OSCR

Does the brain's E:I balance really shape long-range temporal correlations? Lessons learned from 3T MRI.

Code ↔ Paper

9 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 9 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › MRS ↔ EI_Hurst_Measure_Collection_Expanded.sh, lines 88–135 · score 0.74 · Asc, Asp, GPC, NAAG, GSH, Lac
  2. [2] § Methods › MRS ↔ 06_MeasureCollection.sh, lines 188–268 · score 0.73 · Asc, Asp, GPC, NAAG, GSH, Lac
  3. [3] § Methods › MRS ↔ gannetauto.m, the whole file · a weak match · score 0.67 · water suppressed, MEGA PRESS, Philips, co, metabolite, sequences
  4. [4] § Methods › Hurst exponent calculation ↔ dfa/notebook/dfa_simulations.ipynb, lines 16–105 · score 0.65 · power law, Hurst exponent, windows, algorithms, log, density
  5. [5] § Methods › MRS ↔ 06_MeasureCollection.sh, lines 44–114 · score 0.64 · water scaling, LCModel, sLASER, quantified, spectra, Glu
  6. [6] § Methods › Image processing › fMRI ↔ 01_BashPipeline.sh, lines 180–218 · score 0.57 · preprocessed BOLD, fMRIPrep, Tedana, echo
  7. [7] § Methods › Acquisition details ↔ gannetauto.m, the whole file · a weak match · score 0.54 · water suppression, MEGA PRESS, weighted, sequence, scans, voxel
  8. [8] § Methods › Hurst exponent calculation ↔ dfa/dfa.py, lines 39–90 · score 0.52 · power law, windows, algorithms, log, density, exponent
  9. [9] § Methods › Image processing › Structural images ↔ 01_BashPipeline.sh, lines 540–604 · score 0.51 · ANTs, FSL, v2, GM, spaces, mask

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Shell · 371 lines · 38 KB · no license · 2 matches

  1. #!/bin/bash
  3. set -e # exit when any command fails
  5. BIDSdir=/mnt/WeberLab/Projects/EI_Hurst
  6. codedir=${BIDSdir}/code
  7. subjectfile=${codedir}/SubjectDCMInfo.csv
  8. derivatives=${BIDSdir}/derivatives
  9. MEGAPRESSdir=${derivatives}/megapress
  10. SLASERdir=${derivatives}/slaser
  11. hurstdir=${derivatives}/hurst
  12. alffdir=${derivatives}/ALFF
  13. mriqcdir=${derivatives}/mriqc
  14. tedanadir=${derivatives}/tedana
  15. workdir=$HOME/work
  16. fslicense=/mnt/WeberLab
  18. sed 1d $subjectfile | grep -v '^#' | while read d # ignore first row, ignore rows starting with '#'
  19. do
  20. subid=$(echo $d | awk -F',' '{print $1}')
  22. echo "#------------------------------------------------------------------#"
  23. echo "Starting sub-${subid}"
  25. ## Collecing Osprey sLASER data
  26. echo "#------------------------------------------------------------------#"
  27. echo "Step 1: Collecting SLASER measures"
  28. echo "Step 1a: Collecting SLASER Values"
  29. rest_vals=$(awk -F '\t' '(NR>1) {print}' ${SLASERdir}/sub-${subid}/rest/MarkBasisSet/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  30. rest_glu_tcr=$(awk -F '\t' '(NR>1) {print $9}' ${SLASERdir}/sub-${subid}/rest/MarkBasisSet/QuantifyResults/A_tCr_Voxel_1_Basis_1.tsv)
  31. movie_vals=$(awk -F '\t' '(NR>1) {print}' ${SLASERdir}/sub-${subid}/movie/MarkBasisSet/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  32. movie_glu_tcr=$(awk -F '\t' '(NR>1) {print $9}' ${SLASERdir}/sub-${subid}/movie/MarkBasisSet/QuantifyResults/A_tCr_Voxel_1_Basis_1.tsv)
  33. rest_vals_old=$(awk -F '\t' '(NR>1) {print}' ${SLASERdir}/sub-${subid}/rest/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  34. movie_vals_old=$(awk -F '\t' '(NR>1) {print}' ${SLASERdir}/sub-${subid}/movie/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  35. rest_glx_tcr=$(awk -F '\t' '(NR>1) {print $28}' ${SLASERdir}/sub-${subid}/rest/MarkBasisSet/QuantifyResults/A_tCr_Voxel_1_Basis_1.tsv)
  36. movie_glx_tcr=$(awk -F '\t' '(NR>1) {print $28}' ${SLASERdir}/sub-${subid}/movie/MarkBasisSet/QuantifyResults/A_tCr_Voxel_1_Basis_1.tsv)
  37. echo "Step 1b: Collecting FWHM Values"
  38. rest_fwhm_slaser=$(awk -F '\t' '(NR>1) {print $3}' ${SLASERdir}/sub-${subid}/rest/MarkBasisSet/QM_processed_spectra.tsv)
  39. movie_fwhm_slaser=$(awk -F '\t' '(NR>1) {print $3}' ${SLASERdir}/sub-${subid}/movie/MarkBasisSet/QM_processed_spectra.tsv)
  40. rest_fwhm_slaser_old=$(awk -F '\t' '(NR>1) {print $3}' ${SLASERdir}/sub-${subid}/rest/QM_processed_spectra.tsv)
  41. movie_fwhm_slaser_old=$(awk -F '\t' '(NR>1) {print $3}' ${SLASERdir}/sub-${subid}/movie/QM_processed_spectra.tsv)
  42. echo "Step 1: Complete"
  44. ## Collecting LCModel sLASER
  45. echo "#------------------------------------------------------------------#"
  46. echo "Step 2: Collecting LCModel sLASER measures"
  47. rest_lc_vals=$(awk -F ',' '(NR>1) {print $3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21,$22,$24,$25,$27,$28,$30,$31,$33,$34,$36,$37,$39,$40,$42,$43,$45,$46,$48,$49,$51,$52,$54,$55,$57, \
  48. $58,$60,$61,$63,$64,$66,$67,$69,$70,$72,$73,$75,$76,$78,$79,$81,$82,$84,$85,$87,$88}' ${SLASERdir}/sub-${subid}/rest/MarkBasisSet/LCModelFiles/EI_Hurst_sub-${subid}_sLASER_LCModel_Mark.csv)
  49. movie_lc_vals=$(awk -F ',' '(NR>1) {print $3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21,$22,$24,$25,$27,$28,$30,$31,$33,$34,$36,$37,$39,$40,$42,$43,$45,$46,$48,$49,$51,$52,$54,$55,$57, \
  50. $58,$60,$61,$63,$64,$66,$67,$69,$70,$72,$73,$75,$76,$78,$79,$81,$82,$84,$85,$87,$88}' ${SLASERdir}/sub-${subid}/movie/MarkBasisSet/LCModelFiles/EI_Hurst_sub-${subid}_sLASER_LCModel.csv)
  51. ##Old Basis Set
  52. rest_lc_vals_old=$(awk -F ',' '(NR>1) {print $3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21,$22,$24,$25,$27,$28,$30,$31,$33,$34,$36,$37,$39,$40,$42,$43,$45,$46,$48,$49,$51,$52,$54,$55,$57, \
  53. $58,$60,$61,$63,$64,$66,$67,$69,$70,$72,$73,$75,$76,$78,$79,$81,$82,$84,$85,$87,$88}' ${SLASERdir}/sub-${subid}/rest/LCModelFiles/EI_Hurst_sub-${subid}_sLASER_LCModel.csv)
  54. movie_lc_vals_old=$(awk -F ',' '(NR>1) {print $3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21,$22,$24,$25,$27,$28,$30,$31,$33,$34,$36,$37,$39,$40,$42,$43,$45,$46,$48,$49,$51,$52,$54,$55,$57, \
  55. $58,$60,$61,$63,$64,$66,$67,$69,$70,$72,$73,$75,$76,$78,$79,$81,$82,$84,$85,$87,$88}' ${SLASERdir}/sub-${subid}/movie/LCModelFiles/EI_Hurst_sub-${subid}_sLASER_LCModel.csv)
  56. echo "Step 2: Complete"
  58. ## Collecting MEGAPRESS data
  59. echo "#------------------------------------------------------------------#"
  60. echo "Step 3: Collecting GABA measures -- Osprey"
  61. echo "Step 3a: Collecting GABA + Glu Values"
  62. rest_gaba_gabaplus=$(awk -F '\t' '(NR>1) {print $1, $2}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/QuantifyResults/diff1_AlphaCorrWaterScaled_Voxel_1_Basis_1.tsv)
  63. movie_gaba_gabaplus=$(awk -F '\t' '(NR>1) {print $1, $2}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/QuantifyResults/diff1_AlphaCorrWaterScaled_Voxel_1_Basis_1.tsv)
  64. rest_glu_megapress=$(awk -F '\t' '(NR>1) {print $9}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  65. movie_glu_megapress=$(awk -F '\t' '(NR>1) {print $9}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/QuantifyResults/A_TissCorrWaterScaled_Voxel_1_Basis_1.tsv)
  66. rest_gabaplus_tcr=$(awk -F '\t' '(NR>1) {print $31}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/QuantifyResults/diff1_tCr_Voxel_1_Basis_1.tsv)
  67. movie_gabaplus_tcr=$(awk -F '\t' '(NR>1) {print $31}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/QuantifyResults/diff1_tCr_Voxel_1_Basis_1.tsv)
  68. rest_gaba_tcr=$(awk -F '\t' '(NR>1) {print $5}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/QuantifyResults/diff1_tCr_Voxel_1_Basis_1.tsv)
  69. movie_gaba_tcr=$(awk -F '\t' '(NR>1) {print $5}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/QuantifyResults/diff1_tCr_Voxel_1_Basis_1.tsv)
  70. echo "Step 3b: Collecting FWHM Values"
  71. rest_fwhm_osprey=$(awk -F '\t' '(NR>1) {print $3}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/QM_processed_spectra.tsv)
  72. movie_fwhm_osprey=$(awk -F '\t' '(NR>1) {print $3}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/QM_processed_spectra.tsv)
  73. echo "Step 3c: Collecting GABA measures -- Gannet"
  74. gannet_rest=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/MarkBasisSet/GannetQuantify_output/ -type f -name '*.pdf')
  75. pdftotext ${gannet_rest}
  76. txt_gannet_rest=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/MarkBasisSet/GannetQuantify_output/ -type f -name '*.txt')
  77. rest_gaba_gannet_temp=$(awk '(NR==26) {print}' ${txt_gannet_rest} | grep -Eo '[0-9]{1,4}')
  78. rest_gaba_gannet=$(echo $rest_gaba_gannet_temp | tr " " .)
  79. rest_glx_gannet_temp=$(awk '(NR==32) {print}' ${txt_gannet_rest} | grep -Eo '[0-9]{1,4}')
  80. rest_glx_gannet=$(echo $rest_glx_gannet_temp | tr " " .)
  81. gannet_rest_tcr=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/MarkBasisSet/GannetFit_output/ -type f -name '*.pdf')
  82. pdftotext ${gannet_rest_tcr}
  83. txt_gannet_rest_tcr=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/MarkBasisSet/GannetFit_output/ -type f -name '*.txt')
  84. rest_gaba_tcr_gannet=$(sed -n '106p' < ${txt_gannet_rest_tcr})
  85. gannet_movie=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/MarkBasisSet/GannetQuantify_output/ -type f -name '*.pdf')
  86. pdftotext ${gannet_movie}
  87. txt_gannet_movie=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/MarkBasisSet/GannetQuantify_output/ -type f -name '*.txt')
  88. movie_gaba_gannet_temp=$(awk '(NR==26) {print}' ${txt_gannet_movie} | grep -Eo '[0-9]{1,4}')
  89. movie_gaba_gannet=$(echo $movie_gaba_gannet_temp | tr " " .)
  90. movie_glx_gannet_temp=$(awk '(NR==32) {print}' ${txt_gannet_movie} | grep -Eo '[0-9]{1,4}')
  91. movie_glx_gannet=$(echo $movie_glx_gannet_temp | tr " " .)
  92. gannet_movie_tcr=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/MarkBasisSet/GannetFit_output/ -type f -name '*.pdf')
  93. pdftotext ${gannet_movie_tcr}
  94. txt_gannet_movie_tcr=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/MarkBasisSet/GannetFit_output/ -type f -name '*.txt')
  95. movie_gaba_tcr_gannet=$(sed -n '106p' < ${txt_gannet_movie_tcr})
  96. ## Old Basis Set
  97. echo "Step 3d: Collecting GABA Values -- Old Basis Set"
  98. rest_gaba_gabaplus_old=$(awk -F '\t' '(NR>1) {print $1, $2}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/QuantifyResults/diff1_AlphaCorrWaterScaled_Voxel_1_Basis_1.tsv)
  99. movie_gaba_gabaplus_old=$(awk -F '\t' '(NR>1) {print $1, $2}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/QuantifyResults/diff1_AlphaCorrWaterScaled_Voxel_1_Basis_1.tsv)
  100. echo "Step 3e: Collecting FWHM Values -- Old Basis Set"
  101. rest_fwhm_osprey_old=$(awk -F '\t' '(NR>1) {print $3}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/QM_processed_spectra.tsv)
  102. movie_fwhm_osprey_old=$(awk -F '\t' '(NR>1) {print $3}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/QM_processed_spectra.tsv)
  103. echo "Step 3f: Collecting GABA measures -- Gannet; Old Basis Set"
  104. gannet_rest_old=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/GannetQuantify_output/ -type f -name '*.pdf')
  105. pdftotext ${gannet_rest_old}
  106. txt_gannet_rest_old=$(find ${MEGAPRESSdir}/sub-${subid}/rest_gannet/GannetQuantify_output/ -type f -name '*.txt')
  107. rest_gaba_gannet_temp_old=$(awk '(NR==26) {print}' ${txt_gannet_rest_old} | grep -Eo '[0-9]{1,4}')
  108. rest_gaba_gannet_old=$(echo $rest_gaba_gannet_temp_old | tr " " .)
  109. gannet_movie_old=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/GannetQuantify_output/ -type f -name '*.pdf')
  110. pdftotext ${gannet_movie_old}
  111. txt_gannet_movie_old=$(find ${MEGAPRESSdir}/sub-${subid}/movie_gannet/GannetQuantify_output/ -type f -name '*.txt')
  112. movie_gaba_gannet_temp_old=$(awk '(NR==26) {print}' ${txt_gannet_movie_old} | grep -Eo '[0-9]{1,4}')
  113. movie_gaba_gannet_old=$(echo $movie_gaba_gannet_temp_old | tr " " .)
  114. echo "Step 3: Complete"
  116. ## Collecting LCModel MEGAPRESS data
  117. echo "#------------------------------------------------------------------#"
  118. echo "Step 4: Collecting LCModel GABA measures"
  119. rest_lc_gaba=$(awk -F ',' '(NR>1) {print $15,$16}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/MarkBasisSet/LCModelFiles/EI_Hurst_sub-${subid}_MEGAPRESS68_LCModel_DIFF1_Mark.csv)
  120. movie_lc_gaba=$(awk -F ',' '(NR>1) {print $15,$16}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/MarkBasisSet/LCModelFiles/EI_Hurst_sub-${subid}_MEGAPRESS68_LCModel_DIFF1_Mark.csv)
  121. rest_lc_gaba_old=$(awk -F ',' '(NR>1) {print $15,$16}' ${MEGAPRESSdir}/sub-${subid}/rest_osprey/LCModelFiles/EI_Hurst_sub-${subid}_MEGAPRESS68_LCModel_DIFF1.csv)
  122. movie_lc_gaba_old=$(awk -F ',' '(NR>1) {print $15,$16}' ${MEGAPRESSdir}/sub-${subid}/movie_osprey/LCModelFiles/EI_Hurst_sub-${subid}_MEGAPRESS68_LCModel_DIFF1.csv)
  123. echo "Step 4: Complete"
  125. ## Collecting Hurst data
  126. echo "#------------------------------------------------------------------#"
  127. echo "Step 5: Collecting Hurst measures"
  128. rest_hurst_whole=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -M`
  129. rest_hurst_fullfreq_whole=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -M`
  130. rest_hurst_fullfreq=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  131. rest_hurst_fullfreq_blur=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq_7mmblur.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  132. rest_hurst=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.151.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  133. rest_hurst_old=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  134. rest_hurst_vold=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.088.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  135. movie_hurst_whole=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -M`
  136. movie_hurst_fullfreq_whole=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -M`
  137. movie_hurst_fullfreq=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  138. movie_hurst_fullfreq_blur=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq_7mmblur.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  139. movie_hurst=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.151.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  140. movie_hurst_old=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  141. movie_hurst_vold=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.088.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  142. rest_hurst_vn=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.151.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  143. rest_hurst_fullfreq_vn=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  144. rest_hurst_fullfreq_blur_vn=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq_7mmblur.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  145. rest_hurst_vn_old=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  146. rest_hurst_vn_vold=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.088.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  147. movie_hurst_vn=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.151.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  148. movie_hurst_fullfreq_vn=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  149. movie_hurst_fullfreq_blur_vn=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq_7mmblur.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  150. movie_hurst_vn_old=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.101.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  151. movie_hurst_vn_vold=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_0.013_to_0.088.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  153. rest_hurst_dmn=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_DMN_to_native.nii.gz -M`
  154. movie_hurst_dmn=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_DMN_to_native.nii.gz -M`
  155. rest_hurst_fpn=`fslstats ${hurstdir}/sub-${subid}/rest/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_FPN_to_native.nii.gz -M`
  156. movie_hurst_fpn=`fslstats ${hurstdir}/sub-${subid}/movie/desc-optcomDenoised_bold_WelchHurst_fullfreq.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_FPN_to_native.nii.gz -M`
  157. echo "Step 5: Complete"
  159. ## Collecting BOLD data
  160. echo "#------------------------------------------------------------------#"
  161. echo "Step 6: Collecting BOLD data"
  162. rest_bold=`fslstats ${tedanadir}/sub-${subid}/rest/desc-optcomDenoised_bold_Tmean.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  163. rest_bold_vn=`fslstats ${tedanadir}/sub-${subid}/rest/desc-optcomDenoised_bold_Tmean.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  164. movie_bold=`fslstats ${tedanadir}/sub-${subid}/movie/desc-optcomDenoised_bold_Tmean.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  165. movie_bold_vn=`fslstats ${tedanadir}/sub-${subid}/movie/desc-optcomDenoised_bold_Tmean.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  166. echo "Step 6: Complete"
  168. ## Collecting ALFF data
  169. echo "#------------------------------------------------------------------#"
  170. echo "Step 7: Collecting ALFF"
  171. rest_alff=`fslstats ${alffdir}/sub-${subid}/rest/alff.nii -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  172. movie_alff=`fslstats ${alffdir}/sub-${subid}/movie/alff.nii -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  173. rest_alff_vn=`fslstats ${alffdir}/sub-${subid}/rest/alff.nii -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  174. movie_alff_vn=`fslstats ${alffdir}/sub-${subid}/movie/alff.nii -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  175. rest_alff_blur=`fslstats ${alffdir}/sub-${subid}/rest/alff_7mmblur.nii -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  176. movie_alff_blur=`fslstats ${alffdir}/sub-${subid}/movie/alff_7mmblur.nii -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  177. rest_alff_blur_vn=`fslstats ${alffdir}/sub-${subid}/rest/alff_7mmblur.nii -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  178. movie_alff_blur_vn=`fslstats ${alffdir}/sub-${subid}/movie/alff_7mmblur.nii -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  179. echo "Step 7: Complete"
  181. ## Collecting MeanFD data
  182. echo "#------------------------------------------------------------------#"
  183. echo "Step 8: Collecting MeanFD"
  184. rest_meanfd=`jq .fd_mean ${mriqcdir}/sub-${subid}/func/sub-${subid}_task-rest_acq-rest_echo-1_bold.json`
  185. movie_meanfd=`jq .fd_mean ${mriqcdir}/sub-${subid}/func/sub-${subid}_task-rest_acq-movie_echo-1_bold.json`
  186. echo "Step 8: Complete"
  188. ## Parsing TSV file
  189. echo "#------------------------------------------------------------------#"
  190. echo "Step 9a: Parsing TSV"
  191. participants_measures=${BIDSdir}/participant_measures
  192. [ -d $participants_measures ] || mkdir -p $participants_measures
  193. echo "Rest_Glx_tCr Movie_Glx_tCr Rest_GABAplus_tCr Movie_GABAplus_tCr Rest_GABA_tCr Movie_GABA_tCr Rest_Glu_tCR Movie_Glu_tCr Rest_Glu_Megapress Rest_Asc Rest_Asp Rest_Cr Rest_CrCH2 Rest_GABA_slaser Rest_GPC Rest_GSH Rest_Gln Rest_Glu \
  194. Rest_mI Rest_Lac Rest_NAA Rest_NAAG Rest_PCh Rest_PCr Rest_PE Rest_sI Rest_Tau Rest_MM09 Rest_MM12 Rest_MM14 \
  195. Rest_MM17 Rest_MM20 Rest_Lip09 Rest_Lip13 Rest_Lip20 Rest_tNAA Rest_Glx Rest_tCho Rest_tCr Rest_FWHM_SLASER \
  196. Movie_Asc Movie_Glu_Megapress Movie_Asp Movie_Cr Movie_CrCH2 Movie_GABA_slaser Movie_GPC Movie_GSH Movie_Gln \
  197. Movie_Glu Movie_mI Movie_Lac Movie_NAA Movie_NAAG Movie_PCh Movie_PCr Movie_PE Movie_sI Movie_Tau \
  198. Movie_MM09 Movie_MM12 Movie_MM14 Movie_MM17 Movie_MM20 Movie_Lip09 Movie_Lip13 Movie_Lip20 Movie_tNAA \
  199. Movie_Glx Movie_tCho Movie_tCr Movie_FWHM_SLASER Rest_GABA Rest_GABAplus Rest_GABA_Gannet Rest_FWHM_Osprey \
  200. Movie_GABA Movie_GABAplus Movie_GABA_Gannet Movie_FWHM_Osprey Rest_Hurst Rest_Hurst_Old Rest_Hurst_VOld Rest_Hurst_VN \
  201. Rest_Hurst_FullFreq_VN Rest_Hurst_FullFreq_Blur_VN Rest_Hurst_VN_Old Rest_Hurst_VN_VOld Movie_Hurst Movie_Hurst_Old Movie_Hurst_VOld Movie_Hurst_VN \
  202. Movie_Hurst_FullFreq_VN Movie_Hurst_FullFreq_Blur_VN Movie_Hurst_VN_Old Movie_Hurst_VN_VOld Rest_MeanFD \
  203. Movie_MeanFD Rest_ALFF Rest_ALFF_Blur Rest_ALFF_VN Rest_ALFF_Blur_VN Movie_ALFF Movie_ALFF_Blur Movie_ALFF_VN Movie_ALFF_Blur_VN LC_Rest_Ala LC_Rest_AlaSD LC_Rest_Asc LC_Rest_AscSD \
  204. LC_Rest_Asp LC_Rest_AspSD LC_Rest_Cr LC_Rest_CrSD LC_Rest_GABA_sl LC_Rest_GABASD_sl LC_Rest_GSH LC_Rest_GSHSD \
  205. LC_Rest_Gln LC_Rest_GlnSD \
  206. LC_Rest_Glu LC_Rest_GluSD LC_Rest_Lac LC_Rest_LacSD LC_Rest_NAA LC_Rest_NAASD LC_Rest_NAAG LC_Rest_NAAGSD \
  207. LC_Rest_PCr LC_Rest_PCrSD LC_Rest_PE LC_Rest_PESD LC_Rest_Tau LC_Rest_TauSD LC_Rest_mI LC_Rest_mISD \
  208. LC_Rest_sI LC_Rest_sISD LC_Rest_CrCH2 LC_Rest_CrCH2SD LC_Rest_CrPCr LC_Rest_CrPrSD LC_Rest_NAANAAG \
  209. LC_Rest_NAANAAGSD LC_Rest_GluGln LC_Rest_GluGlnSD LC_Rest_Lip13a LC_Rest_Lip13aSD LC_Rest_Lip13b LC_Rest_Lip13bSD \
  210. LC_Rest_Lip09 LC_Rest_Lip09SD LC_Rest_MM09 LC_Rest_MM09SD LC_Rest_Lip20 LC_Rest_Lip20SD LC_Rest_MM20 \
  211. LC_Rest_MM20SD LC_Rest_MM12 LC_Rest_MM12SD LC_Rest_MM14 LC_Rest_MM14SD LC_Rest_MM17 LC_Rest_MM17SD \
  212. LC_Movie_Ala LC_Movie_AlaSD LC_Movie_Asc LC_Movie_AscSD LC_Movie_Asp LC_Movie_AspSD LC_Movie_Cr LC_Movie_CrSD \
  213. LC_Movie_GABA_sl LC_Movie_GABASD_sl LC_Movie_GSH LC_Movie_GSHSD LC_Movie_Gln LC_Movie_GlnSD \
  214. LC_Movie_Glu LC_Movie_GluSD LC_Movie_Lac LC_Movie_LacSD LC_Movie_NAA LC_Movie_NAASD LC_Movie_NAAG \
  215. LC_Movie_NAAGSD LC_Movie_PCr LC_Movie_PCrSD LC_Movie_PE LC_Movie_PESD LC_Movie_Tau LC_Movie_TauSD \
  216. LC_Movie_mI LC_Movie_mISD \
  217. LC_Movie_sI LC_Movie_sISD LC_Movie_CrCH2 LC_Movie_CrCH2SD LC_Movie_CrPCr LC_Movie_CrPrSD LC_Movie_NAANAAG \
  218. LC_Movie_NAANAAGSD LC_Movie_GluGln LC_Movie_GluGlnSD LC_Movie_Lip13a LC_Movie_Lip13aSD LC_Movie_Lip13b \
  219. LC_Movie_Lip13bSD \
  220. LC_Movie_Lip09 LC_Movie_Lip09SD LC_Movie_MM09 LC_Movie_MM09SD LC_Movie_Lip20 LC_Movie_Lip20SD LC_Movie_MM20 \
  221. LC_Movie_MM20SD LC_Movie_MM12 LC_Movie_MM12SD LC_Movie_MM14 LC_Movie_MM14SD LC_Movie_MM17 LC_Movie_MM17SD \
  222. LC_Rest_GABA \
  223. LC_Rest_GABASD LC_Movie_GABA LC_Movie_GABASD Rest_BOLD Rest_BOLD_VN Movie_BOLD Movie_BOLD_VN Rest_Hurst_Whole \
  224. Rest_Hurst_FullFreq Rest_Hurst_FullFreq_Blur Movie_Hurst_Whole Movie_Hurst_FullFreq Movie_Hurst_FullFreq_Blur \
  225. Rest_Hurst_FullFreq_Whole Movie_Hurst_FullFreq_Whole Rest_Glx_Gannet Movie_Glx_Gannet Rest_Hurst_DMN Movie_Hurst_DMN \
  226. Rest_Hurst_FPN Movie_Hurst_FPN Rest_GABA_Gannet_tCr Movie_GABA_Gannet_tCr" > ${participants_measures}/sub-${subid}_EI_Hurst_Measures_Expanded.tsv
  227. echo $rest_glx_tcr $movie_glx_tcr $rest_gabaplus_tcr $movie_gabaplus_tcr $rest_gaba_tcr $movie_gaba_tcr $rest_glu_tcr $movie_glu_tcr $rest_glu_megapress $rest_vals $rest_fwhm_slaser $movie_glu_megapress $movie_vals $movie_fwhm_slaser $rest_gaba_gabaplus $rest_gaba_gannet \
  228. $rest_fwhm_osprey $movie_gaba_gabaplus $movie_gaba_gannet $movie_fwhm_osprey $rest_hurst $rest_hurst_old $rest_hurst_vold \
  229. $rest_hurst_vn $rest_hurst_fullfreq_vn $rest_hurst_fullfreq_blur_vn $rest_hurst_vn_old $rest_hurst_vn_vold $movie_hurst $movie_hurst_old $movie_hurst_vold $movie_hurst_vn \
  230. $movie_hurst_fullfreq_vn $movie_hurst_fullfreq_blur_vn $movie_hurst_vn_old $movie_hurst_vn_vold $rest_meanfd $movie_meanfd \
  231. $rest_alff $rest_alff_blur $rest_alff_vn $rest_alff_blur_vn $movie_alff $movie_alff_blur $movie_alff_vn $movie_alff_blur_vn $rest_lc_vals $movie_lc_vals $rest_lc_gaba $movie_lc_gaba \
  232. $rest_bold $rest_bold_vn $movie_bold $movie_bold_vn $rest_hurst_whole $rest_hurst_fullfreq $rest_hurst_fullfreq_blur $movie_hurst_whole \
  233. $movie_hurst_fullfreq $movie_hurst_fullfreq_blur $rest_hurst_fullfreq_whole $movie_hurst_fullfreq_whole $rest_glx_gannet $movie_glx_gannet $rest_hurst_dmn $movie_hurst_dmn $rest_hurst_fpn \
  234. $movie_hurst_fpn $rest_gaba_tcr_gannet $movie_gaba_tcr_gannet >> ${participants_measures}/sub-${subid}_EI_Hurst_Measures_Expanded.tsv
  235. participants_measures=${BIDSdir}/participant_measures
  236. echo "Step 9b: Parsing TSV: Old Basis Set"
  237. echo "Rest_Asc Rest_Asp Rest_Cr Rest_CrCH2 Rest_GABA_slaser Rest_GPC Rest_GSH Rest_Gln Rest_Glu \
  238. Rest_mI Rest_Lac Rest_NAA Rest_NAAG Rest_PCh Rest_PCr Rest_PE Rest_sI Rest_Tau Rest_MM09 Rest_MM12 Rest_MM14 \
  239. Rest_MM17 Rest_MM20 Rest_Lip09 Rest_Lip13 Rest_Lip20 Rest_tNAA Rest_Glx Rest_tCho Rest_tCr Rest_FWHM_SLASER \
  240. Movie_Asc Movie_Asp Movie_Cr Movie_CrCH2 Movie_GABA_slaser Movie_GPC Movie_GSH Movie_Gln \
  241. Movie_Glu Movie_mI Movie_Lac Movie_NAA Movie_NAAG Movie_PCh Movie_PCr Movie_PE Movie_sI Movie_Tau \
  242. Movie_MM09 Movie_MM12 Movie_MM14 Movie_MM17 Movie_MM20 Movie_Lip09 Movie_Lip13 Movie_Lip20 Movie_tNAA \
  243. Movie_Glx Movie_tCho Movie_tCr Movie_FWHM_SLASER Rest_GABA Rest_GABAplus Rest_GABA_Gannet Rest_FWHM_Osprey \
  244. Movie_GABA Movie_GABAplus Movie_GABA_Gannet Movie_FWHM_Osprey LC_Rest_Ala LC_Rest_AlaSD LC_Rest_Asc LC_Rest_AscSD \
  245. LC_Rest_Asp LC_Rest_AspSD LC_Rest_Cr LC_Rest_CrSD LC_Rest_GABA_sl LC_Rest_GABASD_sl LC_Rest_GSH LC_Rest_GSHSD \
  246. LC_Rest_Gln LC_Rest_GlnSD \
  247. LC_Rest_Glu LC_Rest_GluSD LC_Rest_Lac LC_Rest_LacSD LC_Rest_NAA LC_Rest_NAASD LC_Rest_NAAG LC_Rest_NAAGSD \
  248. LC_Rest_PCr LC_Rest_PCrSD LC_Rest_PE LC_Rest_PESD LC_Rest_Tau LC_Rest_TauSD LC_Rest_mI LC_Rest_mISD \
  249. LC_Rest_sI LC_Rest_sISD LC_Rest_CrCH2 LC_Rest_CrCH2SD LC_Rest_CrPCr LC_Rest_CrPrSD LC_Rest_NAANAAG \
  250. LC_Rest_NAANAAGSD LC_Rest_GluGln LC_Rest_GluGlnSD LC_Rest_Lip13a LC_Rest_Lip13aSD LC_Rest_Lip13b LC_Rest_Lip13bSD \
  251. LC_Rest_Lip09 LC_Rest_Lip09SD LC_Rest_MM09 LC_Rest_MM09SD LC_Rest_Lip20 LC_Rest_Lip20SD LC_Rest_MM20 \
  252. LC_Rest_MM20SD LC_Rest_MM12 LC_Rest_MM12SD LC_Rest_MM14 LC_Rest_MM14SD LC_Rest_MM17 LC_Rest_MM17SD \
  253. LC_Movie_Ala LC_Movie_AlaSD LC_Movie_Asc LC_Movie_AscSD LC_Movie_Asp LC_Movie_AspSD LC_Movie_Cr LC_Movie_CrSD \
  254. LC_Movie_GABA_sl LC_Movie_GABASD_sl LC_Movie_GSH LC_Movie_GSHSD LC_Movie_Gln LC_Movie_GlnSD \
  255. LC_Movie_Glu LC_Movie_GluSD LC_Movie_Lac LC_Movie_LacSD LC_Movie_NAA LC_Movie_NAASD LC_Movie_NAAG \
  256. LC_Movie_NAAGSD LC_Movie_PCr LC_Movie_PCrSD LC_Movie_PE LC_Movie_PESD LC_Movie_Tau LC_Movie_TauSD \
  257. LC_Movie_mI LC_Movie_mISD \
  258. LC_Movie_sI LC_Movie_sISD LC_Movie_CrCH2 LC_Movie_CrCH2SD LC_Movie_CrPCr LC_Movie_CrPrSD LC_Movie_NAANAAG \
  259. LC_Movie_NAANAAGSD LC_Movie_GluGln LC_Movie_GluGlnSD LC_Movie_Lip13a LC_Movie_Lip13aSD LC_Movie_Lip13b \
  260. LC_Movie_Lip13bSD \
  261. LC_Movie_Lip09 LC_Movie_Lip09SD LC_Movie_MM09 LC_Movie_MM09SD LC_Movie_Lip20 LC_Movie_Lip20SD LC_Movie_MM20 \
  262. LC_Movie_MM20SD LC_Movie_MM12 LC_Movie_MM12SD LC_Movie_MM14 LC_Movie_MM14SD LC_Movie_MM17 LC_Movie_MM17SD \
  263. LC_Rest_GABA \
  264. LC_Rest_GABASD LC_Movie_GABA LC_Movie_GABASD Rest_Hurst_DMN Movie_Hurst_DMN Rest_Hurst_FPN Movie_Hurst_FPN" > ${participants_measures}/sub-${subid}_EI_Hurst_Old_Basis.tsv
  265. echo $rest_vals_old $rest_fwhm_slaser_old $movie_vals_old $movie_fwhm_slaser_old $rest_gaba_gabaplus_old $rest_gaba_gannet_old \
  266. $rest_fwhm_osprey_old $movie_gaba_gabaplus_old $movie_gaba_gannet_old $movie_fwhm_osprey_old \
  267. $rest_lc_vals_old $movie_lc_vals_old $rest_lc_gaba_old $movie_lc_gaba_old $rest_hurst_dmn $movie_hurst_dmn $rest_hurst_fpn $movie_hurst_fpn >> ${participants_measures}/sub-${subid}_EI_Hurst_Old_Basis.tsv
  268. echo "Step 9: Complete"
  270. ## Collecting PSD Data
  271. echo "#------------------------------------------------------------------#"
  272. echo "Step 10: Collecting PSD Data"
  273. psd_data=${participants_measures}/psd_data
  274. [ -d $psd_data ] || mkdir -p $psd_data
  275. [ -d ${psd_data}/rest ] || mkdir -p ${psd_data}/rest
  276. [ -d ${psd_data}/movie ] || mkdir -p ${psd_data}/movie
  278. cp ${hurstdir}/sub-${subid}/rest/psd_fullfreq.csv $psd_data/rest/psd_fullfreq_sub-${subid}.csv
  279. cp ${hurstdir}/sub-${subid}/rest/psd_0.013_to_0.151.csv $psd_data/rest/psd_0.013_to_0.151_sub-${subid}.csv
  280. cp ${hurstdir}/sub-${subid}/rest/psd_0.013_to_0.101.csv $psd_data/rest/psd_0.013_to_0.101_sub-${subid}.csv
  281. cp ${hurstdir}/sub-${subid}/rest/psd_0.013_to_0.088.csv $psd_data/rest/psd_0.013_to_0.088_sub-${subid}.csv
  283. cp ${hurstdir}/sub-${subid}/movie/psd_fullfreq.csv $psd_data/movie/psd_fullfreq_sub-${subid}.csv
  284. cp ${hurstdir}/sub-${subid}/movie/psd_0.013_to_0.151.csv $psd_data/movie/psd_0.013_to_0.151_sub-${subid}.csv
  285. cp ${hurstdir}/sub-${subid}/movie/psd_0.013_to_0.101.csv $psd_data/movie/psd_0.013_to_0.101_sub-${subid}.csv
  286. cp ${hurstdir}/sub-${subid}/movie/psd_0.013_to_0.088.csv $psd_data/movie/psd_0.013_to_0.088_sub-${subid}.csv
  287. echo "Step 10: Complete"
  289. ## Collecting Additional Hurst Data
  290. echo "#------------------------------------------------------------------#"
  291. echo "Step 11: Collecting Additional Hurst Data"
  292. add_hurst_data=${participants_measures}/add_hurst_data
  293. [ -d $add_hurst_data ] || mkdir -p $add_hurst_data
  294. [ -d ${add_hurst_data}/rest ] || mkdir -p ${add_hurst_data}/rest
  295. [ -d ${add_hurst_data}/movie ] || mkdir -p ${add_hurst_data}/movie
  297. rest_bp_dfa=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  298. rest_bp_dfa_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  299. rest_bp_ksghe=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  300. rest_bp_ksghe_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  301. rest_bp_rs=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  302. rest_bp_rs_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  303. rest_bp_wavelet=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  304. rest_bp_wavelet_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  305. rest_bp_welch_gt1div=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  306. rest_bp_welch_gt1div_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_BP_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  307. rest_dfa=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  308. rest_dfa_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  309. rest_ksghe=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  310. rest_ksghe_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  311. rest_rs=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  312. rest_rs_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  313. rest_wavelet=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  314. rest_wavelet_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  315. rest_welch_gt1div=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/gm_voxel_mask_space-BOLD_rest.nii.gz -M`
  316. rest_welch_gt1div_vn=`fslstats ${hurstdir}/sub-${subid}/rest/additional/desc-optcomDenoised_bold_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/rest/Yeo2011_Visual_to_native.nii.gz -M`
  317. movie_bp_dfa=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  318. movie_bp_dfa_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  319. movie_bp_ksghe=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  320. movie_bp_ksghe_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  321. movie_bp_rs=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  322. movie_bp_rs_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  323. movie_bp_wavelet=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  324. movie_bp_wavelet_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  325. movie_bp_welch_gt1div=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  326. movie_bp_welch_gt1div_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_BP_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  327. movie_dfa=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  328. movie_dfa_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_DFAHurst_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  329. movie_ksghe=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  330. movie_ksghe_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_KSGHE_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  331. movie_rs=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  332. movie_rs_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_RS_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  333. movie_wavelet=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  334. movie_wavelet_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_Wavelet_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  335. movie_welch_gt1div=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/gm_voxel_mask_space-BOLD_movie.nii.gz -M`
  336. movie_welch_gt1div_vn=`fslstats ${hurstdir}/sub-${subid}/movie/additional/desc-optcomDenoised_bold_Welch-gt1div_Hurst.nii.gz -n -k ${hurstdir}/sub-${subid}/movie/Yeo2011_Visual_to_native.nii.gz -M`
  338. echo "Rest_BP_DFA Rest_BP_DFA_VN Rest_BP_KSGHE Rest_BP_KSGHE_VN Rest_BP_RS Rest_BP_RS_VN \
  339. Rest_BP_Wavelet Rest_BP_Wavelet_VN Rest_BP_Welch_GT1Div Rest_BP_Welch_GT1Div_VN \
  340. Rest_DFA Rest_DFA_VN Rest_KSGHE Rest_KSGHE_VN Rest_RS Rest_RS_VN \
  341. Rest_Wavelet Rest_Wavelet_VN Rest_Welch_GT1Div Rest_Welch_GT1Div_VN \
  342. Movie_BP_DFA Movie_BP_DFA_VN Movie_BP_KSGHE Movie_BP_KSGHE_VN Movie_BP_RS Movie_BP_RS_VN \
  343. Movie_BP_Wavelet Movie_BP_Wavelet_VN Movie_BP_Welch_GT1Div Movie_BP_Welch_GT1Div_VN \
  344. Movie_DFA Movie_DFA_VN Movie_KSGHE Movie_KSGHE_VN Movie_RS Movie_RS_VN \
  345. Movie_Wavelet Movie_Wavelet_VN Movie_Welch_GT1Div Movie_Welch_GT1Div_VN" > ${add_hurst_data}/sub-${subid}_Add_Hurst.tsv
  346. echo $rest_bp_dfa $rest_bp_dfa_vn $rest_bp_ksghe $rest_bp_ksghe_vn $rest_bp_rs $rest_bp_rs_vn \
  347. $rest_bp_wavelet $rest_bp_wavelet_vn $rest_bp_welch_gt1div $rest_bp_welch_gt1div_vn \
  348. $rest_dfa $rest_dfa_vn $rest_ksghe $rest_ksghe_vn $rest_rs $rest_rs_vn \
  349. $rest_wavelet $rest_wavelet_vn $rest_welch_gt1div $rest_welch_gt1div_vn \
  350. $movie_bp_dfa $movie_bp_dfa_vn $movie_bp_ksghe $movie_bp_ksghe_vn $movie_bp_rs $movie_bp_rs_vn \
  351. $movie_bp_wavelet $movie_bp_wavelet_vn $movie_bp_welch_gt1div $movie_bp_welch_gt1div_vn \
  352. $movie_dfa $movie_dfa_vn $movie_ksghe $movie_ksghe_vn $movie_rs $movie_rs_vn \
  353. $movie_wavelet $movie_wavelet_vn $movie_welch_gt1div $movie_welch_gt1div_vn \ >> ${add_hurst_data}/sub-${subid}_Add_Hurst.tsv
  354. echo "Step 11: Complete"
  356. ## Collecting Gannet Spectrum Data
  357. echo "#------------------------------------------------------------------#"
  358. echo "Step 12: Collecting Gannet Spectrum Data"
  359. gannet_spectrum_data=${BIDSdir}/gannet_spectrum_data
  360. [ -d $gannet_spectrum_data ] || mkdir -p $gannet_spectrum_data
  361. [ -d ${gannet_spectrum_data}/rest ] || mkdir -p ${gannet_spectrum_data}/rest
  362. [ -d ${gannet_spectrum_data}/movie ] || mkdir -p ${gannet_spectrum_data}/movie
  364. cp ${MEGAPRESSdir}/sub-${subid}/rest_gannet/gannetout.mat $gannet_spectrum_data/rest/gannet_spectrum_sub-${subid}.mat
  365. cp ${MEGAPRESSdir}/sub-${subid}/movie_gannet/gannetout.mat $gannet_spectrum_data/movie/gannet_spectrum_sub-${subid}.mat
  366. echo "Step 12: Complete"
  368. echo "Finished sub-${subid}"
  371. done

06_MeasureCollection.sh at commit 3e7f845, no license · at the source

Overview

Authors: Lydia Sochan1, Jessica Archibald2, Alexander Mark Weber1,3,4
ORCID iDs: Lydia Sochan, Jessica Archibald, Alexander Mark Weber
  1. School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada
  2. Department of Radiology, Weill Cornell Medicine, New York, NY, United States
  3. BC Children’s Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
  4. Pediatrics, The University of British Columbia, Vancouver, BC, Canada
Institutions: University of British Columbia (Canada); Weill Cornell Medicine (United States); BC Children's Hospital Research Institute (Canada)
Journal: Imaging neuroscience (Cambridge, Mass.), volume 4, article IMAG.a.1252
Dates: received 28 March 2025; accepted 27 April 2026; published online 29 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1162/imag.a.1252 · PMID 42232071 · PMCID PMC13224315 · OpenAlex W4409140605
Open access: diamond, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.03.28.645973
Status: code verified
Categories: structural MRI / diffusion (modality), fMRI (modality), human (organism)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Preprocessing, Connectivity, Complexity, fMRI & imaging
Keywords: Hurst exponent, long range temporal correlation, excitatory/inhibitory balance, criticality, complex systems, visual task, functional magnetic resonance imaging, magnetic resonance spectroscopy, functional magnetic resonance spectroscopy
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Citations: not cited yet (Europe PMC); 144 references in the paper
Research resources: 1999 RRID:SCR_001847, 2017 RRID:SCR_002438, 2001 RRID:SCR_002823

Abstract

A 3T multimodal MR study of healthy adults (n = 18; 10 female; 21.3–53.4 years) was performed to investigate the relationship between functional magnetic resonance imaging (fMRI) long-range temporal correlations and excitatory/inhibitory balance (via single voxel magnetic resonance spectroscopy measurements of glutamate and γ-aminobutyric acid (GABA)). The study objective was to determine whether the Hurst exponent (H)—an estimate of self-correlation and signal complexity—of the blood oxygen level-dependent signal was correlated with the excitatory–inhibitory (E:I) ratio. E:I has been proposed to serve as a control parameter for brain criticality—the theory that the brain operates near a critical point between order and disorder, optimizing information processing and adaptability—which H is believed to be a measure of. Thus, understanding whether H and E:I are indeed correlated would clarify this relationship. Moreover, findings in this domain have implications for neurological and neuropsychiatric conditions with disrupted E:I balance, such as autism, schizophrenia, and Alzheimer’s disease. From a practical perspective, H is easier to accurately measure than E:I ratio at 3T MRI. If H can serve as a proxy for E:I, it may serve as a more practical clinical biomarker for this imbalance and for neuroscience research in general. The study collected functional MRI and magnetic resonance spectroscopy data during rest and movie watching. H and E:I (glutamate/GABA) were not found to be correlated. H was found to increase with movie watching compared with rest, while E:I did not change between conditions. This study represents the first attempt to investigate this connection in vivo in humans. We conclude that, at 3T and with our particular methodologies, no association was found. We end with lessons learned and suggestions for future research.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 9 matches between paragraphs and lines of code.

WeberLab/EI_Hurst_Analysis

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 3e7f84551f18f19b9361a0586b1ff5a0f0231687, 17 February 2025
Languages: Shell (15), Python (8), Jupyter (6), MATLAB (2), R (1)
Size: 45 files, 32 scripts
Software Heritage: not archived
Found in: “Data and Code Availability”
Holds: README, 4 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FSL (11 files), NumPy (11 files), Matplotlib (10 files), NiBabel (10 files), SciPy (10 files), scikit-learn (8 files), seaborn (7 files), pandas (4 files), AFNI (3 files), ANTs (2 files), Dcm2Bids (1 file), fMRIPrep (1 file), FreeSurfer (1 file), MRIQC (1 file), PyWavelets (1 file), reshape2 (1 file), tedana (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
33 files
At the source: github.com/WeberLab/EI_Hurst_Analysis

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 32 scripts, each with its path and the digest of its content;
  • 9 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data and Code Availability

All code used in this paper is available at github.com/WeberLab/EI_Hurst_Analysis. The raw MRI data used in this paper are available by contacting the author. The manuscript was written in a “reproducible manner”: the entire manuscript, including statistics reported, figures, and tables, is reproduced here: weberlab.github.io/EI_Hurst_Manuscript/.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Authors: added Jessica Archibald (0000-0001-6651-183X); removed Jessica Archibald

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 3 authors, 9 keywords, 139 references, 3 RRIDs.

Cite

This paper

Sochan, L., Archibald, J., & Weber, A. M. (2026). Does the brain's E:I balance really shape long-range temporal correlations? Lessons learned from 3T MRI. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1252. https://doi.org/10.1162/imag.a.1252

BibTeX

@article{sochan2026does,
author = {Sochan, Lydia and Archibald, Jessica and Weber, Alexander Mark},
title = {{Does the brain's E:I balance really shape long-range temporal correlations? Lessons learned from 3T MRI}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = may,
volume = {4},
pages = {IMAG.a.1252},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/imag.a.1252},
url = {https://doi.org/10.1162/imag.a.1252},
pmid = {42232071},
pmcid = {PMC13224315}
}

RIS

TY - JOUR
AU - Sochan, Lydia
AU - Archibald, Jessica
AU - Weber, Alexander Mark
TI - Does the brain's E:I balance really shape long-range temporal correlations? Lessons learned from 3T MRI
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/05/29
VL - 4
SP - IMAG.a.1252
SN - 2837-6056
PB - MIT Press
DO - 10.1162/imag.a.1252
UR - https://doi.org/10.1162/imag.a.1252
LA - en
ER -

CSL-JSON

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"id": "10.1162/imag.a.1252",
"type": "article-journal",
"title": "Does the brain's E:I balance really shape long-range temporal correlations? Lessons learned from 3T MRI",
"container-title": "Imaging neuroscience (Cambridge, Mass.)",
"author": [
{
"family": "Sochan",
"given": "Lydia"
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{
"family": "Weber",
"given": "Alexander Mark"
}
],
"container-title-short": "Imaging Neurosci (Camb)",
"volume": "4",
"page": "IMAG.a.1252",
"DOI": "10.1162/imag.a.1252",
"PMID": "42232071",
"PMCID": "PMC13224315",
"ISSN": "2837-6056",
"publisher": "MIT Press",
"URL": "https://doi.org/10.1162/imag.a.1252",
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"issued": {
"date-parts": [
[
2026,
5,
29
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]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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