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Longitudinal changes of choroid plexus volumes and MRI ratios in multiple sclerosis.

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  1. [1] § Materials and methods › Image processing ↔ KUL_T1T2FLAIRMTR_ratio.sh, lines 733–787 · score 0.65 · linear histogram matching, brain tissue, transformation, template, ratios, masks

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  1. #!/bin/bash
  2. # Sarah Cappelle & Stefan Sunaert
  3. # 22/12/2020 - v1.0
  4. # 18/02/2021 - v1.1 (adding calibration)
  5. # 24/10/2022 - v1.2 (accepted for publication)
  6. # 17/08/2023 - v1.3 bug fix (using local path)
  7. #
  8. # This script computes a T1/T2, T1/FLAIR and MTC (magnetisation transfer contrast) ratio
  9. #
  10. # This scripts follows the rationales of
  11. # - D. Pareto et al. AJNR 2020
  12. # - Ganzetti et al. Frontiers in human neuroscience 2014
  13. #
  14. # Starting from 3D-T1w, 3D-FLAIR and 2D-T2w scans we compute:
  15. # bias correct the images using N4biascorrect from ANTs
  16. # ANTs rigid coregister and reslice all images to the 3D-T1w (in isotropic 1 mm space)
  17. # create masked brain images using HD-BET
  18. # calibrate the images according to Ganzetti
  19. # compute a T1FLAIR_ratio, a T1T2_ratio and a MTR
  20. version="1.3"
  22. kul_main_dir=$(dirname "$0")
  23. script=$(basename "$0")
  24. source $kul_main_dir/KUL_main_functions.sh
  25. # $cwd & $log_dir is made in main_functions
  27. # FUNCTIONS --------------
  29. # function Usage
  30. function Usage {
  32. cat <<USAGE
  34. `basename $0` computes a T1/T2, T1/FLAIR and MTC (magnetisation transfer contrast) ratio, using BIDS organised data.
  36. Usage:
  38. `basename $0` <OPT_ARGS>
  40. Example:
  42. `basename $0` -p JohnDoe -f 2 -m -v
  44. Required arguments:
  46. -p: participant name
  49. Optional arguments:
  51. -s: session of the participant
  52. -a: automatic mode (just work on all images in the BIDS folder)
  53. -n: number of cpu to use (default 15)
  54. -m: also run MS lesion segmentation using Freesurfer7 SamSeg
  55. -f: also run fastsurfer (1=full, 2=segmentation with CC & stats, 3=fast segmentation without CC)
  56. -d: only perform part of the workflow
  57. levels:
  58. 1 = bias-correction
  59. 2 = rigid registration of the T2w and/or FLAIR to the T1w
  60. 3 = spatially normalise (warp) the T1w to the MNI atlas
  61. 4 = run fastsufer (req option -f)
  62. 5 = run samseg (req option -m)
  63. 6 = hd-bet the images
  64. 7 = calibration
  65. 8 = compute the T1w/T2w and/or T1w/FLAIR ratio
  66. 9 = compute the MTR
  67. 10 = warp the results to MNI
  68. -c: do not run, but output files for the VSC HPC
  69. -v: show output from commands
  71. Documentation:
  73. This script computes a T1/T2, T1/FLAIR and MTC (magnetisation transfer contrast) ratio, using BIDS organised data.
  75. It follows the rationale of Ganzetti et al. Frontiers in human neuroscience 2014 and D. Pareto et al. AJNR 2020.
  76. The full methodology is described in "T1w/FLAIR ratio standardization as a myelin marker in MS patients,
  77. by S Cappelle, D Pareto, S Sunaert, I Smets, A Laenen, B Dubois, Ph Demaerel" - https://pubmed.ncbi.nlm.nih.gov/36451354/
  79. A T1w is mandatory.
  80. A T1w/T2w ratio is computed if a T2w is present.
  81. A T1w/FLAIR ratio is computed if a FLAIR is present.
  82. A MTR is computed if an MTI pair is available.
  83. It also segments (MS or T1w-hypo/FLAIR-hyper) lesions using Freesurfer Samseg if T1w and FLAIR are present and option -m is given.
  84. It also calculates a FastSurfer parcellation if option -f is used.
  86. Dependecies:
  88. general:
  89. - input images must be supplied in Brain Imaging Data Structure (https://bids.neuroimaging.io/) format in the folder "BIDS"
  91. required:
  92. - MRTrix3 - https://www.mrtrix.org/
  93. - ANTs - http://stnava.github.io/ANTs/
  94. - HD-BET - https://github.com/MIC-DKFZ/HD-BET
  96. optional:
  97. - FastSurfer - https://deep-mi.org/research/fastsurfer/
  98. - Freesurfer Samseg - https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg
  100. References:
  101. @ Sarah Cappelle & Stefan Sunaert
  103. USAGE
  105. exit 1
  106. }
  109. # CHECK COMMAND LINE OPTIONS -------------
  110. #
  111. # Set defaults
  112. auto=0 # default if option -s is not given
  113. silent=1 # default if option -v is not given
  114. outputdir="$cwd/T1T2FLAIRMTR_ratio"
  115. ms=0
  116. ncpu=15
  117. fastsurf=0
  118. hpc=0
  119. deel=10
  121. # Set required options
  122. #p_flag=0
  124. if [ "$#" -lt 1 ]; then
  125. Usage >&2
  126. exit 1
  128. else
  130. while getopts "p:s:f:n:d:acmv" OPT; do
  132. case $OPT in
  133. a) #automatic mode
  134. auto=1
  135. ;;
  136. p) #participant
  137. participant=$OPTARG
  138. ;;
  139. s) #session
  140. session=$OPTARG
  141. ;;
  142. n) #ncpu
  143. ncpu=$OPTARG
  144. ;;
  145. f) #fastsurfer
  146. fastsurf=$OPTARG
  147. ;;
  148. d) #new workflow
  149. deel=$OPTARG
  150. ;;
  151. m) #MS lesion segmentation
  152. ms=1
  153. ;;
  154. c) #VSC HPC
  155. hpc=1
  156. ;;
  157. v) #verbose
  158. silent=0
  159. ;;
  160. \?)
  161. echo "Invalid option: -$OPTARG" >&2
  162. echo
  163. Usage >&2
  164. exit 1
  165. ;;
  166. :)
  167. echo "Option -$OPTARG requires an argument." >&2
  168. echo
  169. Usage >&2
  170. exit 1
  171. ;;
  172. esac
  174. done
  176. fi
  178. # check for required options
  179. #if [ $p_flag -eq 0 ] ; then
  180. # echo
  181. # echo "Option -p is required: give the BIDS name of the participant." >&2
  182. # echo
  183. # exit 2
  184. #fi
  186. export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${ncpu}
  187. ants_verbose=1
  188. fs_silent=""
  189. # verbose or not?
  190. if [ $silent -eq 1 ] ; then
  191. export MRTRIX_QUIET=1
  192. ants_verbose=0
  193. fs_silent=" > /dev/null 2>&1"
  194. fi
  196. d=$(date "+%Y-%m-%d_%H-%M-%S")
  197. log=log/log_${d}.txt
  199. # --- FUNCTIONS ---
  201. function KUL_antsApply_Transform {
  202. antsApplyTransforms -d 3 \
  203. --verbose $ants_verbose \
  204. -i $input \
  205. -o $output \
  206. -r $reference \
  207. -t $transform \
  208. -n Linear
  209. }
  210. function KUL_antsApply_Transform_MNI {
  211. antsApplyTransforms -d 3 \
  212. --verbose $ants_verbose \
  213. -i $input \
  214. -o $output \
  215. -r $reference \
  216. -t $transform1 -t $transform2 \
  217. -n $interpolation_type
  218. }
  220. function KUL_iso_biascorrect {
  221. local input=$1
  222. local output
  223. output=${input##*/}
  224. output=${output%%.*}
  225. bias_output=$outdir/tmp/${output}_iso_biascorrected.nii.gz
  226. if [ ! -f $bias_output ]; then
  227. echo " doing biascorrection on the ${td}"
  228. mrgrid $input regrid -voxel 1 $outdir/tmp/${output}_iso.nii.gz -force
  229. local bias_input=$outdir/tmp/${output}_iso.nii.gz
  230. N4BiasFieldCorrection --verbose $ants_verbose \
  231. -d 3 \
  232. -i $bias_input \
  233. -o $bias_output
  234. else
  235. echo " biascorrection of the ${td} already done"
  236. fi
  237. }
  239. function KUL_MTI_reorient_crop_hdbet_iso {
  240. iso_output=$outdir/tmp/${output}_iso.nii.gz
  241. mrgrid $input regrid -voxel 1 $iso_output -force
  242. }
  244. # Rigidly register the input to the T1w
  245. function KUL_rigid_register {
  246. antsRegistration --verbose $ants_verbose --dimensionality 3 \
  247. --output [$outdir/tmp/${ants_type},$outdir/tmp/${newname}] \
  248. --interpolation BSpline \
  249. --use-histogram-matching 0 --winsorize-image-intensities [0.005,0.995] \
  250. --initial-moving-transform [$outdir/tmp/$ants_template,$outdir/tmp/$ants_source,1] \
  251. --transform Rigid[0.1] \
  252. --metric MI[$outdir/tmp/$ants_template,$outdir/tmp/$ants_source,1,32,Regular,0.25] \
  253. --convergence [1000x500x250x100,1e-6,10] \
  254. --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox
  255. }
  257. # Register and compute the ratio
  258. function KUL_reg2t1 {
  259. local base0=${test_T1w##*/}
  260. local base=${base0%_T1w*}
  261. ants_type="${base}_rigid_${td}_reg2t1_"
  262. ants_template="${base}_T1w_iso_biascorrected.nii.gz"
  263. ants_source="${base}_${td}_iso_biascorrected.nii.gz"
  264. newname="${base}_${td}_iso_biascorrected_reg2T1w.nii.gz"
  265. #finalname="${base}_${td}_reg2T1w.nii.gz"
  266. if [ ! -f $outdir/tmp/${newname} ]; then
  267. echo " rigid registration of the ${td} to the T1w"
  268. KUL_rigid_register
  269. else
  270. echo " skipping rigid registration of the ${td} to the T1w - already done"
  271. fi
  272. }
  274. function KUL_computeratio {
  275. if [ ! -f $outdir/${base}_ratio-T1${td}_calib-nonlin3.nii.gz ];then
  276. echo " computing the ratio T1w/${td}"
  278. #if [[ ${td} == "T2w" ]];then
  279. # factor=42
  280. #else
  281. # factor=1.705
  282. #fi
  284. #mrcalc \
  285. # $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz $factor -div \
  286. # $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz -divide \
  287. # $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  288. # $outdir/${base}_ratio-T1${td}_calib-none.nii.gz -nthreads $ncpu -force
  290. mrcalc \
  291. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  292. $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz -divide \
  293. $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  294. $outdir/${base}_ratio-T1${td}_calib-none.nii.gz -nthreads $ncpu -force
  295. mrcalc \
  296. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-lin.nii.gz \
  297. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-lin_reg2T1w.nii.gz -divide \
  298. $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  299. $outdir/${base}_ratio-T1${td}_calib-lin.nii.gz -nthreads $ncpu -force
  300. mrcalc \
  301. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin.nii.gz \
  302. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin_reg2T1w.nii.gz -divide \
  303. $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  304. $outdir/${base}_ratio-T1${td}_calib-nonlin.nii.gz -nthreads $ncpu -force
  305. if [ $t2 -eq 1 ]; then #need the T2w to calculate the ventricles
  306. mrcalc \
  307. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin2.nii.gz \
  308. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w.nii.gz -divide \
  309. $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  310. $outdir/${base}_ratio-T1${td}_calib-nonlin2.nii.gz -nthreads $ncpu -force
  311. fi
  312. mrcalc \
  313. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin3.nii.gz \
  314. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin3_reg2T1w.nii.gz -divide \
  315. $outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz -multiply \
  316. $outdir/${base}_ratio-T1${td}_calib-nonlin3.nii.gz -nthreads $ncpu -force
  317. else
  318. echo " the ratio T1w/${td} is already computed"
  319. fi
  320. }
  322. function KUL_apply_warp2mni {
  323. echo " warping ${td} results to MNI"
  325. reference=$fix_im
  326. transform1="$outdir/warp2mni/${base}_T1w2MNI_1Warp.nii.gz"
  327. transform2="[$outdir/warp2mni/${base}_T1w2MNI_0GenericAffine.mat,0]"
  328. interpolation_type="LanczosWindowedSinc"
  330. if [[ ${td} == "T1w" ]];then
  331. local ext=""
  332. elif [[ ! ${td} == "MTI" ]];then
  333. local ext="_reg2T1w"
  334. input="$outdir/${base}_ratio-T1${td}_calib-none.nii.gz"
  335. output="$outdir/${base}_space-MNI_ratio-T1${td}_calib-none.nii.gz"
  336. KUL_antsApply_Transform_MNI
  337. input="$outdir/${base}_ratio-T1${td}_calib-lin.nii.gz"
  338. output="$outdir/${base}_space-MNI_ratio-T1${td}_calib-lin.nii.gz"
  339. KUL_antsApply_Transform_MNI
  340. input="$outdir/${base}_ratio-T1${td}_calib-nonlin.nii.gz"
  341. output="$outdir/${base}_space-MNI_ratio-T1${td}_calib-nonlin.nii.gz"
  342. KUL_antsApply_Transform_MNI
  343. if [ $t2 -eq 1 ]; then
  344. input="$outdir/${base}_ratio-T1${td}_calib-nonlin2.nii.gz"
  345. output="$outdir/${base}_space-MNI_ratio-T1${td}_calib-nonlin2.nii.gz"
  346. KUL_antsApply_Transform_MNI
  347. fi
  348. input="$outdir/${base}_ratio-T1${td}_calib-nonlin3.nii.gz"
  349. output="$outdir/${base}_space-MNI_ratio-T1${td}_calib-nonlin3.nii.gz"
  350. KUL_antsApply_Transform_MNI
  351. elif [[ ${td} == "MTI" ]];then
  352. local ext="_reg2T1w"
  353. input="$outdir/${base}_ratio-MTC.nii.gz"
  354. output="$outdir/${base}_space-MNI_ratio-MTC.nii.gz"
  355. KUL_antsApply_Transform_MNI
  356. fi
  358. input="$outdir/${base}_${td}${ext}.nii.gz"
  359. output="$outdir/${base}_space-MNI_${td}${ext}.nii.gz"
  360. KUL_antsApply_Transform_MNI
  361. }
  363. function KUL_MTI_register_computeratio {
  364. base0=${test_T1w##*/}
  365. base=${base0%_T1w*}
  366. # convert the 4D MTI to single 3Ds
  367. input="$outdir/tmp/${base}_${td}_iso.nii.gz"
  368. S0="$outdir/tmp/${base}_${td}_iso_S0.nii.gz"
  369. Smt="$outdir/tmp/${base}_${td}_iso_Smt.nii.gz"
  370. mrconvert $input -coord 3 0 $S0 -force
  371. mrconvert $input -coord 3 1 $Smt -force
  372. # determine the registration
  373. ants_type="${base}_rigid_${td}_reg2t1_"
  374. ants_template="${base}_T1w_iso_biascorrected.nii.gz"
  375. ants_source="${base}_${td}_iso_Smt.nii.gz"
  376. newname="${base}_${td}_iso_Smt_reg2T1w.nii.gz"
  377. finalname="${base}_${td}_reg2T1w.nii.gz"
  378. KUL_rigid_register
  379. Smt="$outdir/tmp/$newname"
  380. # Now apply the coregistration to the 4D MTI
  381. input=$S0
  382. output="$outdir/tmp/${base}_${td}_iso_S0_reg2T1w.nii.gz"
  383. S0=$output
  384. transform="$outdir/tmp/${base}_rigid_${td}_reg2t1_0GenericAffine.mat"
  385. reference="$outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz"
  386. KUL_antsApply_Transform
  387. # make a better mask
  388. mask=$outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz
  389. # MTR formula: (S0 - Smt)/S0
  390. mrcalc $S0 $Smt -subtract $S0 -divide $mask -multiply \
  391. $outdir/${base}_ratio-MTC.nii.gz -nthreads $ncpu -force
  393. # Also warp to MNI space
  394. reference=$ref_im
  395. transform1="$outdir/warp2mni/${base}_T1w2MNI_1Warp.nii.gz"
  396. transform2="[$outdir/warp2mni/${base}_T1w2MNI_0GenericAffine.mat,0]"
  397. interpolation_type="Linear"
  398. input="$outdir/${base}_ratio-MTC.nii.gz"
  399. output="$outdir/${base}_ratio-MTC_MNI.nii.gz"
  400. KUL_antsApply_Transform_MNI
  402. cp $outdir/tmp/$newname $outdir/$finalname
  403. }
  405. # --- MAIN ---
  406. printf "\n\n\n"
  408. # here we give the data
  409. if [ $auto -eq 0 ]; then
  410. if [ -z "$session" ]; then
  411. fullsession1=""
  412. fullsession2=""
  413. else
  414. fullsession1="ses-${session}/"
  415. fullsession2="ses-${session}_"
  416. fi
  417. datadir="$cwd/BIDS/sub-${participant}/${fullsession1}anat"
  418. T1w=("$datadir/sub-${participant}_${fullsession2}T1w.nii.gz")
  419. T2w=("$datadir/sub-${participant}_${fullsession2}T2w.nii.gz")
  420. FLAIR=("$datadir/sub-${participant}_${fullsession2}FLAIR.nii.gz")
  421. MTI=("$datadir/sub-${participant}_${fullsession2}MTI.nii.gz")
  422. else
  423. T1w=($(find $cwd/BIDS -type f -name "*T1w.nii.gz" | sort ))
  424. fi
  426. hpc_counter=0
  427. hpc_task=1
  429. for test_T1w in ${T1w[@]}; do
  431. # defining the basename from the array elements
  432. base0=${test_T1w##*/};base=${base0%_T1w*}
  433. local_participant=${base%_ses*}
  434. local_session="ses-${base##*ses-}"
  435. outdir=$outputdir/$local_participant/$local_session
  436. check_done="$outdir/${base}.done"
  437. # resetting found files
  438. d=0
  439. t2=0
  440. flair=0
  441. mti=0
  442. # read the level of completed workflow
  443. if [ ! -f $check_done ];then
  444. level_done=0
  445. else
  446. level_done=$(cat $check_done)
  447. if [ -z $level_done ];then
  448. #echo "empty"
  449. level_done=10
  450. fi
  451. fi
  454. # only execute if workflow level in not yet reached
  455. if [ $level_done -lt $deel ];then
  456. echo " current level of processing done: $level_done"
  458. # write files for the VSC
  459. if [ $hpc -eq 1 ];then
  461. mkdir -p VSC
  462. if [ $hpc_counter -eq 0 ];then
  463. #echo "#!/bin/bash -e" > VSC/VSC_commands.sh
  464. echo "participant, session" > VSC/pbs_data_${hpc_task}.csv
  465. fi
  466. vsc_participant=${local_participant##*sub-}
  467. vsc_session=${local_session##*ses-}
  468. #vsc_cmd="KUL_T1T2FLAIRMTR_ratio_new.sh -p $vsc_participant -s $vsc_session -m -f 2 -d 3"
  469. #echo $vsc_cmd >> VSC/VSC_commands.sh
  470. echo "${vsc_participant},${vsc_session}" >> VSC/pbs_data_${hpc_task}.csv
  472. hpc_counter=$((hpc_counter+1))
  473. if [ $hpc_counter -ge 34 ];then
  474. hpc_task=$((hpc_task+1))
  475. hpc_counter=0
  476. fi
  478. else
  480. # Test whether T2 and/or FLAIR also exist
  481. test_T2w="${test_T1w%_T1w*}_T2w.nii.gz"
  482. if [ -f $test_T2w ];then
  483. #echo "The T2 exists"
  484. d=$((d+1))
  485. t2=1
  486. fi
  487. test_FLAIR="${test_T1w%_T1w*}_FLAIR.nii.gz"
  488. if [ -f $test_FLAIR ];then
  489. #echo "The FLAIR exists"
  490. d=$((d+1))
  491. flair=1
  492. fi
  493. test_MTI="${test_T1w%_T1w*}_MTI.nii.gz"
  494. if [ -f $test_MTI ];then
  495. #echo "The MTI exists"
  496. d=$((d+1))
  497. mti=1
  498. fi
  500. # If a T1w and a T2w and/or a FLAIR exists
  501. if [ $d -gt 0 ]; then
  502. mkdir -p $outdir/tmp
  503. mkdir -p $outdir/histograms
  504. mkdir -p $outdir/masks
  505. mkdir -p $outdir/rois
  506. mkdir -p $outputdir/log
  507. kul_e2cl "KUL_T1T2FLAIR_ratio is processing $local_participant and session $local_session" ${outputdir}/${log}
  509. # PART 1 - make all images conform and bias-correct
  510. if [ $deel -ge 1 ]; then
  511. # for the T1w
  512. td="T1w"
  513. KUL_iso_biascorrect $test_T1w
  514. cp $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz $outdir/${base}_T1w.nii.gz
  516. if [ $t2 -eq 1 ];then
  517. td="T2w"
  518. KUL_iso_biascorrect $test_T2w
  519. fi
  521. if [ $flair -eq 1 ];then
  522. td="FLAIR"
  523. KUL_iso_biascorrect $test_FLAIR
  524. fi
  525. fi
  527. # PART 2 - register the T2w and/or FLAIR to the T1w
  528. if [ $deel -ge 2 ]; then
  529. if [ $t2 -eq 1 ];then
  530. td="T2w"
  531. KUL_reg2t1
  532. cp $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz $outdir/${base}_${td}_reg2T1w.nii.gz
  533. fi
  535. if [ $flair -eq 1 ];then
  536. td="FLAIR"
  537. KUL_reg2t1
  538. cp $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz $outdir/${base}_${td}_reg2T1w.nii.gz
  539. fi
  540. fi
  542. # PART 3 - Spatially normalise (warp) the T1w to the MNI atlas
  543. if [ $deel -ge 3 ]; then
  544. fix_im="$kul_main_dir/atlasses/Ganzetti2014/mni_icbm152_t1_tal_nlin_sym_09a.nii"
  545. ref_im="$kul_main_dir/atlasses/Ganzetti2014/mni_icbm152_t1_tal_nlin_sym_09a_with_neck.nii"
  546. #input=${test_T1w##*/}
  547. #input=${input%%.*}
  548. #mov_im=$outdir/tmp/${input}_iso_biascorrected.nii.gz
  549. mov_im=$outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz
  550. output="$outdir/warp2mni/${base}_T1w2MNI_"
  551. mkdir -p $outdir/warp2mni
  552. if [ ! -f $outdir/warp2mni/${base}_T1w2MNI_Warped.nii.gz ]; then
  553. echo " computing the spatial normalisation (warp) of the T1w to MNI (takes about 20 minutes)"
  554. my_cmd="antsRegistrationSyN.sh -d 3 -f ${fix_im} -m ${mov_im} \
  555. -o ${output} -n ${ncpu} -j 1 -t s $fs_silent"
  556. eval $my_cmd
  557. else
  558. echo " skipping MNI spatial normalisation, since it's already computed"
  559. fi
  560. fi
  562. # PART 4 - run fastsurfer (optional)
  563. if [ $deel -ge 4 ] && [ $fastsurf -gt 0 ]; then
  564. mkdir -p $outdir/fs
  565. #export FREESURFER_HOME=/usr/local/KUL_apps/freesurfer6
  566. #source $FREESURFER_HOME/SetUpFreeSurfer.sh
  567. if [ ! -f $outdir/fs/$base/mri/aparc.DKTatlas+aseg.deep.mgz ]; then
  568. if [ $fastsurf -eq 1 ]; then
  569. echo " running full fastsufer"
  570. my_cmd="$FASTSURFER_HOME/run_fastsurfer.sh \
  571. --sid $base --sd $outdir/fs \
  572. --t1 $test_T1w \
  573. --fs_license $FS_LICENSE \
  574. --py python --parallel --ignore_fs_version --threads $ncpu $fs_silent"
  575. elif [ $fastsurf -eq 2 ]; then
  576. echo " running segmentation-with-CC & stats fastsufer"
  577. my_cmd="$FASTSURFER_HOME/run_fastsurfer.sh \
  578. --sid $base --sd $outdir/fs \
  579. --t1 $test_T1w \
  580. --fs_license $FS_LICENSE \
  581. --seg_with_cc_only --py python --ignore_fs_version --threads $ncpu $fs_silent"
  582. elif [ $fastsurf -eq 3 ]; then
  583. echo " running segmentation-only fastsufer"
  584. my_cmd="$FASTSURFER_HOME/run_fastsurfer.sh \
  585. --sid $base --sd $outdir/fs \
  586. --t1 $test_T1w \
  587. --seg_only --py python --ignore_fs_version --threads $ncpu $fs_silent"
  588. fi
  589. eval $my_cmd
  590. else
  591. echo " fastsurfer seems to have run already"
  592. fi
  593. fi
  595. # PART 5 - MS lesion segmentation (optional)
  596. MSlesion="$outdir/rois/${base}_MSLesion.nii.gz"
  597. if [ $deel -ge 5 ] && [ $ms -eq 1 ];then
  598. if [ $flair -eq 1 ];then
  599. if [ ! -f $MSlesion ];then
  600. echo " running samseg (takes about 20 minutes)"
  601. T1w_iso="$outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz"
  602. FLAIR_reg2T1w="$outdir/tmp/${base}_FLAIR_iso_biascorrected_reg2T1w.nii.gz"
  603. my_cmd="run_samseg --input $T1w_iso $FLAIR_reg2T1w --pallidum-separate \
  604. --lesion --lesion-mask-pattern 0 1 --output $outdir/samseg \
  605. --threads $ncpu $fs_silent"
  606. eval $my_cmd
  607. SamSeg="$outdir/samseg/seg.mgz"
  608. mrcalc $SamSeg 99 -eq $MSlesion -force -nthreads $ncpu
  609. else
  610. echo " already ran samseg"
  611. fi
  612. else
  613. echo " Warning! No Flair available to do lesion MS segmentation"
  614. fi
  615. fi
  617. # PART 6 - hd-bet and background search
  618. if [ $deel -ge 6 ];then
  619. # hd-bet brain extraction of the T1w
  621. if [ ! -f $outdir/tmp/${base}_T1w_iso_biascorrected_brain.nii.gz ]; then
  622. echo " doing hd-bet on ${base}_T1w_iso_biascorrected.nii.gz"
  623. my_cmd="hd-bet -i $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  624. -o $outdir/tmp/${base}_T1w_iso_biascorrected_brain.nii.gz $fs_silent"
  625. eval $my_cmd
  626. mv $outdir/tmp/${base}_T1w_iso_biascorrected_brain_mask.nii.gz $outdir/masks
  627. else
  628. echo " skipping hd-bet on ${base}_T1w_iso_biascorrected.nii.gz - already done"
  629. fi
  631. # find the background by thresholding the T1w
  632. background="$outdir/masks/${base}_T1w_iso_biascorrected_background.nii.gz"
  633. if [ ! -f $background ]; then
  634. max_T1w=$(mrstats $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz -output max)
  635. echo " thresholding background using 0.5% of max signal of the T1w - $max_T1w"
  636. mrcalc $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz $max_T1w 0.005 -mul -lt \
  637. $background -force -nthreads $ncpu
  638. else
  639. echo " thresholding background already done"
  640. fi
  641. fi
  643. # PART 7 - Calibration
  644. check7="$outdir/histograms/${base}_T1w_iso_biascorrected_calib-nonlin3_histogram.csv"
  645. if [ $deel -ge 7 ] && [ ! -f $check7 ];then
  647. # -----------------------------------------------------------------------------------------------------------------------------
  648. # METHOD 1 - LINEAR histogram matching using eye/muscle tissue
  649. echo " performing linear histogram matching"
  651. M1_template_T1w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T1w.nii.gz"
  652. M1_template_T2w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T2w.nii.gz"
  653. M1_template_FLAIR="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T2w.nii.gz"
  655. M1_template_mask_eye="$kul_main_dir/atlasses/Ganzetti2014/eyemask.nii"
  656. M1_template_mask_tempmuscle="$kul_main_dir/atlasses/Ganzetti2014/tempmask.nii"
  658. # Warp the eye and muscle back to subject space
  659. echo " warping eye/muscle and skull/air back to subject space"
  660. reference=$mov_im
  662. # REVIEW SARAH: There was a bug here in the order of transforms
  663. transform2="$outdir/warp2mni/${base}_T1w2MNI_1InverseWarp.nii.gz"
  664. transform1="[$outdir/warp2mni/${base}_T1w2MNI_0GenericAffine.mat,1]"
  665. interpolation_type="NearestNeighbor"
  667. input=$M1_template_mask_eye
  668. output="$outdir/masks/${base}_method1_eye.nii.gz"
  669. KUL_antsApply_Transform_MNI
  671. input=$M1_template_mask_tempmuscle
  672. output="$outdir/masks/${base}_method1_tempmuscle.nii.gz"
  673. KUL_antsApply_Transform_MNI
  675. # sum the masks
  676. mrcalc $outdir/masks/${base}_method1_eye.nii.gz $outdir/masks/${base}_method1_tempmuscle.nii.gz -add \
  677. $outdir/masks/${base}_method1_eye_and_muscle.nii.gz -nthreads $ncpu -force
  678. mrcalc $M1_template_mask_eye $M1_template_mask_tempmuscle -add \
  679. $outdir/masks/${base}_method1_mni_eye_and_muscle.nii.gz -nthreads $ncpu -force
  681. # do the LINEAR histogram matching using eye/muscle tissue
  682. mrhistmatch \
  683. -mask_input $outdir/masks/${base}_method1_eye_and_muscle.nii.gz \
  684. -mask_target $outdir/masks/${base}_method1_mni_eye_and_muscle.nii.gz \
  685. linear \
  686. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  687. $M1_template_T1w \
  688. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-lin.nii.gz -nthreads $ncpu -force
  690. mrhistogram -bin 100 -ignorezero \
  691. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  692. $outdir/histograms/${base}_T1w_iso_biascorrected_histogram.csv -force
  693. mrhistogram -bin 100 -ignorezero \
  694. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-lin.nii.gz \
  695. $outdir/histograms/${base}_T1w_iso_biascorrected_calib-lin_histogram.csv -nthreads $ncpu -force
  697. if [ $t2 -eq 1 ];then
  698. mrhistmatch \
  699. -mask_input $outdir/masks/${base}_method1_eye_and_muscle.nii.gz \
  700. -mask_target $outdir/masks/${base}_method1_mni_eye_and_muscle.nii.gz \
  701. linear \
  702. $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz \
  703. $M1_template_T2w \
  704. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-lin_reg2T1w.nii.gz -nthreads $ncpu -force
  706. mrhistogram -bin 100 -ignorezero \
  707. $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz \
  708. $outdir/histograms/${base}_T2w_iso_biascorrected_reg2T1w_histogram.csv -force
  709. mrhistogram -bin 100 -ignorezero \
  710. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-lin_reg2T1w.nii.gz \
  711. $outdir/histograms/${base}_T2w_iso_biascorrected_calib-lin_reg2T1w_histogram.csv -nthreads $ncpu -force
  712. fi
  714. if [ $flair -eq 1 ];then
  715. # Note: this is probably not a good calibration, since Ganzetti did not have a MNI-FLAIR
  716. mrhistmatch \
  717. -mask_input $outdir/masks/${base}_method1_eye_and_muscle.nii.gz \
  718. -mask_target $outdir/masks/${base}_method1_mni_eye_and_muscle.nii.gz \
  719. linear \
  720. $outdir/tmp/${base}_FLAIR_iso_biascorrected_reg2T1w.nii.gz \
  721. $M1_template_FLAIR \
  722. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-lin_reg2T1w.nii.gz -nthreads $ncpu -force
  724. mrhistogram -bin 100 -ignorezero \
  725. $outdir/tmp/${base}_FLAIR_iso_biascorrected_reg2T1w.nii.gz \
  726. $outdir/histograms/${base}_FLAIR_iso_biascorrected_reg2T1w_histogram.csv -force
  727. mrhistogram -bin 100 -ignorezero \
  728. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-lin_reg2T1w.nii.gz \
  729. $outdir/histograms/${base}_FLAIR_iso_biascorrected_calib-lin_reg2T1w_histogram.csv -nthreads $ncpu -force
  730. fi
  733. # -----------------------------------------------------------------------------------------------------------------------------
  734. # METHOD 2 - the NON-LINEAR histogram matching using non-brain tissue
  735. echo " performing nonlinear histogram matching"
  736. # Warp the brain_mask and its inverse to subject space
  738. M2_template_T1w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T1w.nii.gz"
  739. M2_template_T2w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T2w.nii.gz"
  740. M2_template_FLAIR="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_T2w.nii.gz"
  742. input="$kul_main_dir/atlasses/Ganzetti2014/brainmask_mni_dilated.nii"
  743. output="$outdir/masks/${base}_method2_MNI2subj_brainmask_mni_dilated.nii.gz"
  744. KUL_antsApply_Transform_MNI
  745. input="$kul_main_dir/atlasses/Ganzetti2014/brainmask_mni_dilated_inverse.nii"
  746. output="$outdir/masks/${base}_method2_MNI2subj_brainmask_mni_dilated_inverse.nii.gz"
  747. KUL_antsApply_Transform_MNI
  749. mrhistmatch \
  750. -mask_input $outdir/masks/${base}_method2_MNI2subj_brainmask_mni_dilated_inverse.nii.gz \
  751. -mask_target $kul_main_dir/atlasses/Ganzetti2014/brainmask_mni_dilated_inverse.nii \
  752. nonlinear \
  753. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  754. $M2_template_T1w \
  755. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin.nii.gz -nthreads $ncpu -force
  757. mrhistogram -bin 100 -ignorezero \
  758. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin.nii.gz \
  759. $outdir/histograms/${base}_T1w_iso_biascorrected_calib-nonlin_histogram.csv -nthreads $ncpu -force
  761. if [ $t2 -eq 1 ];then
  762. mrhistmatch \
  763. -mask_input $outdir/masks/${base}_method2_MNI2subj_brainmask_mni_dilated_inverse.nii.gz \
  764. -mask_target $kul_main_dir/atlasses/Ganzetti2014/brainmask_mni_dilated_inverse.nii \
  765. nonlinear \
  766. $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz \
  767. $M2_template_T2w \
  768. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-nonlin_reg2T1w.nii.gz -nthreads $ncpu -force
  770. mrhistogram -bin 100 -ignorezero \
  771. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-nonlin_reg2T1w.nii.gz \
  772. $outdir/histograms/${base}_T2w_iso_biascorrected_calib-nonlin_reg2T1w_histogram.csv -nthreads $ncpu -force
  773. fi
  775. if [ $flair -eq 1 ];then
  776. mrhistmatch \
  777. -mask_input $outdir/masks/${base}_method2_MNI2subj_brainmask_mni_dilated_inverse.nii.gz \
  778. -mask_target $kul_main_dir/atlasses/Ganzetti2014/brainmask_mni_dilated_inverse.nii \
  779. nonlinear \
  780. $outdir/tmp/${base}_FLAIR_iso_biascorrected_reg2T1w.nii.gz \
  781. $M2_template_FLAIR \
  782. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-nonlin_reg2T1w.nii.gz -nthreads $ncpu -force
  784. mrhistogram -bin 100 -ignorezero \
  785. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-nonlin_reg2T1w.nii.gz \
  786. $outdir/histograms/${base}_FLAIR_iso_biascorrected_calib-nonlin_reg2T1w_histogram.csv -nthreads $ncpu -force
  787. fi
  791. # Method 3 - Cappelle & Sunaert
  792. echo " performing second (Cappelle) nonlinear histogram matching"
  794. M3_template_T1w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_T1w.nii.gz"
  795. M3_template_T2w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_T2w.nii.gz"
  796. M3_template_FLAIR="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_FLAIR.nii.gz"
  798. M3_template_mask_4_T1w="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_mask_4_T1w.nii.gz"
  799. M3_template_mask_4_T2w_and_FLAIR="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_mask_4_T2w_and_FLAIR.nii.gz"
  801. mask1="$outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz"
  802. mask2="$outdir/masks/${base}_T1w_iso_biascorrected_brain_inverted_mask.nii.gz"
  803. mrcalc $mask1 0.1 -lt $mask2 -nthreads $ncpu -force
  805. mask3="$outdir/masks/${base}_T1w_iso_biascorrected_brain_inverted_mask_nobackground.nii.gz"
  806. mrcalc $mask1 0.1 -lt $background -sub 0.1 -gt $mask3 -nthreads $ncpu -force
  809. # do the scond NON-LINEAR histogram matching using non-brain tissue
  810. mrhistmatch \
  811. -mask_input $mask3 \
  812. -mask_target $M3_template_mask_4_T1w \
  813. nonlinear \
  814. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  815. $M3_template_T1w \
  816. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin2.nii.gz -nthreads $ncpu -force
  818. mrhistogram -bin 100 -ignorezero \
  819. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin2.nii.gz \
  820. $outdir/histograms/${base}_T1w_iso_biascorrected_calib-nonlin2_histogram.csv -nthreads $ncpu -force
  822. if [ $t2 -eq 1 ];then
  823. td="T2w"
  824. # find the ventricles by thresholding the T2w
  825. max_T2w=$(mrstats $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz -output max)
  826. echo " max signal of the T2w is $max_T2w"
  827. ventricles="$outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w_ventricules.nii.gz"
  828. mrcalc $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz $max_T2w 0.75 -mul -gt \
  829. $ventricles -nthreads $ncpu -force
  830. skull_and_ventricules="$outdir/masks/${base}_T2w_iso_biascorrected_reg2T1w_skull_and_ventricules.nii.gz"
  831. mrcalc $mask3 $ventricles -add 0.1 -gt $skull_and_ventricules -nthreads $ncpu -force
  833. # do the scond NON-LINEAR histogram matching using non-brain tissue
  834. mrhistmatch \
  835. -mask_input $skull_and_ventricules \
  836. -mask_target $M3_template_mask_4_T2w_and_FLAIR \
  837. nonlinear \
  838. $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz \
  839. $M3_template_T2w \
  840. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w.nii.gz -nthreads $ncpu -force
  841. mrhistogram -bin 100 -ignorezero \
  842. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w.nii.gz \
  843. $outdir/histograms/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w_histogram.csv -nthreads $ncpu -force
  844. fi
  846. if [ $flair -eq 1 ] && [ $t2 -eq 1 ];then
  847. td="FLAIR"
  848. # find the ventricles by thresholding the T2w
  849. max_T2w=$(mrstats $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz -output max)
  850. echo " max signal of the T2w is $max_T2w"
  851. ventricles="$outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w_ventricules.nii.gz"
  852. mrcalc $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz $max_T2w 0.75 -mul -gt \
  853. $ventricles -nthreads $ncpu -force
  854. skull_and_ventricules="$outdir/masks/${base}_FLAIR_iso_biascorrected_reg2T1w_skull_and_ventricules.nii.gz"
  855. mrcalc $mask3 $ventricles -add 0.1 -gt $skull_and_ventricules -nthreads $ncpu -force
  857. # do the scond NON-LINEAR histogram matching using non-brain tissue
  858. mrhistmatch \
  859. -mask_input $skull_and_ventricules \
  860. -mask_target $M3_template_mask_4_T2w_and_FLAIR \
  861. nonlinear \
  862. $outdir/tmp/${base}_${td}_iso_biascorrected_reg2T1w.nii.gz \
  863. $M3_template_FLAIR \
  864. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w.nii.gz -nthreads $ncpu -force
  865. mrhistogram -bin 100 -ignorezero \
  866. $outdir/tmp/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w.nii.gz \
  867. $outdir/histograms/${base}_${td}_iso_biascorrected_calib-nonlin2_reg2T1w_histogram.csv -nthreads $ncpu -force
  868. fi
  872. # Last method of calibration
  873. # do it in the whole image except for the MS lesions
  875. M4_template_T1w=$M3_template_T1w
  876. M4_template_T2w=$M3_template_T2w
  877. M4_template_FLAIR=$M3_template_FLAIR
  878. M4_template_mask="$kul_main_dir/atlasses/Local/Cappelle2021/tpl-MNI152NLin2009aSym_res-1_Cappelle2021_T1w_mask_brain_mask.nii.gz"
  880. mask1="$outdir/masks/${base}_T1w_iso_biascorrected_brain_mask.nii.gz"
  881. mask_subj="$outdir/masks/${base}_method4_brain_mask_without_lesions.nii.gz"
  882. MSlesion_dilated="$outdir/masks/${base}_method4_MSlesion_dilated.nii.gz"
  883. maskfilter $MSlesion dilate $MSlesion_dilated -force
  884. mrcalc $mask1 $MSlesion_dilated -subtract $mask_subj -nthreads $ncpu -force
  887. mrhistmatch \
  888. -mask_input $mask_subj \
  889. -mask_target $M4_template_mask \
  890. nonlinear \
  891. $outdir/tmp/${base}_T1w_iso_biascorrected.nii.gz \
  892. $M4_template_T1w \
  893. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin3.nii.gz -nthreads $ncpu -force
  895. mrhistogram -bin 100 -ignorezero \
  896. $outdir/tmp/${base}_T1w_iso_biascorrected_calib-nonlin3.nii.gz \
  897. $outdir/histograms/${base}_T1w_iso_biascorrected_calib-nonlin3_histogram.csv -nthreads $ncpu -force
  899. if [ $t2 -eq 1 ];then
  900. mrhistmatch \
  901. -mask_input $mask_subj \
  902. -mask_target $M4_template_mask \
  903. nonlinear \
  904. $outdir/tmp/${base}_T2w_iso_biascorrected_reg2T1w.nii.gz \
  905. $M4_template_T2w \
  906. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-nonlin3_reg2T1w.nii.gz -nthreads $ncpu -force
  908. mrhistogram -bin 100 -ignorezero \
  909. $outdir/tmp/${base}_T2w_iso_biascorrected_calib-nonlin3_reg2T1w.nii.gz \
  910. $outdir/histograms/${base}_T2w_iso_biascorrected_calib-nonlin3_histogram.csv -nthreads $ncpu -force
  911. fi
  913. if [ $flair -eq 1 ];then
  914. mrhistmatch \
  915. -mask_input $mask_subj \
  916. -mask_target $M4_template_mask \
  917. nonlinear \
  918. $outdir/tmp/${base}_FLAIR_iso_biascorrected_reg2T1w.nii.gz \
  919. $M4_template_FLAIR \
  920. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-nonlin3_reg2T1w.nii.gz -nthreads $ncpu -force
  922. mrhistogram -bin 100 -ignorezero \
  923. $outdir/tmp/${base}_FLAIR_iso_biascorrected_calib-nonlin3_reg2T1w.nii.gz \
  924. $outdir/histograms/${base}_FLAIR_iso_biascorrected_calib-nonlin3_histogram.csv -nthreads $ncpu -force
  925. fi
  928. fi
  931. # PART 8 - compute the ratio
  932. if [ $deel -ge 8 ];then
  933. if [ $t2 -eq 1 ];then
  934. td="T2w"
  935. KUL_computeratio
  936. fi
  938. if [ $flair -eq 1 ];then
  939. td="FLAIR"
  940. KUL_computeratio
  941. fi
  942. fi
  945. # PART 9 - MTI and MTR
  946. test_done_MTI="$outdir/${base}_ratio-MTC_MNI.nii.gz"
  947. if [ $deel -ge 9 ] && [ $mti -eq 1 ] && [ ! -f $test_done_MTI ];then
  948. input=$test_MTI
  949. output=${test_MTI##*/}
  950. output=${output%%.*}
  951. echo " doing hd-bet of the MTI"
  952. KUL_MTI_reorient_crop_hdbet_iso
  953. td="MTI"
  954. echo " coregistering MTI to T1 and computing the MTC ratio"
  955. KUL_MTI_register_computeratio
  956. fi
  958. # PART 10 - warping results to mni too
  959. if [ $deel -ge 10 ];then
  960. td="T1w"
  961. KUL_apply_warp2mni
  962. if [ $t2 -eq 1 ];then
  963. td="T2w"
  964. KUL_apply_warp2mni
  965. fi
  967. if [ $flair -eq 1 ];then
  968. td="FLAIR"
  969. KUL_apply_warp2mni
  970. fi
  972. if [ $mti -eq 1 ];then
  973. td="MTI"
  974. KUL_apply_warp2mni
  975. fi
  976. fi
  979. #rm -fr $outdir/tmp/${base}*.gz
  980. #cd T1T2FLAIRMTR_ratio/tmp/
  981. #rm -fr *std.nii.gz *iso.nii.gz *ted.nii.gz *reg2T1w.nii.gz *mask.nii.gz *eye.nii.gz *muscle.nii.gz *.csv *MTI* *MNI.nii.gz *verse.nii.gz *inv.nii.gz *brain.nii.gz
  982. #rm -fr *std.nii.gz *iso.nii.gz *ted.nii.gz *reg2T1w.nii.gz *eye.nii.gz *muscle.nii.gz *.csv *MTI* *MNI.nii.gz *verse.nii.gz *inv.nii.gz *brain.nii.gz
  983. #cd ../..
  985. echo ${deel} > $check_done
  987. echo " done"
  989. else
  990. echo " Nothing to do here"
  991. fi
  992. fi
  994. else
  995. echo " $base already done"
  996. fi
  998. done

KUL_T1T2FLAIRMTR_ratio.sh at commit 2c11248, under MPL-2.0 · at the source

Overview

Authors: Britta Krieger1, Barbara Bellenberg1, Dajana Müller1, Hasan Sbaihat1, Anna Katharina Roenneke1, Theodoros Ladopoulos2, Ruth Schneider2, Ralf Gold2, Carsten Lukas1,2
ORCID iDs: Britta Krieger, Barbara Bellenberg, Dajana Müller, Hasan Sbaihat, Anna Katharina Roenneke, Theodoros Ladopoulos, Ruth Schneider, Ralf Gold, Carsten Lukas
  1. Ruhr University Bochum, St. Josef Hospital, Institute of Neuroradiology, 44791 Bochum, Germany
  2. Ruhr University Bochum, St. Josef Hospital, Department of Neurology, 44791 Bochum, Germany
Institutions: St. Josef-Hospital (Germany); Ruhr University Bochum (Germany)
Journal: Brain communications, volume 8, issue 3, article fcag129
Dates: received 1 September 2025; accepted 17 April 2026; published online 18 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag129 · PMID 42158849 · PMCID PMC13180650 · OpenAlex W7154861551
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), multiple sclerosis (population), clinical / translational (subfield)
Methods: Statistics
Keywords: multiple sclerosis, brain MRI, choroid plexus, longitudinal, lesions
Topic: Multiple Sclerosis Research Studies (Pathology and Forensic Medicine, Medicine), according to OpenAlex
Citations: not cited yet (Europe PMC); 46 references in the paper

Abstract

This longitudinal study aimed to identify the predictive role of choroid plexus enlargement for disability progression and its association with tissue damage in early multiple sclerosis patients. Forty patients with clinically isolated syndrome or early relapsing–remitting multiple sclerosis underwent brain MRI scanning at baseline, after 2 and after 6–8 years. FreeSurfer segmentation was used for brain volume estimation, and the choroid plexus was segmented by use of an independent automated segmentation tool. MRI ratios (T1 weighted through fluid attenuated inversion recovery image values) were calculated after calibration and subtracting lesion masks. Lesion masks were eroded to obtain both lesion rims and centres, for which mean ratios were extracted in addition to normal-appearing white matter. Expanded Disability Status Scale and disease duration were collected from neurological examination. Between baseline and last follow-up, choroid plexus volumes increased, and MRI ratios in lesions decreased significantly, which was dominated by the decrease in clinically isolated syndrome rather than relapsing–remitting patients and more pronounced in lesion rims than in their centre. Choroid plexus volumes were significantly related to MRI ratios within rims of lesions at baseline and within lesion centres after 6–8 years, but not within normal-appearing white matter. No associations between choroid plexus volumes or ratios and disability were found. We observed longitudinal changes of both choroid plexus enlargement and MRI ratios over 6–8 years in early multiple sclerosis patients. Choroid plexus enlargement seemed involved in the dynamic development of lesion destructivity.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

treanus/KUL_NIS

License: MPL-2.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 2c11248436041bffa0a63ae7f819317b03efb3ad, 18 August 2023
Languages: Shell (42), MATLAB (8), Python (7)
Size: 171 files, 57 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, license file, documentation
Not found: CITATION.cff, environment file, tests, continuous integration
Tools: MRtrix3 (29 files), ANTs (14 files), FSL (9 files), FreeSurfer (7 files), SPM (6 files), BIDS Validator (4 files), NumPy (4 files), Dcm2Bids (2 files), NiBabel (2 files), SciPy (2 files), fMRIPrep (1 file), Statistics and Machine Learning Toolbox (1 file), MRIQC (1 file), pandas (1 file), SimpleITK (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
59 files
At the source: github.com/treanus/KUL_NIS

Center-of-Imaging-Biomarker-Development/chp_seg

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: c00eaa243d7a2e749a254489d3b8c48197f70f5c, 2 June 2025
Size: 1 file, 0 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
1 file
At the source: github.com/Center-of-Imaging-Biomarker-Development/chp_seg

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 57 scripts, each with its path and the digest of its content;
  • 1 match 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 availability

Raw MRI and clinical data cannot be made available due to data protection regulations. The pipeline used for the creation of T1w/FLAIR ratio maps is publicly available at https://github.com/treanus/KUL_NIS. For choroid plexus segmentation, we used a publicly available toolbox (https://github.com/Center-of-Imaging-Biomarker-Development/chp_seg).

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 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 5 keywords, 43 references.

Cite

This paper

Krieger, B., Bellenberg, B., Müller, D., Sbaihat, H., Roenneke, A. K., Ladopoulos, T., Schneider, R., Gold, R., & Lukas, C. (2026). Longitudinal changes of choroid plexus volumes and MRI ratios in multiple sclerosis. Brain communications, 8(3), fcag129. https://doi.org/10.1093/braincomms/fcag129

BibTeX

@article{krieger2026longitudinal,
author = {Krieger, Britta and Bellenberg, Barbara and Müller, Dajana and Sbaihat, Hasan and Roenneke, Anna Katharina and Ladopoulos, Theodoros and Schneider, Ruth and Gold, Ralf and Lukas, Carsten},
title = {{Longitudinal changes of choroid plexus volumes and MRI ratios in multiple sclerosis}},
journal = {Brain communications},
year = {2026},
month = apr,
volume = {8},
number = {3},
pages = {fcag129},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag129},
url = {https://doi.org/10.1093/braincomms/fcag129},
pmid = {42158849},
pmcid = {PMC13180650}
}

RIS

TY - JOUR
AU - Krieger, Britta
AU - Bellenberg, Barbara
AU - Müller, Dajana
AU - Sbaihat, Hasan
AU - Roenneke, Anna Katharina
AU - Ladopoulos, Theodoros
AU - Schneider, Ruth
AU - Gold, Ralf
AU - Lukas, Carsten
TI - Longitudinal changes of choroid plexus volumes and MRI ratios in multiple sclerosis
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/04/18
VL - 8
IS - 3
SP - fcag129
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag129
UR - https://doi.org/10.1093/braincomms/fcag129
LA - en
ER -

CSL-JSON

{
"id": "10.1093/braincomms/fcag129",
"type": "article-journal",
"title": "Longitudinal changes of choroid plexus volumes and MRI ratios in multiple sclerosis",
"container-title": "Brain communications",
"author": [
{
"family": "Krieger",
"given": "Britta"
},
{
"family": "Bellenberg",
"given": "Barbara"
},
{
"family": "Müller",
"given": "Dajana"
},
{
"family": "Sbaihat",
"given": "Hasan"
},
{
"family": "Roenneke",
"given": "Anna Katharina"
},
{
"family": "Ladopoulos",
"given": "Theodoros"
},
{
"family": "Schneider",
"given": "Ruth"
},
{
"family": "Gold",
"given": "Ralf"
},
{
"family": "Lukas",
"given": "Carsten"
}
],
"container-title-short": "Brain Commun",
"volume": "8",
"issue": "3",
"page": "fcag129",
"DOI": "10.1093/braincomms/fcag129",
"PMID": "42158849",
"PMCID": "PMC13180650",
"ISSN": "2632-1297",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/braincomms/fcag129",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
18
]
]
}
}

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

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