-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathFreeSurfer2HCPWorkbenchConverter.sh
executable file
·456 lines (382 loc) · 34.1 KB
/
FreeSurfer2HCPWorkbenchConverter.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
#!/bin/bash
set -e
#set -x
# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP), wb_command
# environment: FSLDIR , FREESURFER_HOME , HCPPIPEDIR , CARET7DIR
# Author: Alex Cohen, adapted from HCP Pipelines code, cloned at commit b8ea1db
# --------------------------------------------------------------------------------
# Load Function Libraries
# --------------------------------------------------------------------------------
source $HCPPIPEDIR/global/scripts/log.shlib # Logging related functions
source $HCPPIPEDIR/global/scripts/opts.shlib # Command line option functions
########################################## SUPPORT FUNCTIONS ##########################################
# --------------------------------------------------------------------------------
# Usage Description Function
# --------------------------------------------------------------------------------
show_usage() {
echo "This makes a subdir /hcp and creates wb_view .spec files from the FS output"
echo " Inputs:"
echo " --subject=fc_12345"
echo " [--path=/blah/blah/blah] if not specified, assumes pwd"
echo " [--layers=0.33@0.66] to make more cortical surfaces (0->1 ~ white->pial)"
echo " [--subcort=1.3@2] to make subcortical surfaces (mm below white)"
echo " [--target=rawavg] if not specified, assumes T1"
echo " [--lowres=8] 8=8,412nodes, 32=32,492 nodes. Will always make 32k, specify if other resolutions desired"
exit 1
}
defaultopt() {
echo $1
}
# --------------------------------------------------------------------------------
# Establish tool name for logging
# --------------------------------------------------------------------------------
log_SetToolName "FreeSurfer2HCPWorkbenchConverter.sh"
################################################## OPTION PARSING #####################################################
opts_ShowVersionIfRequested $@
if opts_CheckForHelpRequest $@; then
show_usage
fi
log_Msg "Parsing Command Line Options"
# Input Variables
StudyFolder=`opts_GetOpt1 "--path" $@`
Subject=`opts_GetOpt1 "--subject" $@`
Layers=`opts_GetOpt1 "--layers" $@`
Subcort=`opts_GetOpt1 "--subcort" $@`
Target=`opts_GetOpt1 "--target" $@`
LowResMesh=`opts_GetOpt1 "--lowres" $@`
#Initializing Variables with Default Values if not otherwise specified
WD=`pwd`
StudyFolder=`defaultopt $StudyFolder $WD`
Layers=`defaultopt $Layers ""`
Subcort=`defaultopt $Subcort ""`
Target=`defaultopt $Target T1`
LowResMeshes=`echo $LowResMesh "32"`
FreeSurferFolder="$StudyFolder"/"$Subject"
SUBJECTS_DIR="$StudyFolder"
# Hardcoded parameters
HCPFolder="$FreeSurferFolder"/hcp
FreeSurferLabels="${HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
SurfaceAtlasDIR="${HCPPIPEDIR_Templates}/standard_mesh_atlases"
HighResMesh="164"
RegName="FS"
GrayordinatesSpaceDIR="${HCPPIPEDIR_Templates}/91282_Greyordinates"
# Make output folder
if [ ! -e "$HCPFolder" ] ; then
mkdir -p "$HCPFolder"
else
echo "*******"
echo "WARNING: The hcp sub-directory already exists, are you sure you want to re-run this script?"
echo "*******"
read -p "(y or n): " -n 1 -r REPLY
echo ""
if [[ ! $REPLY =~ ^[Yy]$ ]]
then
exit 1
fi
fi
#Find c_ras offset between FreeSurfer surface and volume and generate matrix to transform surfaces
MatrixX=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_r" | cut -d "=" -f 5 | sed s/" "/""/g`
MatrixY=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_a" | cut -d "=" -f 5 | sed s/" "/""/g`
MatrixZ=`mri_info "$FreeSurferFolder"/mri/brain.finalsurfs.mgz | grep "c_s" | cut -d "=" -f 5 | sed s/" "/""/g`
echo "1 0 0 ""$MatrixX" > "$FreeSurferFolder"/mri/c_ras.mat
echo "0 1 0 ""$MatrixY" >> "$FreeSurferFolder"/mri/c_ras.mat
echo "0 0 1 ""$MatrixZ" >> "$FreeSurferFolder"/mri/c_ras.mat
echo "0 0 0 1" >> "$FreeSurferFolder"/mri/c_ras.mat
#Convert FreeSurfer Volumes (and transform to $Target, if not T1.mgz)
for Image in wmparc aparc.a2009s+aseg aparc+aseg ; do
if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
if [ ! $Target = "T1" ] ; then
mri_label2vol --seg "$FreeSurferFolder"/mri/"$Image".mgz --temp "$FreeSurferFolder"/mri/"$Target".mgz --o "$FreeSurferFolder"/mri/"$Image"-in-"$Target".mgz --regheader "$FreeSurferFolder"/mri/"$Image".mgz
NewImage=`echo ${Image}-in-"${Target}"`
touch "$HCPFolder"/All_Files_are_registered_to_"$Target"
else
NewImage=$Image
touch "$HCPFolder"/All_Files_are_registered_to_T1
fi
mri_convert -ot nii "$FreeSurferFolder"/mri/"$NewImage".mgz "$HCPFolder"/"$Image".nii.gz
fslreorient2std "$HCPFolder"/"$Image".nii.gz "$HCPFolder"/"$Image".nii.gz
${CARET7DIR}/wb_command -volume-label-import "$HCPFolder"/"$Image".nii.gz "$FreeSurferLabels" "$HCPFolder"/"$Image".nii.gz -drop-unused-labels
fi
done
#Add Anatomical Volumes
for Image in $Target ; do
if [ -e "$FreeSurferFolder"/mri/"$Image".mgz ] ; then
mri_convert -ot nii "$FreeSurferFolder"/mri/"$Image".mgz "$HCPFolder"/"$Image".nii.gz
fslreorient2std "$HCPFolder"/"$Image".nii.gz "$HCPFolder"/"$Image".nii.gz
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec INVALID ./"$Image".nii.gz
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec INVALID ./"$Image".nii.gz
popd > /dev/null
fi
done
#Loop through left and right hemispheres
for Hemisphere in L R ; do
#Set a bunch of different ways of saying left and right
if [ $Hemisphere = "L" ] ; then
hemisphere="l"
Structure="CORTEX_LEFT"
elif [ $Hemisphere = "R" ] ; then
hemisphere="r"
Structure="CORTEX_RIGHT"
fi
#native Mesh Processing
#Convert and volumetrically register white and pial surfaces makign linear and nonlinear copies, add each to the appropriate spec file
Types="ANATOMICAL@GRAY_WHITE ANATOMICAL@PIAL"
i=1
for Surface in white pial ; do
Type=`echo "$Types" | cut -d " " -f $i`
Secondary=`echo "$Type" | cut -d "@" -f 2`
Type=`echo "$Type" | cut -d "@" -f 1`
if [ ! $Secondary = $Type ] ; then
Secondary=`echo " -surface-secondary-type ""$Secondary"`
else
Secondary=""
fi
if [ ! $Target = "T1" ] ; then
tkregister2 --mov "$FreeSurferFolder"/mri/"$Target".mgz --targ "$FreeSurferFolder"/mri/orig.mgz --reg "$FreeSurferFolder"/mri/register."$Target".dat --noedit --regheader
mri_surf2surf --sval-xyz "$Surface" --reg "$FreeSurferFolder"/mri/register."$Target".dat "$FreeSurferFolder"/mri/"$Target".mgz --tval "$hemisphere"h."$Surface"."$Target" --tval-xyz --hemi "$hemisphere"h --s $Subject
NewSurface=`echo ${Surface}.${Target}`
else
NewSurface=$Surface
fi
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$NewSurface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type $Type$Secondary
${CARET7DIR}/wb_command -surface-apply-affine "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface".native.surf.gii
popd > /dev/null
i=$(($i+1))
done
#Create midthickness by averaging white and pial surfaces and use it to make inflated surfacess
for Folder in "$HCPFolder" ; do
pushd > /dev/null "$Folder"
${CARET7DIR}/wb_command -surface-average "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii -surf "$Folder"/"$Subject"."$Hemisphere".white.native.surf.gii -surf "$Folder"/"$Subject"."$Hemisphere".pial.native.surf.gii
${CARET7DIR}/wb_command -set-structure "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type MIDTHICKNESS
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".midthickness.native.surf.gii
${CARET7DIR}/wb_command -surface-generate-inflated "$Folder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".inflated.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".very_inflated.native.surf.gii -iterations-scale 2.5
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated.native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated.native.surf.gii
#Create subcortical surface by eroding the white surface
if [ -z "$Subcort" ] ; then
echo "Not creating subcortical surfaces"
else
echo "Creating subcortical surfaces"
SubcortList=`echo ${Subcort} | sed 's/@/ /g'`
SubcortNameList=`echo subcortlayer_mm_${Subcort} | sed 's/@/ subcortlayer_mm_/g'`
for EachSubLayer in $SubcortList; do
if [ ! $Target = "T1" ] ; then
TargetSuffix=."$Target"
else
TargetSuffix=""
fi
mris_expand "$FreeSurferFolder"/surf/"$hemisphere"h.white"$TargetSuffix" -${EachSubLayer} "$FreeSurferFolder"/surf/"$hemisphere"h.subcortlayer_mm_"$EachSubLayer""$TargetSuffix"
done
for Surface in $SubcortNameList ; do
if [ ! $Target = "T1" ] ; then
NewSurface=`echo ${Surface}.${Target}`
else
NewSurface=$Surface
fi
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$NewSurface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type INVALID
${CARET7DIR}/wb_command -surface-apply-affine "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii "$FreeSurferFolder"/mri/c_ras.mat "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface".native.surf.gii
done
fi
#Create ADDITIONAL cortical layers by averaging white and pial surfaces with variable distance from the surfaces
if [ -z "$Layers" ] ; then
echo "Not creating additional cortical layer surfaces"
else
echo "Creating additional cortical layer surfaces"
LayersList=`echo ${Layers} | sed 's/@/ /g'`
LayersNameList=`echo corticallayer_${Layers} | sed 's/@/ corticallayer_/g'`
for EachLayer in $LayersList; do
${CARET7DIR}/wb_command -surface-cortex-layer "$Folder"/"$Subject"."$Hemisphere".white.native.surf.gii "$Folder"/"$Subject"."$Hemisphere".pial.native.surf.gii "$EachLayer" "$Folder"/"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$Folder"/"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii ${Structure} -surface-type ANATOMICAL -surface-secondary-type INVALID
${CARET7DIR}/wb_command -add-to-spec-file "$Folder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".corticallayer_"$EachLayer".native.surf.gii
done
fi
popd > /dev/null
done
#Convert original and registered spherical surfaces and add them to the spec file
for Surface in sphere.reg sphere ; do
mris_convert "$FreeSurferFolder"/surf/"$hemisphere"h."$Surface" "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${Structure} -surface-type SPHERICAL
done
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject".native.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere.native.surf.gii
popd > /dev/null
#Add more files to the spec file and convert other FreeSurfer surface data to metric/GIFTI including sulc, curv, and thickness.
for Map in sulc@sulc@Sulc thickness@thickness@Thickness curv@curvature@Curvature ; do
fsname=`echo $Map | cut -d "@" -f 1`
wbname=`echo $Map | cut -d "@" -f 2`
mapname=`echo $Map | cut -d "@" -f 3`
mris_convert -c "$FreeSurferFolder"/surf/"$hemisphere"h."$fsname" "$FreeSurferFolder"/surf/"$hemisphere"h.white "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii ${Structure}
${CARET7DIR}/wb_command -metric-math "var * -1" "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -var var "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii -map 1 "$Subject"_"$Hemisphere"_"$mapname"
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere"."$wbname".native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
done
#Thickness specific operations (we should review the implications of the math...)
${CARET7DIR}/wb_command -metric-math "abs(thickness)" "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -var thickness "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
${CARET7DIR}/wb_command -metric-math "thickness > 0" "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var thickness "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-fill-holes "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-remove-islands "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_ROI
${CARET7DIR}/wb_command -metric-dilate "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii -nearest
${CARET7DIR}/wb_command -metric-dilate "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii 10 "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii -nearest
#Label operations
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
${CARET7DIR}/wb_command -set-structure "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii $Structure
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii -map 1 "$Subject"_"$Hemisphere"_"$Map"
${CARET7DIR}/wb_command -gifti-label-add-prefix "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii "${Hemisphere}_" "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii
fi
done
#End main native mesh processing
#Copy Atlas Files
if [ ! -e "$HCPFolder"/fsaverage ] ; then
mkdir -p "$HCPFolder"/fsaverage
fi
cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fsaverage."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
cp "$SurfaceAtlasDIR"/fs_"$Hemisphere"/fs_"$Hemisphere"-to-fs_LR_fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
cp "$SurfaceAtlasDIR"/fsaverage."$Hemisphere"_LR.spherical_std."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
cp "$SurfaceAtlasDIR"/"$Hemisphere".atlasroi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii
cp "$SurfaceAtlasDIR"/"$Hemisphere".refsulc."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii ] ; then
cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".flat."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
fi
#Concatinate FS registration to FS --> FS_LR registration
${CARET7DIR}/wb_command -surface-sphere-project-unproject "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
#Make FreeSurfer Registration Areal Distortion Maps
${CARET7DIR}/wb_command -surface-vertex-areas "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii
${CARET7DIR}/wb_command -surface-vertex-areas "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -metric-math "ln(spherereg / sphere) / ln(2)" "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -var sphere "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii -var spherereg "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
rm "$HCPFolder"/"$Subject"."$Hemisphere".sphere.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.shape.gii
${CARET7DIR}/wb_command -set-map-names "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii -map 1 "$Subject"_"$Hemisphere"_Areal_Distortion_FS
${CARET7DIR}/wb_command -metric-palette "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii MODE_AUTO_SCALE -palette-name ROY-BIG-BL -thresholding THRESHOLD_TYPE_NORMAL THRESHOLD_TEST_SHOW_OUTSIDE -1 1
RegSphere="${HCPFolder}/${Subject}.${Hemisphere}.sphere.reg.reg_LR.native.surf.gii"
#Ensure no zeros in atlas medial wall ROI
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ${RegSphere} BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -largest
${CARET7DIR}/wb_command -metric-math "(atlas + individual) > 0" "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var atlas "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -var individual "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".curvature.native.shape.gii
#Populate Highres fs_LR spec file. Deform surfaces and other data according to native to folding-based registration selected above. Regenerate inflated surfaces.
for Surface in white midthickness pial $LayersNameList $SubcortNameList; do
${CARET7DIR}/wb_command -surface-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface"."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
done
${CARET7DIR}/wb_command -surface-generate-inflated "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii -iterations-scale 2.5
pushd > /dev/null "$HCPFolder"
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/"$Subject"."$HighResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated."$HighResMesh"k_fs_LR.surf.gii
popd > /dev/null
for Map in thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii -current-roi "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere".roi."$HighResMesh"k_fs_LR.shape.gii "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/"$Subject"."$Hemisphere".sulc."$HighResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/"$Subject"."$Hemisphere".midthickness."$HighResMesh"k_fs_LR.surf.gii
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
${CARET7DIR}/wb_command -label-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$HCPFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/"$Subject"."$Hemisphere"."$Map"."$HighResMesh"k_fs_LR.label.gii -largest
fi
done
for LowResMesh in ${LowResMeshes} ; do
if [ ! -e "$HCPFolder"/fsaverage_LR"$LowResMesh"k ] ; then
mkdir -p "$HCPFolder"/fsaverage_LR"$LowResMesh"k
fi
for Image in $Target ; do
pushd > /dev/null "$HCPFolder"/fsaverage_LR"$LowResMesh"k
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec INVALID ../"$Image".nii.gz
popd > /dev/null
done
#Copy Atlas Files
pushd > /dev/null "$HCPFolder"/fsaverage_LR"$LowResMesh"k
cp "$SurfaceAtlasDIR"/"$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii
cp "$GrayordinatesSpaceDIR"/"$Hemisphere".atlasroi."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".roi."$LowResMesh"k_fs_LR.shape.gii
if [ -e "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii ] ; then
cp "$SurfaceAtlasDIR"/colin.cerebral."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".flat."$LowResMesh"k_fs_LR.surf.gii
fi
#Create downsampled fs_LR spec files.
for Surface in white midthickness pial $LayersNameList $SubcortNameList; do
${CARET7DIR}/wb_command -surface-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Surface".native.surf.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere"."$Surface"."$LowResMesh"k_fs_LR.surf.gii
done
${CARET7DIR}/wb_command -surface-generate-inflated "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii -iterations-scale 0.75
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".inflated."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -add-to-spec-file "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$LowResMesh"k_fs_LR.wb.spec $Structure ./"$Subject"."$Hemisphere".very_inflated."$LowResMesh"k_fs_LR.surf.gii
popd > /dev/null
for Map in sulc thickness curvature ; do
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii -current-roi "$HCPFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii
${CARET7DIR}/wb_command -metric-mask "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".roi."$LowResMesh"k_fs_LR.shape.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.shape.gii
done
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".ArealDistortion_FS.native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".ArealDistortion_FS."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
${CARET7DIR}/wb_command -metric-resample "$HCPFolder"/"$Subject"."$Hemisphere".sulc.native.shape.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii ADAP_BARY_AREA "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sulc."$LowResMesh"k_fs_LR.shape.gii -area-surfs "$HCPFolder"/"$Subject"."$Hemisphere".midthickness.native.surf.gii "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".midthickness."$LowResMesh"k_fs_LR.surf.gii
for Map in aparc aparc.a2009s BA ; do
if [ -e "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot ] ; then
${CARET7DIR}/wb_command -label-resample "$HCPFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii ${RegSphere} "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere".sphere."$LowResMesh"k_fs_LR.surf.gii BARYCENTRIC "$HCPFolder"/fsaverage_LR"$LowResMesh"k/"$Subject"."$Hemisphere"."$Map"."$LowResMesh"k_fs_LR.label.gii -largest
fi
done
done
done
STRINGII=""
for LowResMesh in ${LowResMeshes} ; do
STRINGII=`echo "${STRINGII}${HCPFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR@roi "`
done
#Create CIFTI Files
for STRING in "$HCPFolder"@native@roi "$HCPFolder"@"$HighResMesh"k_fs_LR@roi ${STRINGII} ; do
Folder=`echo $STRING | cut -d "@" -f 1`
Mesh=`echo $STRING | cut -d "@" -f 2`
ROI=`echo $STRING | cut -d "@" -f 3`
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.sulc."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.sulc."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -map 1 "${Subject}_Sulc"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".sulc."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.curvature."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.curvature."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -map 1 "${Subject}_Curvature"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".curvature."$Mesh".dscalar.nii -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.thickness."$Mesh".shape.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.thickness."$Mesh".shape.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -map 1 "${Subject}_Thickness"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii MODE_AUTO_SCALE_PERCENTAGE "$Folder"/"$Subject".thickness."$Mesh".dscalar.nii -pos-percent 4 96 -interpolate true -palette-name videen_style -disp-pos true -disp-neg false -disp-zero false
${CARET7DIR}/wb_command -cifti-create-dense-scalar "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -left-metric "$Folder"/"$Subject".L.ArealDistortion_FS."$Mesh".shape.gii -right-metric "$Folder"/"$Subject".R.ArealDistortion_FS."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -map 1 "${Subject}_ArealDistortion_FS"
${CARET7DIR}/wb_command -cifti-palette "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii MODE_USER_SCALE "$Folder"/"$Subject".ArealDistortion_FS."$Mesh".dscalar.nii -pos-user 0 1 -neg-user 0 -1 -interpolate true -palette-name ROY-BIG-BL -disp-pos true -disp-neg true -disp-zero false
for Map in aparc aparc.a2009s BA ; do
if [ -e "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii ] ; then
${CARET7DIR}/wb_command -cifti-create-label "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -left-label "$Folder"/"$Subject".L.${Map}."$Mesh".label.gii -roi-left "$Folder"/"$Subject".L."$ROI"."$Mesh".shape.gii -right-label "$Folder"/"$Subject".R.${Map}."$Mesh".label.gii -roi-right "$Folder"/"$Subject".R."$ROI"."$Mesh".shape.gii
${CARET7DIR}/wb_command -set-map-names "$Folder"/"$Subject".${Map}."$Mesh".dlabel.nii -map 1 "$Subject"_${Map}
fi
done
done
STRINGII=""
for LowResMesh in ${LowResMeshes} ; do
STRINGII=`echo "${STRINGII}${HCPFolder}/fsaverage_LR${LowResMesh}k@${HCPFolder}/fsaverage_LR${LowResMesh}k@${LowResMesh}k_fs_LR"`
done
#Add CIFTI Maps to Spec Files
for STRING in "$HCPFolder"@"$HCPFolder"@native "$HCPFolder"@"$HCPFolder"@"$HighResMesh"k_fs_LR ${STRINGII} ; do
FolderI=`echo $STRING | cut -d "@" -f 1`
FolderII=`echo $STRING | cut -d "@" -f 2`
Mesh=`echo $STRING | cut -d "@" -f 3`
for STRINGII in sulc@dscalar thickness@dscalar curvature@dscalar aparc@dlabel aparc.a2009s@dlabel BA@dlabel ; do
Map=`echo $STRINGII | cut -d "@" -f 1`
Ext=`echo $STRINGII | cut -d "@" -f 2`
if [ -e "$FolderII"/"$Subject"."$Map"."$Mesh"."$Ext".nii ] ; then
pushd > /dev/null "$FolderI"
${CARET7DIR}/wb_command -add-to-spec-file "$FolderI"/"$Subject"."$Mesh".wb.spec INVALID ./"$Subject"."$Map"."$Mesh"."$Ext".nii
popd > /dev/null
fi
done
done