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Deep-MI / FastSurfer

PyTorch implementation of FastSurferCNN
Apache License 2.0
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Missing files compared to freesurfer #548

Closed VoodooCode14 closed 3 months ago

VoodooCode14 commented 3 months ago

Hello,

when running the surface segmentation step of fastsurfer, I'm missing the following files (compared to FreeSurfer):

(and a couple other ones), also the segmentation step is much faster than indicated (approx. 5 minutes), yet there is no error in the logs.

Running the native version (2.0.0) on linux.

Edit: The fastsurfer cmd: $FAST_SURFER_DIR/run_fastsurfer.sh --t1 $2 --sid $1 --sd $SUBJECTS_DIR --py python --parallel --3T --surf_only

VoodooCode14 commented 3 months ago

Output with the surf_only flag:

Setting ENV variable FASTSURFER_HOME to script directory /home/user/FastSurfer. 
Change via environment to location of your choice if this is undesired (export FASTSURFER_HOME=/dir/to/FastSurfer)
which: no python-s in (/usr/local/freesurfer/7.4.1-1//bin:/usr/local/freesurfer/7.4.1-1/fsfast//bin:/usr/local/freesurfer/7.4.1-1//tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/usr/local/MATLAB/R2023b/bin:/usr/local/freesurfer/7.4.1-1/bin:/usr/local/freesurfer/7.4.1-1/fsfast/bin:/usr/local/freesurfer/7.4.1-1/tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/usr/local/MATLAB/R2023b/bin:/usr/local/freesurfer/7.4.1-1/bin:/usr/local/freesurfer/7.4.1-1/fsfast/bin:/usr/local/freesurfer/7.4.1-1/tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/usr/local/MATLAB/R2023b/bin:/usr/local/freesurfer/7.4.1-1/bin:/usr/local/freesurfer/7.4.1-1/fsfast/bin:/usr/local/freesurfer/7.4.1-1/tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/usr/local/MATLAB/R2023b/bin:/usr/local/freesurfer/7.4.1-1/bin:/usr/local/freesurfer/7.4.1-1/fsfast/bin:/usr/local/freesurfer/7.4.1-1/tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/home/user/.local/bin:/home/user/bin:/usr/local/MATLAB/R2023b/bin:/usr/local/freesurfer/7.4.1-1/bin:/usr/local/freesurfer/7.4.1-1/fsfast/bin:/usr/local/freesurfer/7.4.1-1/tktools:/usr/local/freesurfer/7.4.1-1/mni/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/freesurfer/7.4.1-1/bin/:/usr/local/freesurfer/7.4.1-1/fsfast/bin/)
Version: 2.2.0+818acf1
Running run_fastsurfer.sh on a 
~/FastSurfer/recon_surf ~/code/Pre_FinnPy/finnpy_demo_patient_freesurfer_tmp_dir
./recon-surf.sh --sid demo_patient --sd /home/user/data/working/fastsurfer/anatomy --t1 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz --asegdkt_segfile /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz   --3T   --parallel --threads 1 --py python   

sid demo_patient
T1 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz
asegdkt_segfile /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz

Checking Input Segmentation Quality ...
python /home/user/FastSurfer/recon_surf//../FastSurferCNN/quick_qc.py --asegdkt_segfile /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz
Reading in aparc+aseg: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz ...
Estimating ventricle-background intersection volume...
Ventricle-background intersection volume in mm3: 43.00
Checking total volume ...
Voxel size in mm3: 1.0
Total segmentation volume in liter: 0.85

Thu 18 Jul 2024 05:28:02 AM EDT

export SUBJECTS_DIR=/home/user/data/working/fastsurfer/anatomy
cd /home/user/FastSurfer/recon_surf
./recon-surf.sh --sid demo_patient --sd /home/user/data/working/fastsurfer/anatomy --t1 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz --asegdkt_segfile /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz --3T --parallel --threads 1 --py python

freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
$Id$
Linux opennet-32-48.uhnres.utoronto.ca 6.6.11-200.fc39.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Jan 10 19:25:59 UTC 2024 x86_64 GNU/Linux

 RUNNING both hemis in PARALLEL 
 RUNNING 1 number of OMP THREADS 
 RUNNING 1 number of ITK THREADS 

================== Creating orig and rawavg from input =========================

python /home/user/FastSurfer/recon_surf/../FastSurferCNN/data_loader/conform.py -i /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz --check_only --vox_size min --verbose
Reading input: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz ...
A min-conformed image must satisfy the following criteria:
 - Dimensions 256x256x256:        True
 - Voxel Size 1.0x1.0x1.0:        True
 - Orientation LIA:               True
 - Dtype uint8:                   True
Input /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz is already conformed! Exiting.

@#@FSTIME  2024:07:18:05:28:02 python N 7 e 0.22 S 0.02 U 0.20 P 99% M 86456 F 0 R 17194 W 0 c 12 w 1 I 0 O 0 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:02 python N 7 1.04 1.00 0.83
python /home/user/FastSurfer/recon_surf/../FastSurferCNN/data_loader/conform.py -i /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz --check_only --vox_size 1.0 --dtype any --verbose
Reading input: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz ...
A conformed image must satisfy the following criteria:
 - Dimensions 256x256x256:        True
 - Voxel Size 1.0x1.0x1.0:        True
 - Orientation LIA:               True
Input /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz is already conformed! Exiting.

@#@FSTIME  2024:07:18:05:28:02 python N 9 e 0.17 S 0.01 U 0.16 P 98% M 85992 F 0 R 17087 W 0 c 14 w 1 I 0 O 0 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:02 python N 9 1.04 1.00 0.83
The voxel size 1.0 is not less than 0.999, so we are proceeding with standard options.
mri_convert /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz
mri_convert /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz 
reading from /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz...
TR=12.41, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz...
@#@FSTIME  2024:07:18:05:28:02 mri_convert N 2 e 0.81 S 0.00 U 0.80 P 98% M 23552 F 0 R 4574 W 0 c 3 w 2 I 0 O 12408 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:03 mri_convert N 2 1.04 1.00 0.83
mri_convert /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.orig.mgz
mri_convert /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.orig.mgz 
reading from /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz...
TR=12.41, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.orig.mgz...
@#@FSTIME  2024:07:18:05:28:03 mri_convert N 2 e 0.33 S 0.00 U 0.33 P 99% M 39936 F 0 R 8703 W 0 c 4 w 1 I 0 O 568 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:04 mri_convert N 2 1.04 1.00 0.83
~/data/working/fastsurfer/anatomy/demo_patient/mri ~/FastSurfer/recon_surf
ln -sf orig.mgz rawavg.mgz
@#@FSTIME  2024:07:18:05:28:04 ln N 3 e 0.00 S 0.00 U 0.00 P 100% M 2048 F 0 R 150 W 0 c 0 w 1 I 0 O 32 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:04 ln N 3 1.04 1.00 0.83
~/FastSurfer/recon_surf

============= Computing Talairach Transform and NU (bias corrected) ============

~/data/working/fastsurfer/anatomy/demo_patient/mri ~/FastSurfer/recon_surf
Using the 3T atlas for talairach registration.
talairach_avi --i /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig_nu.mgz --xfm /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig
egrep: warning: egrep is obsolescent; using grep -E
mv -f /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt
Started at Thu 18 Jul 2024 05:28:04 AM EDT
Ended   at Thu 18 Jul 2024 05:28:16 AM EDT
talairach_avi done
@#@FSTIME  2024:07:18:05:28:04 talairach_avi N 6 e 12.16 S 0.55 U 5.60 P 50% M 255488 F 0 R 402189 W 0 c 67 w 165 I 0 O 295256 L 1.04 1.00 0.83
@#@FSLOADPOST 2024:07:18:05:28:16 talairach_avi N 6 0.87 0.96 0.82
cp /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.auto.xfm /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm
@#@FSTIME  2024:07:18:05:28:16 cp N 2 e 0.00 S 0.00 U 0.00 P 100% M 2304 F 0 R 182 W 0 c 0 w 2 I 0 O 0 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:16 cp N 2 0.87 0.96 0.82
lta_convert --src /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz --trg /usr/local/freesurfer/7.4.1-1//average/mni305.cor.mgz --inxfm /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm --outlta /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.4.1

--src: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig.mgz src image (geometry).
--trg: /usr/local/freesurfer/7.4.1-1//average/mni305.cor.mgz trg image (geometry).
--inmni: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm input MNI/XFM transform.
--outlta: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm.lta output LTA.
--s: fsaverage subject name
--ltavox2vox: output LTA as VOX_TO_VOX transform.
 LTA read, type : 1
 1.12263  -0.02749  -0.05509  -1.30774;
 0.03379   1.17662   0.22683  -31.69901;
 0.03964  -0.32241   1.18484   1.27183;
 0.00000   0.00000   0.00000   1.00000;
setting subject to fsaverage
Writing  LTA to file /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm.lta...
lta_convert successful.
@#@FSTIME  2024:07:18:05:28:16 lta_convert N 11 e 0.08 S 0.00 U 0.08 P 98% M 6144 F 0 R 267 W 0 c 2 w 1 I 0 O 8 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:16 lta_convert N 11 0.87 0.96 0.82
~/data/working/fastsurfer/anatomy/demo_patient/mri/transforms ~/data/working/fastsurfer/anatomy/demo_patient/mri ~/FastSurfer/recon_surf
ln -sf talairach.xfm.lta talairach_with_skull.lta
@#@FSTIME  2024:07:18:05:28:16 ln N 3 e 0.00 S 0.00 U 0.00 P 100% M 2048 F 0 R 151 W 0 c 1 w 1 I 0 O 0 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:16 ln N 3 0.87 0.96 0.82
ln -sf talairach.xfm.lta talairach.lta
@#@FSTIME  2024:07:18:05:28:16 ln N 3 e 0.00 S 0.00 U 0.00 P 100% M 1792 F 0 R 146 W 0 c 3 w 1 I 0 O 0 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:16 ln N 3 0.87 0.96 0.82
~/data/working/fastsurfer/anatomy/demo_patient/mri ~/FastSurfer/recon_surf
mri_add_xform_to_header -c /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/talairach.xfm /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/orig_nu.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/nu.mgz
INFO: extension is mgz
@#@FSTIME  2024:07:18:05:28:16 mri_add_xform_to_header N 4 e 0.75 S 0.01 U 0.74 P 99% M 23040 F 0 R 4559 W 0 c 5 w 1 I 0 O 12464 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:17 mri_add_xform_to_header N 4 0.87 0.96 0.82
~/FastSurfer/recon_surf

============ Creating brainmask from aseg and norm, and update aseg ============

mri_mask /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/nu.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/mask.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/norm.mgz
DoAbs = 0
maskval=0, outval=0
Writing masked volume to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/norm.mgz...done.
@#@FSTIME  2024:07:18:05:28:17 mri_mask N 3 e 0.30 S 0.01 U 0.28 P 99% M 73728 F 0 R 17256 W 0 c 4 w 1 I 0 O 2024 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:17 mri_mask N 3 0.87 0.96 0.82
mri_normalize -g 1 -seed 1234 -mprage /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/nu.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/T1.mgz
using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/nu.mgz...
normalizing image...
NOT doing gentle normalization with control points/label
talairach transform
 1.12263  -0.02749  -0.05509  -1.30774;
 0.03379   1.17662   0.22683  -31.69901;
 0.03964  -0.32241   1.18484   1.27183;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 9
Starting OpenSpline(): npoints = 9
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 104
gm peak at 77 (74), valley at 63 (60)
csf peak at 38, setting threshold to 64
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 92
gm peak at 74 (71), valley at 58 (55)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/T1.mgz
3D bias adjustment took 0 minutes and 37 seconds.
@#@FSTIME  2024:07:18:05:28:17 mri_normalize N 7 e 37.37 S 0.19 U 37.13 P 99% M 583436 F 0 R 267353 W 0 c 84 w 1 I 0 O 12496 L 0.87 0.96 0.82
@#@FSLOADPOST 2024:07:18:05:28:54 mri_normalize N 7 0.94 0.97 0.83
mri_mask /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/T1.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/mask.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brainmask.mgz
DoAbs = 0
maskval=0, outval=0
Writing masked volume to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brainmask.mgz...done.
@#@FSTIME  2024:07:18:05:28:54 mri_mask N 3 e 0.34 S 0.01 U 0.32 P 99% M 73728 F 0 R 17259 W 0 c 4 w 1 I 0 O 2000 L 0.94 0.97 0.83
@#@FSLOADPOST 2024:07:18:05:28:55 mri_mask N 3 0.94 0.97 0.83
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/cc_up.lta demo_patient
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/transforms/cc_up.lta
reading aseg from /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aseg.auto_noCCseg.mgz
reading norm from /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/norm.mgz
11669 voxels in left wm, 24203 in right wm, xrange [123, 129]
searching rotation angles z=[-5  9], y=[-6  8]

searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.9  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.4  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.9  
searching scale 1 Z rot 9.1  global minimum found at slice 126.6, rotations (0.55, 2.37)
final transformation (x=126.6, yr=0.554, zr=2.371):
 0.99910  -0.04137   0.00966   4.86499;
 0.04136   0.99914   0.00040   14.80945;
-0.00967  -0.00000   0.99995   9.22957;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
min_x_fornix = 119
min_x_fornix = 121
min_x_fornix = 132
min_x_fornix = 121
min_x_fornix = 119
cc center is found at 128 108 120
eigenvectors:
 0.00140   0.00441   0.99999;
-0.09762  -0.99521   0.00453;
 0.99522  -0.09763  -0.00096;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.1 minutes
#VMPC# mri_cc VmPeak  382356
mri_cc done
@#@FSTIME  2024:07:18:05:28:55 mri_cc N 7 e 6.72 S 0.04 U 6.67 P 99% M 142212 F 0 R 62975 W 0 c 20 w 1 I 0 O 456 L 0.94 0.97 0.83
@#@FSLOADPOST 2024:07:18:05:29:02 mri_cc N 7 0.94 0.97 0.83
python /home/user/FastSurfer/recon_surf/paint_cc_into_pred.py -in_cc /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aseg.auto.mgz -in_pred /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz -out /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.withCC.mgz
Reading inputs: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aseg.auto.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.mgz...
Writing segmentation with corpus callosum to: /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/aparc.DKTatlas+aseg.deep.withCC.mgz
@#@FSTIME  2024:07:18:05:29:02 python N 7 e 0.33 S 0.03 U 0.29 P 99% M 166724 F 0 R 31194 W 0 c 14 w 4 I 0 O 1048 L 0.94 0.97 0.83
@#@FSLOADPOST 2024:07:18:05:29:02 python N 7 0.94 0.97 0.83

========= Creating filled from brain (brainfinalsurfs, wm.asegedit, wm)  =======

recon-all -s demo_patient -asegmerge -normalization2 -maskbfs -segmentation -fill
egrep: warning: egrep is obsolescent; using grep -E
egrep: warning: egrep is obsolescent; using grep -E
fs-check-version --s demo_patient --o /tmp/tmp.hoEpM4
Thu Jul 18 05:29:02 EDT 2024

setenv SUBJECTS_DIR /home/user/data/working/fastsurfer/anatomy
cd /home/user/FastSurfer/recon_surf
/usr/local/freesurfer/7.4.1-1//bin/fs-check-version --s demo_patient --o /tmp/tmp.hoEpM4
-rwxrwxr-x. 1 prerana meg 18565 Jun 13  2023 /usr/local/freesurfer/7.4.1-1//bin/fs-check-version

freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
$Id$
Linux opennet-32-48.uhnres.utoronto.ca 6.6.11-200.fc39.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Jan 10 19:25:59 UTC 2024 x86_64 GNU/Linux
pid 177063
Current FS Version freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
Subject does not have a bstampfile, copying /usr/local/freesurfer/7.4.1-1//build-stamp.txt
Subject FS Version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /home/user/data/working/fastsurfer/anatomy
Actual FREESURFER_HOME /usr/local/freesurfer/7.4.1-1
Linux opennet-32-48.uhnres.utoronto.ca 6.6.11-200.fc39.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Jan 10 19:25:59 UTC 2024 x86_64 GNU/Linux
egrep: warning: egrep is obsolescent; using grep -E
~/data/working/fastsurfer/anatomy/demo_patient/mri/transforms ~/data/working/fastsurfer/anatomy/demo_patient 
~/data/working/fastsurfer/anatomy/demo_patient 
#--------------------------------------
#@# Merge ASeg Thu Jul 18 05:29:03 EDT 2024

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Jul 18 05:29:03 EDT 2024
/home/user/data/working/fastsurfer/anatomy/demo_patient/mri

 mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 

setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src from norm.mgz...
Reading aseg aseg.presurf.mgz
aseg read with width 256 (src width 256)
************** resampling aseg to account for mismatch with source image ***************
normalizing image...
NOT doing gentle normalization with control points/label
processing with aseg
removing outliers in the aseg WM...
1728 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 79 (79), valley at 47 (47)
csf peak at 21, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 78 (78), valley at 46 (46)
csf peak at 21, setting threshold to 59
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 0 minutes and 54 seconds.
@#@FSTIME  2024:07:18:05:29:03 mri_normalize N 9 e 54.47 S 0.48 U 53.91 P 99% M 1100492 F 0 R 604135 W 0 c 126 w 2 I 416 O 2128 L 0.94 0.97 0.83
@#@FSLOADPOST 2024:07:18:05:29:57 mri_normalize N 9 1.14 1.02 0.86
#--------------------------------------------
#@# Mask BFS Thu Jul 18 05:29:57 EDT 2024
/home/user/data/working/fastsurfer/anatomy/demo_patient/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1131942 voxels in mask (pct=  6.75)
maskval=0, outval=0
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2024:07:18:05:29:57 mri_mask N 5 e 0.40 S 0.01 U 0.38 P 99% M 73728 F 0 R 17267 W 0 c 4 w 1 I 0 O 2000 L 1.14 1.02 0.86
@#@FSLOADPOST 2024:07:18:05:29:57 mri_mask N 5 1.14 1.02 0.86
cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
#--------------------------------------------
#@# WM Segmentation Thu Jul 18 05:29:58 EDT 2024

 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz 

@#@FSTIME  2024:07:18:05:29:58 AntsDenoiseImageFs N 4 e 12.88 S 0.06 U 12.80 P 99% M 350720 F 0 R 86517 W 0 c 23 w 1 I 0 O 2008 L 1.14 1.02 0.86
@#@FSLOADPOST 2024:07:18:05:30:10 AntsDenoiseImageFs N 4 1.10 1.02 0.86

 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz 

wsizemm = 13, voxres = 1, wsize = 13
Widening wm low from 89 to 79
assuming input volume is MGH (Van der Kouwe) MP-RAGE
wm mean:  110
wsize:    13
wm low:   79
wm hi:    125
gray low: 30
gray hi:  99
Doing initial trinary intensity segmentation 
MRIintensitySegmentation() wm_low=79, wm_hi=125, gray_hi=99
white = 181917, nonwhite = 16290572, ambig = 304727, nmask = 0
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (100.0): 99.7 +- 6.3 [79.0 --> 125.0]
CCS GM (75.0) : 72.9 +- 12.5 [30.0 --> 95.0]
 white_mean 99.7056
 white_sigma 6.30992
 gray_mean 72.9303
 gray_sigma 12.5332
setting bottom of white matter range wm_low to 85.5
setting top of gray matter range gray_hi to 98.0
 wm_low 85.4635
 wm_hi  125
 gray_low 30
 gray_hi  97.9967
Redoing initial intensity segmentation...
MRIintensitySegmentation() wm_low=85.4635, wm_hi=125, gray_hi=97.9967
white = 206405, nonwhite = 16416058, ambig = 154753, nmask = 0
Recomputing local statistics to label ambiguous voxels...
 wm_low 85.4635
 wm_hi  125
 gray_low 30
 gray_hi  97.9967
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 97.9967, wm_low = 85.4635
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=97.9967, wmlow=85.4635
    119099 voxels processed (0.71%)
     58450 voxels white (0.35%)
     60649 voxels non-white (0.36%)

Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=80.4635, gray_hi=97.9967, wsize=13
    241036 voxels tested (1.44%)
     46669 voxels changed (0.28%)
     35290 multi-scale searches  (0.21%)
Recovering bright white
MRIrecoverBrightWhite()
 wm_low 85.4635
 wm_hi 125
 slack 6.30992
 pct_thresh 0.33
 intensity_thresh 131.31
 nvox_thresh 8.58
       24 voxels tested (0.00%)
       12 voxels changed (0.00%)

removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=80.4635, hithr=97.9967
  smoothing input volume with sigma = 0.250
   119512 voxels tested (0.71%)
    13247 voxels changed (0.08%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
 2856 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
1753 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
  20 segments, 4141 filled
MRIfindBrightNonWM(): 77 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 0.4 minutes
writing output to wm.seg.mgz...
@#@FSTIME  2024:07:18:05:30:10 mri_segment N 5 e 24.97 S 0.13 U 24.80 P 99% M 134948 F 0 R 290343 W 0 c 81 w 1 I 0 O 752 L 1.10 1.02 0.86
@#@FSLOADPOST 2024:07:18:05:30:35 mri_segment N 5 1.07 1.02 0.87

 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 

mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 
preserving editing changes in input volume...
auto filling took 0.15 minutes
reading wm segmentation from wm.seg.mgz...
761 voxels added to wm to prevent paths from MTL structures to cortex
5534 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 103197 voxels turned on, 14974 voxels turned off.
propagating editing to output volume from wm.seg.mgz
writing edited volume to wm.asegedit.mgz....
@#@FSTIME  2024:07:18:05:30:35 mri_edit_wm_with_aseg N 5 e 9.06 S 0.03 U 9.01 P 99% M 158208 F 0 R 58264 W 0 c 43 w 1 I 0 O 600 L 1.07 1.02 0.87
@#@FSLOADPOST 2024:07:18:05:30:44 mri_edit_wm_with_aseg N 5 1.14 1.03 0.87

 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 

Iteration Number : 1
pass   1 (xy+):  19 found -  19 modified     |    TOTAL:  19
pass   2 (xy+):   0 found -  19 modified     |    TOTAL:  19
pass   1 (xy-):  22 found -  22 modified     |    TOTAL:  41
pass   2 (xy-):   0 found -  22 modified     |    TOTAL:  41
pass   1 (yz+):  20 found -  20 modified     |    TOTAL:  61
pass   2 (yz+):   0 found -  20 modified     |    TOTAL:  61
pass   1 (yz-):  28 found -  28 modified     |    TOTAL:  89
pass   2 (yz-):   0 found -  28 modified     |    TOTAL:  89
pass   1 (xz+):  15 found -  15 modified     |    TOTAL: 104
pass   2 (xz+):   0 found -  15 modified     |    TOTAL: 104
pass   1 (xz-):  20 found -  20 modified     |    TOTAL: 124
pass   2 (xz-):   0 found -  20 modified     |    TOTAL: 124
Iteration Number : 1
pass   1 (+++):  18 found -  18 modified     |    TOTAL:  18
pass   2 (+++):   0 found -  18 modified     |    TOTAL:  18
pass   1 (+++):  17 found -  17 modified     |    TOTAL:  35
pass   2 (+++):   0 found -  17 modified     |    TOTAL:  35
pass   1 (+++):  29 found -  29 modified     |    TOTAL:  64
pass   2 (+++):   0 found -  29 modified     |    TOTAL:  64
pass   1 (+++):  15 found -  15 modified     |    TOTAL:  79
pass   2 (+++):   0 found -  15 modified     |    TOTAL:  79
Iteration Number : 1
pass   1 (++):  71 found -  71 modified     |    TOTAL:  71
pass   2 (++):   0 found -  71 modified     |    TOTAL:  71
pass   1 (+-):  85 found -  85 modified     |    TOTAL: 156
pass   2 (+-):   0 found -  85 modified     |    TOTAL: 156
pass   1 (--):  69 found -  69 modified     |    TOTAL: 225
pass   2 (--):   1 found -  70 modified     |    TOTAL: 226
pass   3 (--):   0 found -  70 modified     |    TOTAL: 226
pass   1 (-+): 100 found - 100 modified     |    TOTAL: 326
pass   2 (-+):   0 found - 100 modified     |    TOTAL: 326
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   6 found -   6 modified     |    TOTAL:  10
pass   2 (xy-):   0 found -   6 modified     |    TOTAL:  10
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:  13
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:  13
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  16
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  16
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  18
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  18
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  19
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  19
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   1 found -   1 modified     |    TOTAL:   3
pass   2 (--):   0 found -   1 modified     |    TOTAL:   3
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 560 (out of 382006: 0.146595)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

@#@FSTIME  2024:07:18:05:30:45 mri_pretess N 4 e 1.26 S 0.01 U 1.25 P 99% M 56320 F 0 R 12958 W 0 c 3 w 1 I 0 O 608 L 1.14 1.03 0.87
@#@FSLOADPOST 2024:07:18:05:30:46 mri_pretess N 4 1.14 1.03 0.87
#--------------------------------------------
#@# Fill Thu Jul 18 05:30:46 EDT 2024
/home/user/data/working/fastsurfer/anatomy/demo_patient/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /usr/local/freesurfer/7.4.1-1//SubCorticalMassLUT.txt wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.presurf.mgz...
done.
searching for cutting planes...voxel to talairach voxel transform
 1.12263  -0.05509   0.02749  -12.21729;
 0.03964   1.18484   0.32241  -69.92929;
-0.03379  -0.22683   1.17662   0.77576;
 0.00000   0.00000   0.00000   1.00000;
reading input volume... wm.mgzvoxel to talairach voxel transform
 1.12263  -0.05509   0.02749  -12.21729;
 0.03964   1.18484   0.32241  -69.92929;
-0.03379  -0.22683   1.17662   0.77576;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.presurf.mgz
removing CC from segmentation
Looking for area (min, max) = (350, 1400)
area[0] = 1700 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75)
need search nearby
using seed (128, 125, 157), TAL = (0.0, 29.0, 3.0)
talairach voxel to voxel transform
 0.88860   0.03548  -0.03048   13.36121;
-0.03485   0.80054  -0.21854   55.72478;
 0.01880   0.15535   0.80688   10.46719;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (128,  125,  157) --> (0.0, 29.0, 3.0)
done.
filling took 0.4 minutes
talairach cc position changed to (0.00, 29.00, 3.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(18.00, 29.00, 3.00) SRC: (110.76, 117.65, 158.63)
search lh wm seed point around talairach space (-18.00, 29.00, 3.00), SRC: (142.75, 116.39, 159.31)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram for separating WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
Embedding colortable
mri_fill done, writing output to filled.mgz...
@#@FSTIME  2024:07:18:05:30:46 mri_fill N 10 e 21.39 S 0.36 U 20.99 P 99% M 866944 F 0 R 465748 W 0 c 61 w 1 I 0 O 336 L 1.14 1.03 0.87
@#@FSLOADPOST 2024:07:18:05:31:07 mri_fill N 10 1.10 1.03 0.88
 cp filled.mgz filled.auto.mgz

Started at Thu Jul 18 05:29:02 EDT 2024 
Ended   at Thu Jul 18 05:31:07 EDT 2024
#@#%# recon-all-run-time-hours 0.035
recon-all -s demo_patient finished without error at Thu Jul 18 05:31:07 EDT 2024
done
@#@FSTIME  2024:07:18:05:29:02 recon-all N 7 e 125.31 S 1.63 U 123.55 P 99% M 1100492 F 2 R 1622227 W 0 c 565 w 1013 I 416 O 8760 L 0.94 0.97 0.83
@#@FSLOADPOST 2024:07:18:05:31:07 recon-all N 7 1.10 1.03 0.88
echo 
echo "================== Creating surfaces lh - orig.nofix =================="
echo 
echo "mri_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled.mgz 255 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brain.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz" 
/home/user/FastSurfer/recon_surf/fs_time mri_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled.mgz 255 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brain.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz 
echo "mri_mc /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz 255 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mri_mc /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz 255 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix 
echo "python /home/user/FastSurfer/recon_surf/rewrite_mc_surface.py --input /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix --output /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix --filename_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/rewrite_mc_surface.py --input /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix --output /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix --filename_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess255.mgz 
echo "mris_info /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix | tr -s ' ' | grep -q 'vertex locs : surfaceRAS'" 
/home/user/FastSurfer/recon_surf/fs_time mris_info /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix | tr -s ' ' | grep -q 'vertex locs : surfaceRAS' 
echo "mris_extract_main_component /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mris_extract_main_component /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix 
echo "mris_smooth -n 10 -nw -seed 1234 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.smoothwm.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mris_smooth -n 10 -nw -seed 1234 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.smoothwm.nofix 
echo  
echo "=================== Creating surfaces lh - qsphere ===================="
echo 
echo "recon-all -subject demo_patient -hemi lh -inflate1 -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi lh -inflate1 -no-isrunning   
echo "python /home/user/FastSurfer/recon_surf/spherically_project_wrapper.py --hemi lh --sdir /home/user/data/working/fastsurfer/anatomy/demo_patient/surf --subject demo_patient --threads=1 --py python --binpath /home/user/FastSurfer/recon_surf/" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/spherically_project_wrapper.py --hemi lh --sdir /home/user/data/working/fastsurfer/anatomy/demo_patient/surf --subject demo_patient --threads=1 --py python --binpath /home/user/FastSurfer/recon_surf/ 
echo 
echo "=================== Creating surfaces lh - fix ========================"
echo 
echo "recon-all -subject demo_patient -hemi lh -fix -autodetgwstats -white-preaparc -cortex-label -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi lh -fix -autodetgwstats -white-preaparc -cortex-label -no-isrunning   
echo " "
echo "================== Creating surfaces lh - inflate2 ===================="
echo " "
echo "recon-all -subject demo_patient -hemi lh -smooth2 -inflate2 -curvHK -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi lh -smooth2 -inflate2 -curvHK -no-isrunning   
echo " "
echo "=========== Creating surfaces lh - map input asegdkt_segfile to surf ==============="
echo " "
echo "mris_sample_parc -ct /usr/local/freesurfer/7.4.1-1//average/colortable_desikan_killiany.txt -file /home/user/FastSurfer/recon_surf/lh.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc demo_patient lh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot" 
/home/user/FastSurfer/recon_surf/fs_time mris_sample_parc -ct /usr/local/freesurfer/7.4.1-1//average/colortable_desikan_killiany.txt -file /home/user/FastSurfer/recon_surf/lh.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc demo_patient lh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot 
echo "python /home/user/FastSurfer/recon_surf/smooth_aparc.py --insurf /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.white.preaparc --inaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.prefix.annot --incort /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.cortex.label --outaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.annot" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/smooth_aparc.py --insurf /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.white.preaparc --inaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.prefix.annot --incort /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.cortex.label --outaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.annot 
echo " "
echo "============ Creating surfaces lh - FS sphere, surfreg ==============="
echo " "
echo "recon-all -subject demo_patient -hemi lh -sphere  -no-isrunning " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi lh -sphere  -no-isrunning  
echo "python /home/user/FastSurfer/recon_surf//rotate_sphere.py        --srcsphere /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere        --srcaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.annot        --trgsphere /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/surf/lh.sphere        --trgaparc /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/label/lh.aparc.annot        --out /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.angles.txt" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf//rotate_sphere.py        --srcsphere /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere        --srcaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/lh.aparc.DKTatlas.mapped.annot        --trgsphere /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/surf/lh.sphere        --trgaparc /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/label/lh.aparc.annot        --out /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.angles.txt 
echo "mris_register -curv -norot -rotate `cat /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.angles.txt`        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere        /usr/local/freesurfer/7.4.1-1//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere.reg" 
/home/user/FastSurfer/recon_surf/fs_time mris_register -curv -norot -rotate `cat /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.angles.txt`        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere        /usr/local/freesurfer/7.4.1-1//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/lh.sphere.reg 
echo " "
echo "================ Creating surfaces lh - white and pial direct ==================="
echo " "
echo "mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.DKTatlas.mapped.annot" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.DKTatlas.mapped.annot 
echo "mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.DKTatlas.mapped.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.DKTatlas.mapped.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 
echo "ln -sf lh.pial.T1 lh.pial" 
/home/user/FastSurfer/recon_surf/fs_time ln -sf lh.pial.T1 lh.pial 
echo "mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white" 
/home/user/FastSurfer/recon_surf/fs_time mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white 
echo "mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv 
echo "mris_place_surface --area-map ../surf/lh.white ../surf/lh.area" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --area-map ../surf/lh.white ../surf/lh.area 
echo "mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial 
echo "mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial 
echo "mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 
echo "recon-all -subject demo_patient -hemi lh -curvstats -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi lh -curvstats -no-isrunning   
echo 
echo "================== Creating surfaces rh - orig.nofix =================="
echo 
echo "mri_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled.mgz 127 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brain.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz" 
/home/user/FastSurfer/recon_surf/fs_time mri_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled.mgz 127 /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/brain.mgz /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz 
echo "mri_mc /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz 127 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mri_mc /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz 127 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix 
echo "python /home/user/FastSurfer/recon_surf/rewrite_mc_surface.py --input /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix --output /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix --filename_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/rewrite_mc_surface.py --input /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix --output /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix --filename_pretess /home/user/data/working/fastsurfer/anatomy/demo_patient/mri/filled-pretess127.mgz 
echo "mris_info /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix | tr -s ' ' | grep -q 'vertex locs : surfaceRAS'" 
/home/user/FastSurfer/recon_surf/fs_time mris_info /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix | tr -s ' ' | grep -q 'vertex locs : surfaceRAS' 
echo "mris_extract_main_component /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mris_extract_main_component /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix 
echo "mris_smooth -n 10 -nw -seed 1234 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.smoothwm.nofix" 
/home/user/FastSurfer/recon_surf/fs_time mris_smooth -n 10 -nw -seed 1234 /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.orig.nofix /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.smoothwm.nofix 
echo  
echo "=================== Creating surfaces rh - qsphere ===================="
echo 
echo "recon-all -subject demo_patient -hemi rh -inflate1 -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi rh -inflate1 -no-isrunning   
echo "python /home/user/FastSurfer/recon_surf/spherically_project_wrapper.py --hemi rh --sdir /home/user/data/working/fastsurfer/anatomy/demo_patient/surf --subject demo_patient --threads=1 --py python --binpath /home/user/FastSurfer/recon_surf/" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/spherically_project_wrapper.py --hemi rh --sdir /home/user/data/working/fastsurfer/anatomy/demo_patient/surf --subject demo_patient --threads=1 --py python --binpath /home/user/FastSurfer/recon_surf/ 
echo 
echo "=================== Creating surfaces rh - fix ========================"
echo 
echo "recon-all -subject demo_patient -hemi rh -fix -autodetgwstats -white-preaparc -cortex-label -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi rh -fix -autodetgwstats -white-preaparc -cortex-label -no-isrunning   
echo " "
echo "================== Creating surfaces rh - inflate2 ===================="
echo " "
echo "recon-all -subject demo_patient -hemi rh -smooth2 -inflate2 -curvHK -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi rh -smooth2 -inflate2 -curvHK -no-isrunning   
echo " "
echo "=========== Creating surfaces rh - map input asegdkt_segfile to surf ==============="
echo " "
echo "mris_sample_parc -ct /usr/local/freesurfer/7.4.1-1//average/colortable_desikan_killiany.txt -file /home/user/FastSurfer/recon_surf/rh.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc demo_patient rh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot" 
/home/user/FastSurfer/recon_surf/fs_time mris_sample_parc -ct /usr/local/freesurfer/7.4.1-1//average/colortable_desikan_killiany.txt -file /home/user/FastSurfer/recon_surf/rh.DKTatlaslookup.txt -projmm 0.6 -f 5  -surf white.preaparc demo_patient rh aparc.DKTatlas+aseg.orig.mgz aparc.DKTatlas.mapped.prefix.annot 
echo "python /home/user/FastSurfer/recon_surf/smooth_aparc.py --insurf /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.white.preaparc --inaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.prefix.annot --incort /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.cortex.label --outaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.annot" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf/smooth_aparc.py --insurf /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.white.preaparc --inaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.prefix.annot --incort /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.cortex.label --outaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.annot 
echo " "
echo "============ Creating surfaces rh - FS sphere, surfreg ==============="
echo " "
echo "recon-all -subject demo_patient -hemi rh -sphere  -no-isrunning " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi rh -sphere  -no-isrunning  
echo "python /home/user/FastSurfer/recon_surf//rotate_sphere.py        --srcsphere /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere        --srcaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.annot        --trgsphere /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/surf/rh.sphere        --trgaparc /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/label/rh.aparc.annot        --out /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.angles.txt" 
/home/user/FastSurfer/recon_surf/fs_time python /home/user/FastSurfer/recon_surf//rotate_sphere.py        --srcsphere /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere        --srcaparc /home/user/data/working/fastsurfer/anatomy/demo_patient/label/rh.aparc.DKTatlas.mapped.annot        --trgsphere /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/surf/rh.sphere        --trgaparc /usr/local/freesurfer/7.4.1-1//subjects/fsaverage/label/rh.aparc.annot        --out /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.angles.txt 
echo "mris_register -curv -norot -rotate `cat /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.angles.txt`        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere        /usr/local/freesurfer/7.4.1-1//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere.reg" 
/home/user/FastSurfer/recon_surf/fs_time mris_register -curv -norot -rotate `cat /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.angles.txt`        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere        /usr/local/freesurfer/7.4.1-1//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif        /home/user/data/working/fastsurfer/anatomy/demo_patient/surf/rh.sphere.reg 
echo " "
echo "================ Creating surfaces rh - white and pial direct ==================="
echo " "
echo "mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.DKTatlas.mapped.annot" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.DKTatlas.mapped.annot 
echo "mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.DKTatlas.mapped.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.DKTatlas.mapped.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 
echo "ln -sf rh.pial.T1 rh.pial" 
/home/user/FastSurfer/recon_surf/fs_time ln -sf rh.pial.T1 rh.pial 
echo "mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white" 
/home/user/FastSurfer/recon_surf/fs_time mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white 
echo "mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv 
echo "mris_place_surface --area-map ../surf/rh.white ../surf/rh.area" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --area-map ../surf/rh.white ../surf/rh.area 
echo "mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial 
echo "mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial 
echo "mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness" 
/home/user/FastSurfer/recon_surf/fs_time mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 
echo "recon-all -subject demo_patient -hemi rh -curvstats -no-isrunning  " 
/home/user/FastSurfer/recon_surf/fs_time recon-all -subject demo_patient -hemi rh -curvstats -no-isrunning   

 RUNNING HEMIs in PARALLEL !!! 

RunBatchJobs: Logfile: /home/user/data/working/fastsurfer/anatomy/demo_patient/scripts/recon-surf.log
RunBatchJobs: CMDF: /home/user/data/working/fastsurfer/anatomy/demo_patient/scripts/lh.processing.cmdf
RunBatchJobs: CMDF: /home/user/data/working/fastsurfer/anatomy/demo_patient/scripts/rh.processing.cmdf
Waiting for PID 178264 of (178264 178266) to complete...
Waiting for PID 178266 of (178264 178266) to complete...
PIDs (178264 178266) completed and logs appended.
dkuegler commented 3 months ago

[I overlooked the version string in the log. It is 2.2.0-818acf1]

Generally, it looks like the surface reconstruction is not working. You will find more info in /home/user/data/working/fastsurfer/anatomy/demo_patient/scripts/lh.processing.cmdf.log and /home/user/data/working/fastsurfer/anatomy/demo_patient/scripts/rh.processing.cmdf.log.

VoodooCode14 commented 3 months ago

Those files don't exist either, only lh.processing.cmdf and rh.processing.cmdf.

Took a look at recon-surf.log, there's an error: ``` Fill Round: 1 rows: 305 reduced to 191 Traceback (most recent call last): File "/home/max/finnpy2/FastSurfer/recon_surf/smooth_aparc.py", line 367, in smooth_aparc(options.insurf, options.inaparc, options.incort, options.outaparc) File "/home/max/finnpy2/FastSurfer/recon_surf/smooth_aparc.py", line 333, in smooth_aparc labels_new = mode_filter(adjM, labels, fillonlylabel, np.array([fillonlylabel])) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/max/finnpy2/FastSurfer/recon_surf/smooth_aparc.py", line 238, in mode_filter labels_new[ids[row]] = mvals[0]


IndexError: invalid index to scalar variable. ```
dkuegler commented 3 months ago

I have seen this error before.

This issue has been fixed for the next release. I think this popped up because of a change of an upstream package (scipy or numpy).

As a short-term solution, I would recommend using the docker or singularity installation method or to make sure you use the recommended versions of packages. You can check which packages FastSurfer uses with $FASTSUFER_HOME/run_fastsurfer.sh --version +pip.

VoodooCode14 commented 3 months ago

Yeah, this is the issue, thanks a lot for looking into it! I fixed it in the version I'm using at the moment.