@SUMA_Make_Spec_FS some files missing, including lh.pial

AFNI Message Board
1

Hi there, I am using @SUMA_Make_Spec_FS -GIFTI (full code below)

There is something going wrong. It produces less files (90) than normal (97), with missing files including lh.pial.

I used to run this code on my uni’s HPC and it worked fine. I am now working on a local machine at my institute. Could it have something to do with tcsh on our system? I had to ask for it to be installed, and some things don’t work as I would expect, e.g., module load does not work. I wondered this after reading this post who had tcsh issues causing problems with SUMA_Make_Spec_FS NO COR files for @SUMA_Make_Spec_FS function

Running other afni processes on this new local computer all seems to work fine.

Any help would be very appreciated. Code and more details/ output below.

Thank you!

Harriet

Code

#!/bin/tcsh

set base_dir = /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer

set sub = sub-050
set ses = ses-01

# Go to sub surf dir
set surf_dir = $base_dir/${sub}/${ses}
cd $surf_dir
    
# Run make_spec
@SUMA_Make_Spec_FS -GIFTI -sid ${sub}_${ses}

Here is the -ver info and output

Precompiled binary linux_ubuntu_24_64: Oct  1 2024 (Version AFNI_24.3.00 'Elagabalus')

(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ tcsh 3_run_suma_make_spec 
++ Running @SUMA_Make_Spec_FS version: 2.2.4
++ creating directory './SUMA' for results...
-- found 5 LH surfaces
-- found 5 RH surfaces
mri_convert -ot nii /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/mri/orig.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/orig.nii 
reading from /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/mri/orig.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/orig.nii...
++ 3drefit: AFNI version=AFNI_24.3.00 (Oct  1 2024) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/sub-050_ses-01_SurfVol.nii
 + changing ID code
 + loading and re-writing dataset /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/sub-050_ses-01_SurfVol.nii (/90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/SUMA/sub-050_ses-01_SurfVol.nii in NIFTI storage)
++ 3drefit processed 1 datasets
++ created AFNI file './SUMA/sub-050_ses-01_SurfVol.nii'
Made roi label table for AFNI - fs_table.niml.lt
mri_convert -ot nii mri/T1.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/T1.nii 
reading from mri/T1.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/T1.nii...
mri_convert -ot nii mri/aseg.auto.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/aseg.auto.nii 
reading from mri/aseg.auto.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/aseg.auto.nii...
mri_convert -ot nii mri/aseg.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/aseg.nii 
reading from mri/aseg.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_24.3.00 (Oct  1 2024) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/SUMA/aseg.nii to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aseg.nii
 + setting labeltable
 + loading and re-writing dataset aseg.nii (/90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/SUMA/aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
mri_convert -ot nii mri/brain.finalsurfs.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brain.finalsurfs.nii 
reading from mri/brain.finalsurfs.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brain.finalsurfs.nii...
mri_convert -ot nii mri/brain.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brain.nii 
reading from mri/brain.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brain.nii...
mri_convert -ot nii mri/brainmask.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brainmask.nii 
reading from mri/brainmask.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/brainmask.nii...
mri_convert -ot nii mri/norm.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/norm.nii 
reading from mri/norm.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/norm.nii...
mri_convert -ot nii mri/nu.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/nu.nii 
reading from mri/nu.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/nu.nii...
mri_convert -ot nii mri/lh.ribbon.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/lh.ribbon.nii 
reading from mri/lh.ribbon.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/lh.ribbon.nii...
mri_convert -ot nii mri/rh.ribbon.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/rh.ribbon.nii 
reading from mri/rh.ribbon.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/rh.ribbon.nii...
mri_convert -ot nii mri/wm.asegedit.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.asegedit.nii 
reading from mri/wm.asegedit.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.asegedit.nii...
mri_convert -ot nii mri/wm.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.nii 
reading from mri/wm.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.nii...
mri_convert -ot nii mri/wm.seg.mgz /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.seg.nii 
reading from mri/wm.seg.mgz...
TR=0.00, 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 /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
Saving lh.smoothwm.asc as a surface in TKREGISTER space
Reading lh.smoothwm.asc ...
Comment: #!ascii version of lh.smoothwm

Performing affine transform...
Writing surface...
-- running 'mris_convert lh.inflated lh.inflated.asc'
Saving lh.inflated.asc as a surface in TKREGISTER space
Reading lh.inflated.asc ...
Comment: #!ascii version of lh.inflated

Performing affine transform...
Writing surface...
-- running 'mris_convert lh.sphere lh.sphere.asc'
Saving lh.sphere.asc as a surface in TKREGISTER space
Reading lh.sphere.asc ...
Comment: #!ascii version of lh.sphere

Performing affine transform...
Writing surface...
-- running 'mris_convert lh.white lh.white.asc'
Saving lh.white.asc as a surface in TKREGISTER space
Reading lh.white.asc ...
Comment: #!ascii version of lh.white

Performing affine transform...
Writing surface...
-- running 'mris_convert lh.sphere.reg lh.sphere.reg.asc'
Saving lh.sphere.reg.asc as a surface in TKREGISTER space
Reading lh.sphere.reg.asc ...
Comment: #!ascii version of lh.sphere.reg

Performing affine transform...
Writing surface...
-- running 'mris_convert rh.smoothwm rh.smoothwm.asc'
Saving rh.smoothwm.asc as a surface in TKREGISTER space
Reading rh.smoothwm.asc ...
Comment: #!ascii version of rh.smoothwm

Performing affine transform...
Writing surface...
-- running 'mris_convert rh.inflated rh.inflated.asc'
Saving rh.inflated.asc as a surface in TKREGISTER space
Reading rh.inflated.asc ...
Comment: #!ascii version of rh.inflated

Performing affine transform...
Writing surface...
-- running 'mris_convert rh.sphere rh.sphere.asc'
Saving rh.sphere.asc as a surface in TKREGISTER space
Reading rh.sphere.asc ...
Comment: #!ascii version of rh.sphere

Performing affine transform...
Writing surface...
-- running 'mris_convert rh.white rh.white.asc'
Saving rh.white.asc as a surface in TKREGISTER space
Reading rh.white.asc ...
Comment: #!ascii version of rh.white

Performing affine transform...
Writing surface...
-- running 'mris_convert rh.sphere.reg rh.sphere.reg.asc'
Saving rh.sphere.reg.asc as a surface in TKREGISTER space
Reading rh.sphere.reg.asc ...
Comment: #!ascii version of rh.sphere.reg

Performing affine transform...
Writing surface...
++ Converting surf dsets:  lh.thickness
++ Converting surf dsets:  lh.curv
++ Converting surf dsets:  lh.sulc
++ Converting surf dsets:  rh.thickness
++ Converting surf dsets:  rh.curv
++ Converting surf dsets:  rh.sulc
++ created spec file'./SUMA/sub-050_ses-01_lh.spec'
++ created spec file'./SUMA/sub-050_ses-01_rh.spec'
++ created spec file'./SUMA/sub-050_ses-01_both.spec'

------------------------------------------------------------------
Running MapIcosahedron for both hemispheres at ld values of 141 60

**               **
    To view in SUMA, run:
  suma -spec std.141.sub-050_ses-01_lh.spec 
**               **

**               **
    To view in SUMA, run:
  suma -spec std.141.sub-050_ses-01_rh.spec 
**               **

**               **
    To view in SUMA, run:
  suma -spec std.60.sub-050_ses-01_lh.spec 
**               **

**               **
    To view in SUMA, run:
  suma -spec std.60.sub-050_ses-01_rh.spec 
**               **

------------------------------------------------------------------
Please verify that the datasets are aligned properly in both
afni and suma.  You may do this by running the following commands:

    cd ./SUMA
    afni -niml &
    suma -spec sub-050_ses-01_both.spec -sv sub-050_ses-01_SurfVol.nii

++ Going to make renumbered ROIs now.
    --> done for colorbar and making tissue maps.
        See '@SUMA_renumber_FS -help' for description.

++ Running @SUMA_renumber_FS version: 1.6
** Trouble finding 'aparc+aseg.nii*'! Check /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/SUMA

++ Going to make a nice WB mask.
       ... and some useful QC images.
       ... and some useful ROI info tables.

++ Prepare for running adjunct_suma_fs_mask_and_qc (ver = 0.33)
set: No match.
++ Prepare for running adjunct_suma_fs_roi_info (ver = 0.3)
++ Executing 3dcalc()
 argv[0]=3dcalc argv[1]=-a argv[2]=brainmask.nii argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_lcFqRCr7g6YQ2KbJuVyh1w argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_24.3.00 (Oct  1 2024) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0: no scale factor
++ Computing output statistics
++ Output dataset /tmp/3dcalc_AFN_lcFqRCr7g6YQ2KbJuVyh1w+orig.BRIK
set: No match.

++ Compressing all remaining .nii files, except for SurfVol.

@SUMA_Make_Spec_FS ... finished

Apparent issues

++ Running @SUMA_renumber_FS version: 1.6
** Trouble finding 'aparc+aseg.nii*'! Check /90days/uqhdemp1/Data/MND/bids/derivatives/Fastsurfer/sub-050/ses-01/SUMA

++ Prepare for running adjunct_suma_fs_mask_and_qc (ver = 0.33)
set: No match.

Then some more set: No match. Later on

Below is the output of afni_system_check.py -check_all

(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
cpu type:             x86_64
system:               Linux
release:              6.8.0-49-generic
version:              #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov  6 17:42:15 UTC 2
distribution:         ubuntu 24.04 Noble Numbat
number of CPUs:       80
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /usr/local/abin/afni
afni version         : Precompiled binary linux_ubuntu_24_64: Oct  1 2024 
                     : AFNI_24.3.00 'Elagabalus'
AFNI_version.txt     : AFNI_24.3.00, linux_ubuntu_24_64, Oct 01 2024, official
which python         : /usr/bin/python
python version       : 3.12.3
which R              : /usr/bin/R
R version            : R version 4.3.3 (x86_64-pc-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/usr/local/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.12)
    python2 : 0 
    python3 : 1   (/usr/bin/python3.12)

** have python3 but not python2

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    uber_subject.py      : success
    3dMVM                : success

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh           : /usr/bin/tcsh
tcsh version         : 6.24.10
which Xvfb           : /usr/bin/Xvfb

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /usr/lib/R

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
   matplotlib version : 3.6.3

++ module loaded: flask
   module file : /usr/lib/python3/dist-packages/flask/__init__.py
   flask version : 3.0.2

++ module loaded: flask_cors
   module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
   flask_cors version : 4.0.0

-------------------------------- env vars --------------------------------
PATH                       = /opt/freesurfer-7.4.1/bin:/opt/freesurfer-7.4.1/fsfast/bin:/opt/freesurfer-7.4.1/tktools:/opt/freesurfer-7.4.1/mni/bin:/usr/local/abin:/home/ubuntu/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/.local/bin

PYTHONPATH                 = 
R_LIBS                     = /usr/local/share/R-4.3
LD_LIBRARY_PATH            = /.singularity.d/libs
DYLD_LIBRARY_PATH          = 
DYLD_FALLBACK_LIBRARY_PATH = 
CONDA_SHLVL                = 
CONDA_DEFAULT_ENV          = 
CC                         = 

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : missing

--------- shell startup files ----------

   -- no .tcshrc, will create one as a follower of .cshrc
   -- considered operations: path, apsearch
   
   -- note: followers should not need edits, so edit flags should be 0
      (have 1 follower(s), which can be ignored)
   
   dot file test : want 4 modifications across 3 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           1     0        1               0     
      .tcshrc          0     0        0               1     
      .bashrc          1     0        1               0     
   
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /usr/local/abin

------------------------------ OS specific -------------------------------
which apt-get        : /usr/bin/apt-get
apt-get version      : apt 2.7.14 (amd64)

have Ubuntu system: ubuntu 24.04 Noble Numbat
have Ubuntu afni  : Precompiled binary linux_ubuntu_24_64: Oct  1 2024 

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  'afni' executable is owned by root
*  please run: apsearch -update_all_afni_help
*  dot file test : want 4 modifications across 3 files:
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)





I tried to run the same code as above, but with debug mode on:
-debug 2

But got this error:
(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ -debug 2
Command '-debug' not found, did you mean:
  command 'udebug' from deb openafs-client (1.8.10-2ubuntu1~22.04.2)
Try: apt install <deb name>




Also adding this from the forum example above:

(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ file_tool -show_bad_all -infiles `which @SUMA_Make_Spec_FS`
/data/lfs2/neurocommand/local/containers/afni_24.3.00_20241003/@SUMA_Make_Spec_FS has 0 bad characters

/data/lfs2/neurocommand/local/containers/afni_24.3.00_20241003/@SUMA_Make_Spec_FS file type: UNIX

Also following that example from the forum above, I tried changing my code to the following:

@SUMA_Make_Spec_FS -fs_setup -GIFTI -sid ${sub}_${ses} -fspath ./${sub}_${ses} |& tee output.3_run_suma_make_spec_${sub}_${ses}.txt

But it came back with this, so I may not have understood the instructions:

(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ tcsh 3_run_suma_make_spec
++ Running @SUMA_Make_Spec_FS version: 2.2.4
++ sourcing $FREESURFER_HOME/SetUpFreeSurfer.csh
INFO: /data/home/uqhdemp1/matlab/startup.m does not exist ... creating

failure: directory not found - './sub-050_ses-01'
program failure: exiting...

Tcsh is installed, and some things work normally with it

(base) uqhdemp1@cai-wks2:/90days/uqhdemp1/Parent_scripts/Anat2Surfaces$ which tcsh
/usr/bin/tcsh

Thank you once again!

2

Possibly relevant extra information - these files were generated with Fastsurfer, not Freesurfer. But, the same @SUMA_Make_Spec_FS previously worked on the same Fastsurfer files, but does not work now.

3

Is there the parcellation file generated by Fastsurfer for subj_id/mri/aparc+aseg.mgz ? It looks like that conversion may not have succeeded.

4

From Fastsurfer's github, that parcellation is not part of Freesurfer.

You can create the aparc+aseg.mgz (Desikian atlas) the same way as the a2009s (either running FastSurfer with --fsaparc or using the FreeSurfer commands):

cd $SUJECTS_DIR/<subjid>/mri

mris_ca_label -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ../label/?h.aparc.annot

mri_aparc2aseg --s <subjid> --volmask --aseg aseg.presurf.hypos
5

Hi Daniel,

Thanks for getting back, and for the info on the atlases.

Looks like the answer was quite boring. It turns out Fastsurfer makes some files I am unfamiliar with (highlighted in blue in right image below) that look like links to other files? They have no size, and an arrow icon next to them. They exist for various files that are not made by Fastsurfer or are named differently by Fastsurfer, like aparc_aseg.mgz (made by freesurfer, not fastsurfer, as they use the DTKatlas - as your link points out). Same for lh.pial in the surf folder (called lh.pial.T1 by Fastsurfer). I guess then when programs like SUMA_Make_Spec_FS are looking for lh.pial, this other file points it to lh.pial.T1?

Anyway, when I have been copying files between my local and HPC, these link files have not been copied over. Also, these files don't show up with some methods of counting/ comparing if files are similar/ different/ missing between folders, so took me a while to find what was up.

Not very interesting I am afraid, but useful info maybe for people using Fastsurfer!

Thanks again for your help!

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