and:

mris_seg2annot --seg /.../hammers_lh_INDI_0021.mgh --s 0021 --h lh --ctab /.../ExploreDTI_Pcode/Source/Misc/My_FS_LUT.txt --o .../lh.hammersmithINDI.annot

My question now is how can I create a suitable LUT with the correct labels for the cortical parcellations? I have only a .csv file with the labels for the volumetric atlas?

My goal is to use

mris_anatomical_stats -a .../0021/label/lh.hammersmithINDI.annot -b 0021 lh

to get the cortical thickness values of each segment in the annot for every participant file.

Thanks again,

Boris

Am 27.01.2019 um 23:58 schrieb Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

Hi Boris

vol2surf samples a scalar overlay in the volume to be a scalar overlay on the surface. This is NOT the same as a surface itself - it contains no geometry or topology information. Try giving freeview a surface (which I guess you have for subject 0021). Something like

freeview -f \
0021/surf/lh.inflated:overlay=lhHammers_mith_atlas_n30r83_SPM5surf.mgh

cheers
Bruce

On Sun, 27 Jan 2019, Boris Rauchmann wrote:

        External Email - Use Caution
Hi,
I used the following commands:
mri_vol2surf —src .../Hammers_mith_atlas_n30r83_SPM5.nii --out lhHammers_mith_atlas_n30r83_SPM5surf.mgh
--out_type mgh --hemi lh --regheader 0021
srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using .../0021/mri/orig.mgz as target reference.
Reading surface .../0021/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 76207
Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
Dim: 125545 1 1
it creates the .mgh file but when I try to open in in Freeview or tksurfer to check the surface file I get the
following error message:
my_computer$ freeview
ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 vertices!
Probably trying to use a scalar data file as a surface!
nquads=65537, nvertices=0
ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision:
4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris Sun Jan 27 23:12:45 2019
[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0
--download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault
Hoe can I actually check the surface file?
Thanks,
Boris

     Am 25.01.2019 um 17:45 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:
Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is
not working?
On 1/25/19 10:56 AM, Boris Rauchmann wrote:

             External Email - Use Caution

     Dear FreeSurfer Developers,


I´m trying to extract the cortical thickness of individuals from a study cohort based on an
hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run
recon-all on all subjects. I tried mri_vol2surf and then mris_seg2annot but without success so far.
What commands would you recommend me to run?

Thanks,
Boris
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