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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#Sig... 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:

...

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<>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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Hi Bruce,

thank you for your quick answer. I managed it now to create cannot files based on the atlas volumetric segmentations.

I first created:

mri_vol2surf —src .../Hammers_mith_atlas_n30r83_SPM5.nii --out .../Hammers_AVG.nii --out_type mgh --hemi lh --mni152reg

then applied:

mris_apply_reg --src .../hammers_lh_avg_surf.mgh --trg .../hammers_lh_INDI_0021.mgh --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg .../0021/surf/lh.sphere

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:

...

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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#Sig... 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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