External Email - Use Caution 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 <fis...@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. >> <dgr...@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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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