Hi Elena, it looks like the aseg.mgz has several unexpected segments in it. The aseg.auto.mgz looks ok, so I think FS is working properly. It looks like you made some changes to the aseg. What did you do?
On 12/06/2017 03:51 PM, Douglas N Greve wrote: > Did you run this through the standard FS pipeline? If so, can you send > me the FS analysis for this subject? You can upload it here > > https://gate.nmr.mgh.harvard.edu/filedrop2 > > > On 12/06/2017 09:46 AM, Herranz Muelas, Elena wrote: >> Dear Freesurfers, >> >> >> I am trying to apply partial volume correction to my PET images, >> following the steps explained in the PetSurfer wiki. >> >> >> When I run the mri_gtmpvc command, it works fine for most of the >> subjects but for some of them I get the following error message: >> >> >> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space >> Loading input >> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz >> done loading input 1 frames >> $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ >> setenv SUBJECTS_DIR >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 >> cd /autofs/space/alicudi_002/users/mscat/users/elena/scripts/PVC >> mri_gtmpvc --i >> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz >> --reg >> /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.reg.lta >> --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx >> .01 --o >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output >> sysname Linux >> hostname alicudi.nmr.mgh.harvard.edu >> machine x86_64 >> user ehmuelas >> vgthresh 0.001000 >> nReplace 18 >> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >> 40 avail.processors, using 1 >> Creating output directory >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output >> Loading seg for gtm >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.mgz >> Loading seg ctab >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.ctab >> Reading >> /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.lta >> Replacing 18 >> Pruning ctab >> *Checking tissue type >> ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set >> Failed tissue type check >> * >> >> >> And the command line that I ran: >> >> mri_gtmpvc --i $path_to_suvr/SUVR.nii.gz --reg >> $path_to_suvr/SUVR.reg.lta --psf 6 --seg gtmseg.mgz >> --default-seg-merge --auto-mask PSF .01 --mgx .01 --o >> $path_to_recon/$subj"_recon"/gtmpvc.output >> >> >> Could you please help me out with this? >> >> >> Many thanks in advance! >> >> >> Elena >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
