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.
