Hi Doug,
Thanks for your response. Actually, we do modify the aseg.mgz (Sorry, I didn't realized and I shouldn't have considered this a 'standard FS pipeline'). We work with Multiple Sclerosis patients and because of the size and number of lesions in some of them, the pial and WM surfaces that we obtain after a first run of “recon-all -all ” are not accurate. FreeSurfer pipeline for healthy subjects or small lesions requires to edit wm.mgz -- but these edits don't fix our issue of WM & GM surface getting pulled in by lesions. Given the size and number of lesions in some of our MS patients, using control points make the entire recon worse. So after repeated testing, the solution we arrived at was to insert manually drawn lesion masks into segmentation volumes as "WM-hypointensities". We label manually drawn lesion masks as "WM-hypointensities" on aseg.mgz, and wm.mgz. We then do a second run of recon-all and check the surfaces again. Once they are ok we run “recon-all -autorecon3” and check the final output. In principle, we only change voxels in aseg.mgz to "WM-hypointensities", so I don't know why these unexpected values appear. Just to check, I renamed the 'aseg.auto.mgz' as 'aseg.mgz' and re-run again the steps for PVC: 1. Segmentation for GTM: gtmseg --s $subj"_recon" --xcerseg In this step I get the following warnings: WARNING: segid 59 Right-Substancia-Nigra tissue type is not set WARNING: segid 61 Right-undetermined tissue type is not set WARNING: segid 64 Right-F3orb tissue type is not set WARNING: segid 73 Left-Interior tissue type is not set WARNING: segid 81 Left-non-WM-hypointensities tissue type is not set WARNING: segid 86 Left_future_WMSA tissue type is not set 2. Registration: mri_coreg --s $subj"_recon" --mov $path_to_suvr/SUVR.nii.gz --reg $path_to_suvr/SUVR.reg.lta 3. PVC: 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. And still get the same error (below) (maybe because there are other files that are based in the previous aseg.mgz? ) Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set Failed tissue type check Any help with this would be very much appreciate it! Thanks! Elena ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, December 07, 2017 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error 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 FileDrop v2.0 - Martinos Center for Biomedical Imaging<https://gate.nmr.mgh.harvard.edu/filedrop2> gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ... > > > 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 Freesurfer -- Freesurfer support list - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. 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