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
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
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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Herranz Muelas, Elena