Hi Doug,
I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine: $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ mri_gtmseg --s $s etc, exited fine
Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error: [weckl:FDG_2017-11-15] (nmr-stable6-env) cat MR_2017-11-07/pvc.psf06/mri_gtmpvc.log $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR $SUBJECTS_DIR mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg $PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta Failed tissue type check [weckl:FDG_2017-11-15] (nmr-stable6-env)
I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this thread (I left out --no-xcerseg since I think it's now the default): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.h... But I got a different error, where it's trying to write to a file called (null): [weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ cwd $PET_DIR cmdline mri_gtmseg --s $s--keep-cc sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz subject $s USF 2 OutputUSF 2 apasfile apas+head.mgz wmannotfile NULL ctxannotfile aparc.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 1 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz Loading surfaces t = 2.1280 Loading annotations t = 6.2390 Not segmenting WM reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 32.3010 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using aparc.annot t = 83.9890 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 1517 unknown, filled with 257 Not subsegmenting WM Found 115 segs in the final list MRIgtmSeg() done, t = 358.8340 Computing colortable WARNING: segid 29 Left-undetermined tissue type is not set Writing output file to $SUBJECTS_DIR/$s/mri/(null) unknown file type for file ($SUBJECTS_DIR/$s/mri/(null)) [weckl:FDG_2017-11-15] (nmr-stable6-env)
I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). Do you have any advice?
Thank you in advance for any help! Sara
Hi Doug,
I'm still stuck on this subject and am wondering if you have any advice.
Thanks for any help!
Sara
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Makaretz, Sara Johanna SMAKARETZ@mgh.harvard.edu Sent: Friday, December 15, 2017 12:04:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_gtmpvc & mri_gtmseg errors - failed tissue type check
Hi Doug,
I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine: $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ mri_gtmseg --s $s etc, exited fine
Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error: [weckl:FDG_2017-11-15] (nmr-stable6-env) cat MR_2017-11-07/pvc.psf06/mri_gtmpvc.log $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR $SUBJECTS_DIR mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg $PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta Failed tissue type check [weckl:FDG_2017-11-15] (nmr-stable6-env)
I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this thread (I left out --no-xcerseg since I think it's now the default): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.h... But I got a different error, where it's trying to write to a file called (null): [weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ cwd $PET_DIR cmdline mri_gtmseg --s $s--keep-cc sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz subject $s USF 2 OutputUSF 2 apasfile apas+head.mgz wmannotfile NULL ctxannotfile aparc.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 1 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz Loading surfaces t = 2.1280 Loading annotations t = 6.2390 Not segmenting WM reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 32.3010 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using aparc.annot t = 83.9890 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 1517 unknown, filled with 257 Not subsegmenting WM Found 115 segs in the final list MRIgtmSeg() done, t = 358.8340 Computing colortable WARNING: segid 29 Left-undetermined tissue type is not set Writing output file to $SUBJECTS_DIR/$s/mri/(null) unknown file type for file ($SUBJECTS_DIR/$s/mri/(null)) [weckl:FDG_2017-11-15] (nmr-stable6-env) [Freesurfer] Reading values from overlays with PETcoreghttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.html mail.nmr.mgh.harvard.edu The problem is that --default-seg-merge merges the CC with WM, so you can't use that option, which means that you'll have to specify the rest of the default seg merge ...
I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). Do you have any advice?
Thank you in advance for any help! Sara
freesurfer@nmr.mgh.harvard.edu
-
Makaretz, Sara Johanna