That is a bug in mri_compute_volume_fractions. That seg (29) has not been given a tissue type. Probably there are like 5 voxels in there with that label. In the short term, you can just replace it with another label, eg 2 for left white matter or 41 for right white matter. You can do this with mri_binarize --replaceonly 29 2 ...

On 9/22/2023 4:38 AM, Óscar Peña-Nogales wrote:

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Hi,

I'm trying to perform mri_compute_volume_fractions --o output/ --regheader FREESURFER FREESURFER/mri/rawavg.mgz

and it apparently works in most of the subjects except in one which gives the following output:

$Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname  Linux hostname oscar machine  x86_64 user     oscar setenv SUBJECTS_DIR /home/oscar/Downloads/FS_12/ cd /home/oscar/Downloads/FS_12 mri_compute_volume_fractions --o output/ --regheader FREESURFER FREESURFER/mri/rawavg.mgz --debug outstem output/ regfile (null) regtype 0 segfile aseg.mgz wsurf white psurf pial TempVolFile (null) USF 2 Reading in aseg and surfs from /home/oscar/Downloads/FS_12_69463//FREESURFER Loading /home/oscar/Downloads/FS_12/FREESURFER/mri/aseg.mgz Filling empty voxels with extracerebral CSF (if not there already), nDil=3 Computing registration from header -0.98185   0.17682  -0.06858   199.82191; -0.11189  -0.24810   0.96225   50.90987; -0.15313  -0.95246  -0.26338   303.22836;  0.00000   0.00000   0.00000   1.00000;   t = 15.599 Computing PVF (USF=2, resmm=0.500000)   MRIhiresSeg(): filling unknowns with 257 ERROR: MRIseg2TTypeMap() tissue type for seg 29 Left-undetermined not set

Are you familiar on how to solve this error? In previous Q&A I saw this happened in PETsurfer to some people, but that solution does not seem to work in this case (or might might not be doing it correctly)

Any help is very welcome. Thank you in advance Óscar

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