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:
External Email - Use Caution
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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