Your first command should do the trick. What version of FS are you
using? The version of that program is over 7 years old. I just ran it
with that command line in 7.3.2, and it worked.
On 9/28/2022 8:35 AM, Bauer, Martin wrote:
External Email - Use Caution
Dear Freesurfer experts,
I’m trying to get a 5TT output from freesurfer data as FSL would
provide it using MRtrix wrapper 5ttgen fsl.
mri_compute_volume_fractions looks like doing the job, but I can’t
wrap my head around some tissue type that seemed to be missing.
For clarification, its infant data but it comes from a freesurfer
based processing pipeline. If I’m using it like this:
mri_compute_volume_fractions --o test --regheader 2035
/Users/path/to/data/2035/mri/norm.mgz
I’ll get this error:
$Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl
Exp $
sysname Darwin
hostname xxx.charite.de
<http://secure-web.cisco.com/1duNm437197YxIoR1NUN7k5zEN8kZoKQenYNRSG9UrqckbQcfgTpqtkmt2AUd_xJ9QYI2rLBuVCcLWIryaPU6jKFxAO9oS4FHXXN9Gh6iRGu_WLAmfg9ZqrF8fI5OP0ga-bbXPxbxOHDFZGqvFcwl5lK9jNHcqtZFtD046E7BcRH18-6fyRCfAqp_UoChNLj-KNSIM5TQCPuoITbJCif2Y4vfRlf9IMV_FfBpDYnRDj4CbXX0ceG44aDzCBXwzHGVcFkXFeJlHJkM5tjAzBIydAQqtmqw6nfCvfA4j7ulKGk_bkp_Ssb3Up795rALytuXZhgLQ5QZMLbfvEvOyfrvtQ/http%3A%2F%2Fxxx.charite.de>
machine x86_64
user martinbauer
setenv SUBJECTS_DIR /Users/martinbauer/Daten/MRI/FS_corrected
cd /Users/martinbauer
mri_compute_volume_fractions --o test --regheader 2035
/Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/norm.mgz
outstem test
regfile (null)
regtype 0
segfile aseg.mgz
wsurf white
psurf pial
TempVolFile (null)
USF 2
Reading in aseg and surfs from
/Users/martinbauer/Daten/MRI/FS_corrected/2035
Loading /Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/aseg.mgz
Changing type of seg from UCHAR to INT
Filling empty voxels with extracerebral CSF (if not there already), nDil=3
Computing registration from header
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
t = 4.53563
Computing PVF (USF=2, resmm=0.500000)
MRIhiresSeg(): filling unknowns with 257
ERROR: MRIseg2TTypeMap() tissue type for seg 172 Vermis not set
Fair enough, so I force it using finer parcellations doing:
mri_compute_volume_fractions --o test --regheader
2035 /Users/path/to/data/2035/mri/norm.mgz --seg aparc.a2009s+aseg.mgz
Vermis is now part of the game but:
$Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl
Exp $
sysname Darwin
hostname xxx.charite.de
<http://secure-web.cisco.com/1duNm437197YxIoR1NUN7k5zEN8kZoKQenYNRSG9UrqckbQcfgTpqtkmt2AUd_xJ9QYI2rLBuVCcLWIryaPU6jKFxAO9oS4FHXXN9Gh6iRGu_WLAmfg9ZqrF8fI5OP0ga-bbXPxbxOHDFZGqvFcwl5lK9jNHcqtZFtD046E7BcRH18-6fyRCfAqp_UoChNLj-KNSIM5TQCPuoITbJCif2Y4vfRlf9IMV_FfBpDYnRDj4CbXX0ceG44aDzCBXwzHGVcFkXFeJlHJkM5tjAzBIydAQqtmqw6nfCvfA4j7ulKGk_bkp_Ssb3Up795rALytuXZhgLQ5QZMLbfvEvOyfrvtQ/http%3A%2F%2Fxxx.charite.de>
machine x86_64
user martinbauer
setenv SUBJECTS_DIR /Users/martinbauer/Daten/MRI/FS_corrected
cd /Users/martinbauer
mri_compute_volume_fractions --o test --regheader 2035
/Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/norm.mgz --seg
aparc.a2009s+aseg.mgz
outstem test
regfile (null)
regtype 0
segfile aparc.a2009s+aseg.mgz
wsurf white
psurf pial
TempVolFile (null)
USF 2
Reading in aseg and surfs from
/Users/martinbauer/Daten/MRI/FS_corrected/2035
Loading
/Users/martinbauer/Daten/MRI/FS_corrected/2035/mri/aparc.a2009s+aseg.mgz
Filling empty voxels with extracerebral CSF (if not there already), nDil=3
Computing registration from header
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
t = 4.40752
Computing PVF (USF=2, resmm=0.500000)
MRIhiresSeg(): filling unknowns with 257
ERROR: MRIseg2TTypeMap() tissue type for seg 12104
ctx_rh_G_and_S_subcentral not set
What files are exactly read and can those files be adjusted? In
FreeSurferColorLUT.txt Vermis and 12104 are included, I tried to add
12104 to the parcellation stats LUT but it didn’t solve the problem.
I’m also open to go another way.
Thank you so much in advance for pointing me towards the right direction!
All the best,
Martin
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