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:
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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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