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aparc+aseg does not have the thalamic nuclei. You need to run it on ThalamicNuclei.v10.T1.FSvoxelSpace.mgz
On 7/22/2020 6:26 PM, Al Qadi, Ameen wrote:
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Hi Douglas,
mri_segstats wouldn't generate binary ROI masks, so I tried using mri_binarize and mri_extract_label to produce masks for thalamic nuclei, but I run into the same problem of generating empty masks (these commands worked for other ROIs):
- $: mri_extract_label aparc+aseg.nii 8005 thalamus_vent_lat.nii
reading volume from aparc+aseg.nii...
extracting label 8005 ()
writing output to thalamus_vent_lat.nii.
- $: mri_binarize --i aparc+aseg.nii --o thalamus_vent_lat.nii --match 8005
7.1.0
cwd /data/freesurfer/subjects/S12452/mri
cmdline mri_binarize --i aparc+aseg.nii --o thalamus_vent_lat.nii --match 8005
sysname #####
hostname #####
machine #####
user ######
input aparc+aseg.nii
frame 0
nErode3d 0
nErode2d 0
output thalamus_vent_lat.nii
Binarizing based on matching values
nMatch 1
0 8005
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
Found -1 voxels in final mask
Count: -1 -0.343000 32768000 -0.000003
mri_binarize done
I'd appreciate any feedback you may have.
Best,
Ameen
On Tue, Jul 21, 2020 at 10:34 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
I don't know. I'm not that familiar with FSL programs. If you want our help, try using mri_segstats. If something goes wrong send the command line
On 7/21/2020 10:26 AM, Al Qadi, Ameen wrote:
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Hi Douglas,
--
I see the CLUT file, it's the same one I've been using. I have been using FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the CLUT indices as thresholds. This normally works, but results in empty ROIs for thalamic nuclei (but not for whole thalamus). What do you think could be the problem?
Best,Ameen
On Fri, Jul 17, 2020 at 10:33 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
_______________________________________________
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
They should be in $FREESURFER/FreeSurferColorLUT.txtExternal Email - Use Caution
Dear Freesurfer Developers,
I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer:
- Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROIs, but got empty ROI files.
How are you extracting?
You can run the hippocamal and thalamic segs on FS version 6 subjects.
- Given that Freesurfer version 7 contains segmentations not previously generated in recon-all (i.e. hippocampal subfields), is it possible to extract these ROIs using aparc+aseg images generated using previous versions of Freesurfer? Or do we need to repeat the cortical parcellations (i.e. rerun recon-all) using FS7?
I’d highly appreciate your time and feedback on this matter. Thank you.
Best,
Ameen
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Ameen Al QadiMSBS CandidateIcahn School Of Medicine at Mount Sinai '20+1-646-500-1521
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Ameen Al QadiMSBS CandidateIcahn School Of Medicine at Mount Sinai '20+1-646-500-1521
Ameen Al QadiMSBS CandidateIcahn School Of Medicine at Mount Sinai '20+1-646-500-1521
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Ameen Al QadiMSBS CandidateIcahn School Of Medicine at Mount Sinai '20+1-646-500-1521