http://freesurfer.net/fswiki/ThalamicNuclei
On 7/23/2020 11:04 AM, Al Qadi, Ameen wrote:
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Thank you. How do I generate this image? It wasn't generated using
recon-all.
On Thu, Jul 23, 2020 at 10:55 AM Douglas N. Greve
<[email protected] <mailto:[email protected]>> wrote:
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 ######
inputaparc+aseg.nii
frame0
nErode3d 0
nErode2d 0
output thalamus_vent_lat.nii
Binarizing based on matching values
nMatch 1
08005
binval1
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
<[email protected] <mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> wrote:
On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
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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.
They should be in $FREESURFER/FreeSurferColorLUT.txt
How are you extracting?
* 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?
You can run the hippocamal and thalamic segs on FS
version 6 subjects.
I’d highly appreciate your time and feedback on this
matter. Thank you.
Best,
Ameen
--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
[email protected]
<mailto:[email protected]>
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--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
[email protected] <mailto:[email protected]>
--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
[email protected] <mailto:[email protected]>
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--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
[email protected] <mailto:[email protected]>
--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
[email protected] <mailto:[email protected]>
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