Oops, slight edit
import nibabel as nib
file_list = [os.path.join(os.getenv(‘SUBJECTS_DIR’), subject, ‘mri’,
‘brainmask.mgz’)for subject in subject_list]
mri_list = [nib.load(fname) for fname in file_list]
On Feb 22, 2022, at 9:53 PM, Fischl, Bruce wrote:
In python you should be able to
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Hello,
The output of mri_info --dim VOI.mgz is 344 344 344 1.
VOI.mgz is a mask of the MRS "voxel". "Voxel" is a slightly misleading term in
this context, as the MRS "voxel" is the small rectangular volume from which
the MRS data is acquired. I
In python you should be able to do (assuming you have a list of subject ids in
subject_list):
import nibabel as nib
file_list = [os.path.join(os.getenv(‘SUBJECTS_DIR’), subject) for subject in
subject_list]
mri_list = [nib.load(fname) for fname in file_list]
even for 1000 subjects it won’t
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Hello FreeSurfer experts,
I want to run a classification task using deep learning on data
processed by Freesurfer recon-all and I have some queries. I will use
brainmask .mgz
First of all, based on my simple knowledge, I cannot feed my model
with
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Sorry about that!
I'm resending with previous emails.
---
On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:
Thanks so much for the explanation!
There is
What is the size of your VOI.mgz? Ie, if you run
mri_info --dim VOI.mgz
It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the
You don't need to go that far. You can run mris_annotoical_stats. Look
in recon-all.log to find the command line used to create the
?h.aparc.annot and just change the annot and output file
On 2/22/2022 10:02 AM, Jacoby, John wrote:
Hi all,
We were sent a FreeSurfer annotation file that
Try just adding a line at the end of the lta file like
subject 126346
On 2/22/2022 9:45 AM, Tisdall, Dylan wrote:
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>
> Hi Doug and Matt,
>
> I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for
> recon-all on this subject and the
I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:
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If I only want to extract intensity from gray matter, do I need to add
an additional mask?
Thanks!
Jennifer
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Thank you! I ran the development version of the mri_glmfit-sim command on my
data, and it did not crash and seems to give reasonable outputs (smaller
clusters disappear after correction). Whenever your tests are done, it will be
good to know if they confirm that everything is working.
Best,
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal
output. The output files generated (i.e, cortex.mgz) are the partial volume
segmentations for the whole brain. There were no output files that segmented
the
Hi all,
We were sent a FreeSurfer annotation file that denotes some ROIs we're
interested in. What's the proper way to map this annotation to the cortical
ribbon volume and get an estimate of that volume for each ROI? I've already
registered the annotations to the subject from fsaverage space
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Hi Doug and Matt,
I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for
recon-all on this subject and the files seem to be in the right place; wee
below:
[mtisdall@ftdc-gpu01 126346]$ echo $SUBJECTS_DIR
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Thanks so much for the explanation!
There is something different in the analysis of volume and surface area in
relation to the analysis of cortical thickness? Like some more command, or some
other detail that must be changed (besides, of course, the
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If I only want to extract intensity from gray matter, do I need to add an
additional mask?
Thanks!
Jennifer
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