Hi Mason
You should be able to load the overlay and the ROIs into matlab, then pick out
the vertices in each ROI from the overlay and save them separately. Just be
careful about the one-based indexing in matlab. That is, if your ROI is in a
label file and you read the vertex indices from it,
seg is usually a volume-based segmentation (like the aseg)
parc is usually a surface-based segmentation (like lh.aparc.annot)
unfortunately, I misnamed "wmparc". It is a volume-based segmentation
that incorporates surface-based information
On 6/12/2020 3:12 PM, Zeng, Qi wrote:
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I am using the OpenNeuro dataset "Reconstructing Faces from fMRI Patterns
using Deep Generative Neural Networks":
https://openneuro.org/datasets/ds001761/versions/2.0.0. In this dataset,
four subjects go through eight sessions each, and each session
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Hi All,
I am a little confused with the stats output. So seg/aparc are cortical
white /grey matter and wmparc are subcortical white matter. Is that correct?
Best,
Qi
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That is what I did for us, based on tables from web, existing make file and
trial and error. But now my make file does not work and without more
information about steps it looks very difficult for me to do.
I am glad FreeSurfer decided to go the
You could also do it pretty easily in matlab or python
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, June 12, 2020 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Splitting surface overlay into separate files
When
When you say "surface" do you mean a surface overlay or a surface with
xyz and neighbor relations? Assuming you mean an overlay (eg, something
in an mgh or mgz file), you can try fscalc. Or do you have 25 frames in
a single file and you want to split them into separate files? You might
be
On 6/10/2020 9:54 AM, Avi Gharehgazlou wrote:
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Hi experts,
I am a bit confused with visualizing my significant clusters after
having corrected my results for multiple comparisons. after running
mri_glmfit, I corrected with monte carlo and permutation as
Also, verify that they are shifted (or not) in freeview
On 6/10/2020 8:39 AM, Tim Schäfer wrote:
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>
> Without the code used to plot it's hard to tell why they are not aligned, but
> my guess would be that are misaligned by exactly 1 voxel (=mm) as a
>
Hard to tell from just that view. Was there a lot of brain change with
that time point? Or was there an MRI artifact? If no to both, then you
can upload all the cross, the base, and that one long. Follow
instructions below (you can make one tarball for all subjects)
From the linux command
Can we back up a moment? Is this the same subject scanned at different
time points? If so, why are you using CVS? That is probably not
necessary unless there is a lot of anatomical change between the two
time points.
On 6/9/2020 3:22 PM, Paul Soulos wrote:
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On 6/9/2020 11:27 AM, Avi Gharehgazlou wrote:
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Thank you so much for your input, it was very helpful and I
really appreciate it.
Regarding your question with relation to my 4th question, when I run
the below command line to visualize my results after
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Hi Experts,
Apologies if this is a rather simple question. Is there a FreeSurfer equivalent
of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz
file. I want to separate each atlas region into a different file, so that I
Sorry, we don't have a plan for v7. Unfortunately, it became too
difficult to maintain. We'd like to reprogram recon-all entirely to have
make-like functionality from the ground up.
On 6/9/2020 11:17 AM, Roman Fleysher wrote:
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Thank you, Douglas. I will
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