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Hi,
I'm assuming the .annot is wrong because it doesn't map the entire gray matter
ribbon, whereas when the .annot is mapped unto the gray matter ribbon using
mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture
as illustr
Hello Jim,
All subjects should be processed with the same version of freesurfer,
especially for longitudinal studies.
Either v6.x or 7.x should work for your purposes.
If you decide to go with v7.x, you can make a copy of the subjects run in v6.0,
then run v7.x using the outputs of v6.0, and th
Hi Sarah
It is something like:
100 * (mean(abs(distance error)) / mean(original_distances))
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Sarah Lavelle
Sent: Tuesday, November 8, 2022 12:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Calculating Disto
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Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK atlas
(i.e. output of recon-all). I need average cortical thickness in frontal,
parietal, temporal, cingulate
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Hi freesurfers,
Does anyone know how to measure the distortion of your inflated surface ->
flatmap transformation (using mris_flatten)?
When being run, the function outputs "final distance error ...%" in the
terminal. What exactly does this mean? and
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Hello Yujing,
Thank you so much for your reply!
I understand.
It helps me a lot.
Thank you!
Best regards
Haiyun
On Mon, Nov 7, 2022 at 3:39 PM Huang, Yujing
wrote:
> Hi Haiyun,
>
>
>
> You can convert lh.pial.native to GIFTI using mris_convert - mri
Just as a quick verification and follow up using
1. Specifying the number of components eg. if I want 5 -nuisreg the various
components I want to regress out “-comp 6 – comp 7 comp 8 comp 9
2. Also just a follow up, how do I go ahead and run an ICA instead of the
regular connectivity ana
I'm not sure what you are saying. Are you saying that the annot/surf
looks right but the seg in the volume looks wrong or that they both look
wrong?
On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Hi Freesurfer devs,
We have us
can you send the mkanalysis-sess command?
On 10/31/2022 12:17 PM, Loeffler, Martin wrote:
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Dear experts,
I’m running into an error when running selxavg3. It says the design is
ill-conditioned. I’m a bit stuck, because the same pipeline works in
most subje
Try running recon-all on the unskull stripped data. Alternatively, if
you just want hippo you can run mri_synthseg or samseg
On 10/31/2022 5:32 AM, PRASAD D wrote:
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Hello everyone. I’m new to FREESURFER
I would like to segment the sMRI images.
I have ext
can you send the terminal output from selxavg3-sess?
On 10/31/2022 4:38 AM, Noam Khayat wrote:
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Hi again Douglas,
Do you know the answer to my last mail?
Do I need to compress all functional nii files to one single file?
Thanks!
Noam
בתאריך יום ב׳, 24 באו
are you looking at a surface or a volume? for volume, there is an
opacity slider in freeview
On 10/28/2022 11:06 PM, Yoshito Saito wrote:
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Hello.
I would like to ask a question about the color look-up table.
I want to change the opacity of color on a brain
the intensity is the T1-weight instensity of the norm.mgz image (after
intensity normalization, white matter mean ~= 110). It may or may not be
useful. In some cases, the intensity changes, so you could test that
On 10/28/2022 1:55 AM, Zeng, Qi wrote:
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Hi
just install FS
On 10/27/2022 4:56 PM, Jang, Woo Ju Albert W.,PhD wrote:
Hi, I need to unpack dcm files to my local workstation via /dcmunpack/
command. Is it possible to install this command on my local workstation?
Best,
Albert
___
Freesurfer
is it in $FREESURFER/bin ? If so, is that folder in your path?
On 10/27/2022 12:49 PM, Gillian Grennan wrote:
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Realized I sent this to the support list not back to you! But it says
"command not found" when I run 3dvolreg and 3dvolreg.afni
On Wed, Oct 26,
Also see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 10/27/2022 12:00 PM, Wighton, Paul wrote:
Hi Padma,
You can use the --like flag of mri_convert to convert the output of
the skull stripping back to the dimensions of the original file
https://surfer.nmr.mgh.harvard.edu
On 10/26/2022 10:05 PM, Lyna Mariam El Haffaf wrote:
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Hi!
I hope you are doing well!
I am working on a paper where we used Freesurfer for whole brain
analysis in intergroup comparison (g2v1). The objective of the
analysis is to see if there is an assoc
When you run fcseed-sess, specify -pca instead of -mean. When you run
mkanaysis-sess, specify the number of components you want when specify
-nuisreg
On 10/26/2022 6:29 PM, Addison, Reuben wrote:
Hi,
I am running resting State functional connectivity and I want to run
everything in freesurfe
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Hi,
I’m wondering if there’s a way to get the properties of individual vertices
such as:
1)Coordinates
2)Surface area
3)angles
4) Side lengths
5) distance matrix from other vertices
And can you get these properties for individual surfaces/ transforma
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