I have created some python and bash scripts to pull items from FreeSurfer
data. I've found tools like aparcstats2table and asegstats2table to be very
useful, and I'm grateful for them, but I've had some more specific needs. My
scripts are available at https://github.com/mfschmidt/freesurfer-managem
Hi Antonin,
Thank you for your input. I will give mri_cvs_register a try.
Best,
Corinna
On Mon, Apr 24, 2017 at 10:24 AM, Antonin Skoch wrote:
> Dear Corinna,
>
> I am not sure what is (or whether is) something wrong with your commands,
> but in any case I would be cautious of interpretation
https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table
On 04/24/2017 12:55 PM, shi yao wang wrote:
> Dear FS experts:
> Would you pls provide freesurferstats2table_bash script?
> The link of http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table
> does not work.
>
> thanks
> Shiyao
>
>
Dear FS experts:
Would you pls provide freesurferstats2table_bash script?
The link of http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table
does not work.
thanks
Shiyao
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Dear Doug,
the subject with leak of white surface outside brain (my first post with
screenshots) is subject 1. Slice number (coronal) around 100.
The subject in second post (with text below) is subject 2, slice number
(coronal) also 100.
I have processed the subjects with v 6.0 (in fact dev ver
tksurfer will always report the coordinate of the ?h.orig surface
On 04/24/2017 03:35 AM, Zhiliang Long wrote:
> Dear FS experts:
>
> I am studying the coordinate system in FS. I met a problem that
> confused me. I run tksurfer: tksurfer fsaverage lh inflated. Then I
> chose a point on su
If you want a table of ROI values, then you can run asegstats2table and
aparcstats2table. If you want a map, then you can run mris_preproc
followed by mri_concat stack.mgh --mean --o stack.mean.mgh
On 04/24/2017 11:08 AM, shi yao wang wrote:
> Dear FS expert,
> We have running around 500 sample
And what slice number?
On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> Anonin, of the three subjects you sent, which one is shown in these
> pictures?
>
>
> On 04/19/2017 05:23 PM, Antonin Skoch wrote:
>> Dear experts,
>>
>> I am sending just one more example to illustrate issue with white
>>
Dear FS expert,
We have running around 500 samples by FS. I am wondering if there are easy
way to summary these data. i.e., generate mean of cortical thickness.
thanks
Shiyao
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Dear Corinna,
I am not sure what is (or whether is) something wrong with your commands, but
in any case I would be cautious of interpretation of results using such method,
mainly from following reasons:
1.
mni152reg uses 12 DOF whole-brain registration. You cannot expect to get
perfect alignme
Thank you!
Julie
On 19/04/2017 11:49 pm, "Harms, Michael" wrote:
>
>I??ve previously created an .annot version of the Gordon parcellation. It
>is attached.
>
>--
>Michael Harms, Ph.D.
>
>---
>Conte Center for the Neuroscience of Mental
Dear FS experts:
I am studying the coordinate system in FS. I met a problem that confused
me. I run tksurfer: tksurfer fsaverage lh inflated. Then I chose a point on
surface. It showed that the Vertex Index is 80321, and the Vertex RAS is
(-38.53 9.05 40.01). I thought that the Vertex
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