Hi Noam
if you want your outputs in a specific coordinate system, why not just
run recon-all, then mri_conver to whatever orientation you want?
Internally we have a consistent orientation that you can't easily change
cheers
Bruce
On
Sat, 9 Mar 2019, Peled, Noam wrote:
Dear group,
I ran
Dear group,
I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz
turn out to be in LIA orientation.
I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS
--out_orientation RAS ...), and rerun recon-all, but it didn't change the
results.
How do I
When you have such a low threshold, the resulting p-values are very
liberal. See our paper https://www.ncbi.nlm.nih.gov/pubmed/29288131
Should be fine for exploratory
On 3/7/19 7:48 PM, Arsenije Subotic wrote:
> External Email - Use Caution
>
> Hello,
>
> I am planning on running a
Dear Doug
Thank you so very much for your time and helps.
Yes It works perfectly.
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, March 7, 2019 6:07:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
Yea, the real hard part is figuring out how to model the twins that are split
between groups. You might be able to create a bunch of groups. If you've
already created a design in FSL that you like, you can extract the design
matrix and use it in mri_glmfit with the --X option. Not sure about
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Hi Stefano,
You can try the following
1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
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Hi Doug,
my apologies, I have tried to do it with some errors. Could you suggest the
command line, please?
Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D."
> ha scritto:
>
> You have to convert the annotation to a volume
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Hi Bruce,
my apologies, I have tried to do it with some errors. Could you suggest the
command line, please?
Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D."
> ha scritto:
>
> You have to convert the annotation to a
External Email - Use Caution
You could load the aseg in freeview and navigate to the voxel (you can enter
the CRS at the bottom, no need to scroll there). Then you have its intensity
value, which you can check against FreeSurferColorLUT.txt.
Tim
--
Dr. Tim Schäfer
Postdoc
