Hi Bronwyn,
You can first create a striatum mask in the native subject's space:
>> mri_binarize --i subject/mri/aparc+aseg.mgz --match 11 --match 12
--match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
Then use the resulting mask to mask the striatum parcellation:
>> fslmaths Ch
Hi Thomas,
Thanks, I have taken your advise and used the LooseMask for the 7
network parcellation in steps 3a and b. How do I now mask it again with
FreeSurfer's segmentation of striatal regions as you have suggested?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Aus
Hi Bronwyn,
I was using that as a placeholder. You can use any of these:
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI15
Hi Thomas,
I am not sure which file you are referring to when you say
"Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
Choi_JNeurophysiol12_MNI152_README
Choi2012_7Networks_ColorLUT.txt
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Ne
Hi Bronwyn,
Perhaps you can try something like this:
mri_surf2surf --srcsubject fsaverage --trgsubject testsubj --hemi lh --sval-
annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.
annot --tval $SUBJECTS_DIR/testsubj/label/lh.Yeo2011_7Networks_N1000.annot
Regards,
Thomas
Hi Doug,
I tried to run the mri_surf2surf command as follows and got this error:
[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval
lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval
lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot
ERROR: Option --save-annot
Hi Doug, the Choi file is a striatal functional connectivity atlas which we
distribute. It's under the average directory.
Hi Bronwyn,
To transform the Choi's striatal atlas to your individual subject, Here's a
(non-ideal) suggestion I previously suggested to another user:
1) Assuming you are qui
On 5/4/16 11:40 PM, Bronwyn Overs wrote:
Hi Freesurfer Mailing List,
I wish to extract stats for my sample for the Yeo 2011 cortical
parcellations and the Choi 2012 striatal parcellations (7 networks)
that are provided for download on the freesurfer wiki. My questions
are as follows:
1. I
Hi Bronwyn
it depends on the type of stats, but you would either map the Yeo
annotations to your subjects, or map the stats from your subjects to
fsaverage.
cheers
Bruce
On Thu, 5 May 2016, Bronwyn Overs wrote:
> Hi Freesurfer Mailing List,
>
> I wish to extract stats for my sample for the Y
