[Freesurfer] [Freesurfer/FSFAST]

[Dave Yas]

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY

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Re: [Freesurfer] Freesurfer for canine

[Douglas N. Greve]

To my knowledge, it does not work with canine data, but maybe someone 
has done it.


On 04/02/2018 04:41 PM, Khoi Mai wrote:
> Hi,
>
> I am interested in the automated volumetric analysis for canine. My 
> question is how can we go about adjusting the pipeline to accommodate 
> canine data.
>
> Thank you for your reply
>
> Best,
>
> Khoi
>
>
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[Freesurfer] Freesurfer for canine

[Khoi Mai]

Hi,

I am interested in the automated volumetric analysis for canine. My
question is how can we go about adjusting the pipeline to accommodate
canine data.

Thank you for your reply

Best,

Khoi
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Re: [Freesurfer] mirroring fsaverage labels between hemispheres

[Douglas Greve]

If you have a label defined on the lh or rh of fsaverage, you can map it 
to the contralateral hemi with something like


mris_apply_reg --src-label lh.your.label --streg lh.sphere.left_right 
rh.sphere.left_right --trg rh.your.label


where the left_right files are in fsaverage/surf


On 3/29/18 2:02 PM, Abigail Noyce wrote:
Hi, I have pored over (I think) all of the mailing list postings about 
cross-hemisphere mapping and I can't quite figure out how to do this.


I have a bunch of labels on fsaverage, and I want to be able to 
check/visualize the relationship between lh and rh versions of the 
labels.


I can do mri_label2label to map from fsaverage to fsaverage_sym, but 
that doesn't do the right thing, and fsaverage doesn't have the same 
kind of xhemi registration structure that "normal" subjects get with 
surfreg --xhemi. I guess I could back-project onto a normal subject 
and then project to fsaverage_sym, but that seems like an unnecessary 
step.


How can I get mirror-projected labels from fsaverage on fsaverage_sym?

Thanks!
Abby
--
Abigail L. Noyce, Ph.D.
Psychological & Brain Sciences
Boston University

ano...@bu.edu 
617-440-3640


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