Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html