Re: [Freesurfer] preproc-sess

Actually, before you do that, can you check two things 1. Does the raw data (eg, f.nii) look ok? 2. Does the talairach transform for this subject look ok? doug

On 09/24/2012 04:02 PM, Douglas N Greve wrote:

Can you upload it to our file drop at www.nmr.mgh.harvard.edu/facility/filedrop/

On 09/24/2012 02:58 PM, Andrew Bock wrote:

...

It looks like a very patchy, warped version of the brain. I find that this is true for all subjects (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). I used both freeview and fslview to visualize the images.

On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:

 yes, you would expect that. what does it look like? how are you
 visualizing it?

 On 09/20/2012 06:18 PM, Andrew Bock wrote:
 >  Hello,
 >
 >  I am attempting to run preproc-sess on my functional data, and am
 >  following the tutorial found here:
 >
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
 >
 >  I downloaded the tutorial data, and find that when I view
 >  fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does
 not look
 >  like a brain).  I would expect this file to look like the fsaverage
 >  brain, is that not correct?
 >
 >  Andrew
 >
 >
 >
 >
 >
 >
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>
 Phone Number: 617-724-2358<tel:617-724-2358>
 Fax: 617-726-7422<tel:617-726-7422>

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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