Re: [Freesurfer] preproc-sess

Oh, I see now. There is not a problem here. The volume data has the cortical structure masked out (since those are analyzed in the cortical stream). doug

On 09/24/2012 04:22 PM, Andrew Bock wrote:

Hi Doug,

I uploaded two example files, as far as I can tell the raw f.nii and talairach transform look okay. I obtained these files from the tutorial data set, so I'm assuming they were processed properly.

Andrew

On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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/
<http://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.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu <mailto: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><mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>>      Phone Number: 617-724-2358
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<tel:617-726-7422>>
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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
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