[caret-users] mapping functional data from SPM5

[John Harwell]

Gene,

On the "Spec File And Surface Selection" page of the Map Volumes to  
Surfaces Dialog are buttons "Map to Caret...", which places the  
results into Caret's loaded Metric Data, and "Map to Spec File...",  
which places the results into a Metric File.  If the D/C metric  
selection is disabled, it is likely that "Map To Spec File..." was  
used and the results are in a metric file.  If this is the case, you  
just need to load the metric file into Caret.

-----------------------------------
John Harwell
john at brainmap.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110



On Feb 20, 2008, at 11:36 AM, Eugene Tunik wrote:

>
> Hi Donna,
> I have a quick question about a caret problem.
> I installed v.5.51 on a new windows machine. (and the tutorial sept  
> 06 toolbox).
> I just want to map functional volume to surface so I do the following:
>
> 1) load spec file (in mapping procedures->PALs for fmri mapping
>
> 2) attributes-=> map to surface...and go through the whole deal of  
> loading my image file (SPM space).
>
> When the whole thing is done, and I click D/C, the metric icon  
> doesn't become active so I cannot overlay anything.
>
> (The same functional works fine on a different machine that has an  
> older installation of caret).
>
> Any suggestions?
> Thanks and best,
> Gene
>
>
>
>
> Eugene Tunik, PhD, PT
> Dept. of Physical Therapy, NYU
> http://homepages.nyu.edu/~et38/
>
> ----- Original Message -----
> From: Donna Dierker <donna at brainvis.wustl.edu>
> Date: Wednesday, April 11, 2007 9:28 am
> Subject: Re: [caret-users] mapping functional data from SPM5
> To: "Caret, SureFit, and SuMS software users" <caret-users at brainvis.wustl.edu 
> >
>
>
>> Hi Gene,
>>
>> It might take you 15 minutes to wade through this whole thread, but  
>> it
>>
>> will resonate:
>>
>> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01088.html
>>
>> Here are the highlights:
>>
>> * Caret only reads NIFTI files that are a single file with the ".nii"
>>
>> extension. The next release of Caret will be able to read NIFTI files
>>
>> that are in an Analyze hdr/img pair.  Caret still reads the files as
>> if
>> they were Analyze, but without the SPM99/SPM2-style "originator" info
>> in
>> the .hdr, it's clueless about the location of the origin.
>>
>> * Use Volume: Edit volume attributes to set the origin to  
>> -90,-126,-72.
>>
>> * When opening the functional volume in Caret, select the "Volume is
>> an
>> SPM2 Volume with Right on Left" if your volume is stored in a
>> left-handed coordinate system (aka radilogical or right on left --  
>> see
>>
>> http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q15).  If you  
>> need
>>
>> to map several functional volumes and want to use the caret_map_fmri
>> command line utility, then you'll probably need to convert your
>> volumes
>> to *.nii, AFNI, or SPM2-style .hdr.
>>
>> Donna
>>
>> On 04/11/2007 07:50 AM, Eugene Tunik wrote:
>>> Dear all,
>>> I am mapping a contrast image (the spmT.hdr/img) that is output in  
>>> SPM5.
>>> However, Caret is not mapping it to the fiducial. This works fine
>> using an spmT image output from SPM2.
>>>
>>> Is there something special about the SPM5 output that makes it
>> incompatible with caret?
>>>
>>> Any suggestions are appreciated.
>>>
>>> Best,
>>> Gene
>>>
>>>
>>>
>>>
>>> Eugene Tunik, PhD, PT
>>> Dept. of Physical Therapy, NYU
>>> http://homepages.nyu.edu/~et38/
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>>
>>
>> -- 
>> Donna L. Dierker
>> (Formerly Donna Hanlon; no change in marital status -- see
>> http://home.att.net/~donna.hanlon for details.)
>>
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