[caret-users] mapping SPM2 activations volume to caret surface (activation in wrong place)

Donna Dierker donna at brainvis.wustl.edu
Fri Sep 4 17:46:10 CDT 2009


You didn't specify the format -- .nii or .hdr/.img.  Try to write your
volume as .nii and see how it maps.  If you must use .hdr/.img (e.g., it
really is SPM2 data), then use File: Open Data File: Volume Functional
file to open the volume.  Specify the data is right on left (checkbox on
file open dialog, I believe).  Then map loaded volume, rather than volume
from disk.

> Hi Donna:
>
> The is Caret version 5. I used the same version with another set of data
> analyzed on SPM5 and no problem, it is mostly as you expected, hemispheres
> flipped, can I flip them back on caret using the same spmT files?
>
> Thank you!
>
> Soha
> On Fri, Sep 4, 2009 at 3:21 PM, Donna Dierker
> <donna at brainvis.wustl.edu>wrote:
>
>> I'm not sure how old your Caret version is, but older versions of Caret
>> couldn't read NIfTI files as .hdr/.img; you had to write them as .nii to
>> get sensible results.  I suspect the left is getting mapped to right and
>> vice versa, because your Caret version isn't reading the NIfTI volume
>> properly.
>>
>> If you're not using NIfTI, then fixing that is step 1.
>>
>> On 09/04/2009 01:28 PM, soha saleh wrote:
>> > Dear Caret users:
>> >
>> > I am trying to import fMRI data from a group study analyzed using SPM2
>> > as a metric file so that I can view it on the PALS atlas. *However,
>> > the activations are shown in the wrong anatomical place!*
>> >
>> > This is what I do to map the volume to surface and to open the spec
>> file:
>> >
>> > Attributes\Map volumes to surface
>> > data mapping type : metric
>> > add volumes from disk : the spmT files Umt_Pmt_mask
>> > map to spec with atlas:
>> >                                  Output spec file: select
>> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec from this
>> > tutorial ( CARET_TUTORIAL_SEPT06/MAPPING_PROCEDURES)
>> >                                  Mapping Atlas: SPM2
>> >                                  Atlas:
>> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec
>> > Mapping algorithm: Metric enclosing voxel
>> >
>> > Now load spec file
>> > file\open spec file :
>> > Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec
>> > SPACE: SPM2
>> > category: atlas
>> > species: human
>> > subject: PALS-B12
>> >
>> > select (Fiducial) and (Inflated) coordinates, and the metric file
>> > created after I did map volume to surface. I convert metric to RGB, I
>> > overlay the RGB data, and I have wrong activations.
>> >
>> > I attached a ppt. file that has 2 slides each showing the same spmT
>> > file on either Caret or SPM2 result figure, both at threshold T=3.
>> >
>> > Between, I did the same procedure with data analyzed using SPM5 and
>> > had no problem.
>> >
>> > I hope anybody can help, thanks in advance!
>> >
>> > Soha Saleh
>> > phD candidate
>> > Department of Biomedical Engineering
>> > New Jersey Institute of Technology
>> > shs25 at njit.edu <mailto:shs25 at njit.edu>
>> > 1 (201) 951 0029
>> >
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > caret-users mailing list
>> > caret-users at brainvis.wustl.edu
>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users at brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>




More information about the caret-users mailing list