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

soha saleh shs25 at njit.edu
Fri Sep 4 18:54:11 CDT 2009


the format is hdr/img not nii and I must use it (SPM2 data).. I will follow
your instructions, thanks!

Soha

On Fri, Sep 4, 2009 at 6:46 PM, Donna Dierker <donna at brainvis.wustl.edu>wrote:

> 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
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------
> >> >
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