Note that when opening functional volumes in Caret, there's a checkbox:
Volume is an SPM2 Volume with Right on Left
Make sure it is either selected or deselected as needed.
On 03/26/2007 09:52 AM, Tobias Egner wrote:
> Donna,
>
> thanks very much indeed, I think for now I will just go with the fix
> of manually re-setting the origin in the way you suggest.
>
> best wishes,
>
> Tobias.
>
> On 3/26/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
>> Hi Tobias,
>>
>> Your metric files were only 30 lines long -- header but no data.
>> Anyway, I suspect this is a case where Caret doesn't recognize your
>> nifti1 .img and .hdr format. It's reading it as Analyze, which
works,
>> except you need to then set the origin. The attached captures
>> overlay_bad.jpg and overlay_good.jpg show how the volume
intersects the
>> average fiducial surface before and after using Volume: Edit Volume
>> Attributes: to set the origin to -90,-126,-72. (I didn't
double-check
>> that this is precisely the right origin!) Saving the volume with the
>> tweaked origin results in a reasonable looking metric, as the
attached
>> capture shows.
>>
>> If you can export a flavor of NIFTI that gets along better with
Caret,
>> then perhaps a way around this problem is to do this one; save the
.hdr
>> as something like "make_caret_happy.hdr"; and copy this .hdr over
your
>> existing (or copied) .hdr for mapping purposes. If you do this,
please
>> check two things: 1) The left-right orientation is good; 2) the
origin
>> is exactly right.
>>
>> For what it's worth, I've used the .nii style NIFTI files with good
>> success.
>>
>> Donna
>>
>> On 03/26/2007 08:37 AM, Tobias Egner wrote:
>> > Dear Donna,
>> >
>> > thanks for your help: I've uploaded a couple of volumes
>> > ('Tobias_feature.hdr', etc) and the metric files (note that in the
>> > metric files, my volumes are referred to by different names). I'm
>> > actually using Windows though, not Linux.
>> >
>> > Many thanks and best wishes,
>> >
>> > Tobias.
>> >
>> > On 3/26/07, Donna Dierker <[EMAIL PROTECTED]> wrote:
>> >> Hi Tobias,
>> >>
>> >> I don't recognize this problem. Hmmm. How about if I give it a
>> try on
>> >> my end. Can you upload one or more of your volumes here:
>> >>
>> >> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>> >>
>> >> From the "'QEventDispatcherUNIX::unregisterTimer" error, I guess
>> you're
>> >> running Linux. We'll see if my Linux box acts the same.
>> >>
>> >> Also, would you mind also uploading one of the metric files? Or
>> you can
>> >> just verify that it is all zeros like so:
>> >>
>> >> caret_file_convert -text my.metric
>> >>
>> >> cut -f2 -d' ' my.metric |sort -un
>> >>
>> >> If you get a bunch of lines with scalars in them, then the metric
>> file
>> >> contains non-zero nodes; however, if you just get a bunch of lines
>> with
>> >> alpha characters, one line with 0.000000, and one with 73730, then
>> it is
>> >> all zeroes.
>> >>
>> >> Donna
>> >>
>> >> On 03/24/2007 03:08 PM, Tobias Egner wrote:
>> >> > Dear all,
>> >> >
>> >> > I am trying (unsuccessfully) to display some SPM T-images
>> generated in
>> >> > SPM5 in Caret 5.5. Here's what I am doing:
>> >> >
>> >> > The T-images are in nifti1 format (with .img and .hdr
>> extensions), and
>> >> > the original functional data were converted to nifti via the
DICOM
>> >> > import function in SPM5. The images are normalized (and
>> resliced) to
>> >> > the SPM5 MNI T1.nii template (voxel size 2x2x2, dimensions:
>> 91x109x91,
>> >> > origin: 46 64 37).
>> >> >
>> >> > In Caret 5.5, I follow the steps indicated in the
>> >> > Caret_Tutorial_Sep22.pdf section 5.1. (and using the Caret
Tutorial
>> >> > Sept06 data set).
>> >> >
>> >> > 1- I open the fMRI mapping template Spec file, select all, then
>> save
>> >> > under a new name, and load scenes.
>> >> > 2- Attributes: Map volumes to surface, then add my SPM t-maps
>> and set
>> >> > thresholds.
>> >> > 3- Map to spec file with atlas: As output I select my newly
created
>> >> > spec file, and then I select the SPM2 space, and the
corresponding
>> >> > SPM2 left hem atlas, then repeat those steps with the SPM2 right
>> hem
>> >> > atlas. I accept the default settings on the next page.
>> >> > 4- The I name my metric files (left, right) in accrodance
with the
>> >> > left/right aspects of the 'surface family'.
>> >> > 5- As Mapping Algorithm, I accept the 'enclosing voxel'
>> default, then
>> >> > I press Finish and the computing starts...
>> >> >
>> >> > At the end of the number crunching, I get a little warning sound
>> and
>> >> > in the command line window it reads:
>> >> >
>> >> > 'QEventDispatcherUNIX::unregisterTimer: invalid argument'
>> >> >
>> >> > Regardless, I next load the Scene No 4 (FLAT etc..), and then
>> open the
>> >> > two metric files I have created. I then also load the SPM2
fiducial
>> >> > coord files. I select Metric as the Primary Overlay, and select
>> L-to-L
>> >> > R-to-R matching. With great anticipation, I select one of my
metric
>> >> > files, but no cigar: I don't see any surface overlays
whatsoever.
>> >> >
>> >> > Any idea where I am going wrong? Many thanks for any advice!
>> >> > Best wishes,
>> >> >
>> >> > Tobias.
