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help > RE: Transform individual ROIs to MNI space
Nov 10, 2015 03:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Transform individual ROIs to MNI space
Hi Jalmar,
Yes you may use the syntax:
M = spm_get_space('myfile1.nii');
spm_get_space('myfile2.nii', M);
to copy the voxel-to-world mapping info from myfile1.nii to myfile2.nii (this, of course, will only make sense if both volumes have the same dimensions and are in the same space)
Best
Alfonso
Originally posted by Jalmar Teeuw:
Yes you may use the syntax:
M = spm_get_space('myfile1.nii');
spm_get_space('myfile2.nii', M);
to copy the voxel-to-world mapping info from myfile1.nii to myfile2.nii (this, of course, will only make sense if both volumes have the same dimensions and are in the same space)
Best
Alfonso
Originally posted by Jalmar Teeuw:
I got it to work by using FSL's fslcpgeom to
copy the header information from the translated T1 scan to the
tissue maps (since they were created in the same space and
geometry). Then after structural normalisation on the T1, apply the
same transformation to the tissue maps using SPM. CONN/SPM and
Freesurfer's freeview show the tissue maps and T1 are transformed
to MNI and are nicely aligned again. FSL's fslview show a mismatch
where the tissue maps are still offset by some translation factor,
but we're good to go with CONN/SPM.
I'd still love to know if there is any easy way to copy the header information from the translated T1 to the tissue maps using functions from Matlab, CONN or SPM, so we can put everything in a single batch script.
Originally posted by Jalmar Teeuw:
I'd still love to know if there is any easy way to copy the header information from the translated T1 to the tissue maps using functions from Matlab, CONN or SPM, so we can put everything in a single batch script.
Originally posted by Jalmar Teeuw:
Hi Alfonso,
Thanks for the quick response. We tried option 2, but we do have the problem that we require the 'set origin to (0,0,0)' option during preprocessing, otherwise SPM complains about to little overlap between scans during structural normalisation. How is this 'set origin' step performed? Is there a way to get the translation parameters? Because if we can apply it to the structural scan and then the same translation to our tissue maps prior to using CONN it should work with option 2.
Regards,
Jalmar
Thanks for the quick response. We tried option 2, but we do have the problem that we require the 'set origin to (0,0,0)' option during preprocessing, otherwise SPM complains about to little overlap between scans during structural normalisation. How is this 'set origin' step performed? Is there a way to get the translation parameters? Because if we can apply it to the structural scan and then the same translation to our tissue maps prior to using CONN it should work with option 2.
Regards,
Jalmar
Threaded View
| Title | Author | Date |
|---|---|---|
| Matthew Defenderfer | Oct 27, 2015 | |
| Alfonso Nieto-Castanon | Nov 10, 2015 | |
| Jalmar Teeuw | Nov 10, 2015 | |
| Alfonso Nieto-Castanon | Nov 10, 2015 | |
| Jalmar Teeuw | Nov 11, 2015 | |
| Jalmar Teeuw | Nov 10, 2015 | |
| Alfonso Nieto-Castanon | Nov 10, 2015 | |
| Jalmar Teeuw | Nov 9, 2015 | |