I am currently performing an analysis of some fMRI data I've collected. I've had a lot of trouble coregistering the functional images to my high-res structural. SPMs automatic functions can't do it; I've tried almost every possible option. I assume the problem is due to my rather small functionals (12 slices of .75 x .75 x 1 mm i.e. 192 x 96 x 12 voxels).
I have therefore turned to manual coregistration through tkregister2 (the interface is a lot easier to use than SPMs 'display' option). I launch the registration process using: - tkregister2 --s <subjectid> --mov <functional.nii> --surf orig --reg fregister.dat --regheader and then do the manual registration and save the manipulations I've done (in fregister.dat). Now I take the registration from 'freesurfer space' back to 'spm space' using: - mri_vol2vol --reg fregister.dat --mov <functional.nii> --fstarg --o --<functional_in_anatomical.nii> And now I'm ready to perform my SPM analysis on this image. This seems to work pretty well, but now my problem is that I have 619 volumes per subject and so calling the mri_vol2vol function 619 times per subject is not really feasible. My idea for solving this problem was simply to convert the 619 realigned functionals into a single 4D.nii and then perform the exact same operations as above. This results in an error: MRIalloc(256, 256, 256): could not allocate 262144 bytes for 56253th slice > Cannot allocate memory To me it looks as if mri_vol2vol tries to load the entire dataset into memory and then perform the operation, and fails to do so because that's just too much memory needed. Furthermore, I wonder why it fails at slice number 56.253 since I believe I only have (619 x 12) 7.428 slices in total pr. subject. I am fairly new to the freesurfer/unix environment so I am certain than I am missing something obvious/doing something wrong. Any idea how apply my fregister.dat to all my functionals at once? Any help will be much appreciated, Daniel Gramm. -- Med venlig hilsen / Best regards, Daniel Gramm Kristensen Bachelor of Arts (BA) in Philosophy and Cognitive Semiotics Stud. Msc. Res. Cognitive Neuroscience
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