if they are named orig/00[012345].mgz then I think they will be averaged but without motion correction, which is almost certainly not what you want
On Sun, 2 Jun 2013, obregon@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thanks for responding! For the sake of clarification, let's say I have multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i switch in recon-all to point to one of them, exclusively. If I additionally include the -nomotioncor option, will the multiple source volumes be averaged without correcting for motion between them, yielding orig.mgz as output?
Best,
Gabriel
Hi Gabriel
if you want to process only one volume, then point recon-all at it with the -i switch. You can also use freeview instead of tkmedit for browsing the volumes - it's much more flexible.
The two volumes vs. one is an empirical question. I've found that a single high-quality volume is better than motion-correcting and averaging two, particularly if one of the two is lower quality, but that's an ad hoc assessment on my part and depends a lot on field strength, coil, subject motion, etc....
cheers Bruce
On Sun, 2 Jun 2013, Gabriel Obregon wrote:
Hi,
Could someone please help me with the following concerns:
A. If I have multiple source volumes in mri/orig/ and run recon-all using the -nomotioncor option, how are these inputs processed compared to the case in which motion correction is employed, and what should I expect as my output?
B. If I want to process only one of the multiple source volumes, i.e., the "best", how should I proceed?
C. I've been encountering displaying issues of the raw volumes using tkmedit. What other interfaces are readily available for browsing through the source volumes in order to assess their quality?
D. Finally, if in one of my studies I could afford running only two MPRAGE sessions per subject, is motion correction advisable for segmenting the surfaces?
Thanks!
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