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!

Gabriel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

isn't that a feature? Freeview saves state to try to preserve the appropriate settings.

As for recon-all, yes that is the way it works. If you want to start with a new volume with -i you have to delete the subject dir (or specify a newly named one)

cheers Bruce

On Tue, 4 Jun 2013, obregon@nmr.mgh.harvard.edu wrote:

Hi Bruce,

This is certainly something I want to avoid, I guess I won't be using the -<no>motioncor flag in any of my studies!

I ran recon-all using both only one and two (motion corrected and averaged) source volumes, and the results do seem to suggest that using one vs. two volumes is an empirical issue. In the former case, I tried using the -i switch to point to a specific source volume (as you suggested), but failed to do so for I had already created the subjects' folders. Therefore, in order to use a single source volume, I had to move the remaining ones outside their corresponding mri/orig/ folders. Is there a way around this?

I also started using Freeview and I'm finally being able to display the raw volumes "cleanly". However, I want to find out why is it that when you change the contrast of your volumes, and avoid saving these changes, every time you reload the volumes they're displayed using the contrast settings you last employed? Why aren't these settings reset to their default values?

Thanks!

--G

...

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!

Gabriel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer