Hi All,

since the new version seems to be just around the corner, I would like to ask nicely, if you could make sure the following functionality of mri_motion_correct.fsl is restored? I am not sure whether this ever reached anybody the first time I tried to send it, so I just resend it, please ignore if you already fixed this.

Many Thanks for your exceptionally nice software...

best Sebastian

Begin forwarded message:

From: Sebastian Moeller sebastian.moeller@lur.rwth-aachen.de Date: April 7, 2010 5:28:53 PM PDT To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Bcc: Sebastian Moeller sebastian.moeller@lur.rwth-aachen.de Subject: mri_motion_correct.fsl buglet

Dear Freesurfers,

I just tried to use mri_motion_correct.fsl with the -tmpdir and -nocleanup options. Since I currently average around 10 to 16 mprage volumes per subject (NHPs) I want to look at the variance in addition to the average. And it seemed simplest to just keep the co-registered volumes in the tmpdir around and calculate the variance from those. But, it turns out that the -nocleanup does not work (nor does the implied -nocleanup that is set from -tmpdir (set CleanUp = 0)). The problem seems to be fixable by changing:

cleanup:

if($#CleanUp > 0) then foreach f ($CleanUpList) rm -f $f end endif

rm -r $tmpdir

goto cleanup_return;

to:

cleanup:

if($#CleanUp > 0) then if (${CleanUp} == 1) then echo "cleaning up..." foreach f ($CleanUpList) rm -f $f end endif endif if (${CleanUp} == 1) then rm -r $tmpdir endif

goto cleanup_return;

or even simpler:

goto cleanup; cleanup_return:

to:

if (${CleanUp} == 1) then goto cleanup; cleanup_return: endif

it would be great if this could be included into the next version. (It would certainly make my life easier :))

Best Regards Sebastian