can you paste in the errors? i'll forward them to the freesurfer list

On Thu, Sep 22, 2011 at 3:43 PM, Chelsea Cummiford <chelsea.cummiford@gmail.com> wrote:

ok, so the xhemireg command ran fine, but I can't run recon-all -all - it exits with errors.  says that there is no 001.mgz file.

I can pull it up in tkmedit (albeit, none of the control points or grey/white matter lines show up).  the brain is flipped compared to the original though.

On Thu, Sep 22, 2011 at 3:30 PM, Chelsea Cummiford <chelsea.cummiford@gmail.com> wrote:

oh, got it.  i thought you meant check both commands... will do.

On Thu, Sep 22, 2011 at 3:26 PM, Ilana Hairston <hairstonster@gmail.com> wrote:

no this one, to invert the brains that are already processed

xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg

On Thu, Sep 22, 2011 at 3:24 PM, Chelsea Cummiford <chelsea.cummiford@gmail.com> wrote:

do you mean running the --in-orientation ras command and then running recon-all??  because we did that and it looks fine in tkmedit and tksurfer - right heng?  this is what FS00wh is...

On Thu, Sep 22, 2011 at 2:57 PM, Ilana Hairston <hairstonster@gmail.com> wrote:

Seems like we need to be 100% sure that our analyze/nifti is RAS.

Chelsea, could you check the second command, followed by recon-all (i assume recon-all all) ?

thx

i

 

We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert.  Is that correct?

 

That might work. The orientation string is actually more specific than just "RAS". You data might in an RAS cooridnate system, but this means that the orientation string could be RAS, or it could be SAR, or ARS, or ARS, etc. See what I mean? If it shows up correctly in tkmedit, then you're got it right (assuming that you are sure that it is really in an RAS coordinate system).

The other question is - now that we have processed some 50 subjects, is there a way of flipping the results so that we wont have to start from scratch (this is a longitudinal study and participants will be scanned again).?

You can try using
xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg

This script was never intended for this purpose, so I don't know whether it will work fully or not. It should at least reverse all the volumes after which you can run recon-all on it. It should keep any edits you have made, but the control points won't be copied (and would be wrong in the reversed subject).

doug

Thanks
Ilana

 





--

******************************
Ilana Hairston ,PhD
Research Assistant Professor
4250 Plymouth Rd. (rm 2439)
Psychiatry Department, Addiction Research Center
University of Michigan, Ann Arbor MI 48109-2700
Tel: 734-232-0232; Mobile: 650-906-8449

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****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

--

****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

--

****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property