Ilana Hairston wrote: > Hi Doug, > The the subject data is uploaded, however it seems that we have > figured out the issue - so you may not need to look at it. Below is > what we think the problem and its solution are. Let me know if it > makes sense. > > the reconstruction scripts at our campus imaging facility have two > flaws: [1] there's is no orientation information in header of either > Analyze or NIFTII outputs; [2] the Analyze format is non-standard (RAS > instead of LAS). > As a result the first mri_convert step which converts our file to .mgz > format assumes that the orientation is neurological resulting in a > flip of left to right (albeit with an error message saying that it did > not have that info). > this flipping can only be seen when comparing images in tkmedit and > SPM, which should have been inveresed, but were not. > > 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 >> >> ******************** >> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >> and own 1% of the world's property > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
