I don't know what that is about. Can you try using this version: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg
Ilana Hairston wrote: > Hi Doug, > Sorry, that this is turning into a saga. > The xhemireg command ran, but then recon-all failed (we used recon-all > -all). > Also it seems there are missing surfaces, we can't load wm and pial, > the surf directory is empty. Although that maybe because the recon > didn't run. > Thanks > i. > > > > ---------- Forwarded message ---------- > From: *Chelsea Cummiford* <chelsea.cummif...@gmail.com > <mailto:chelsea.cummif...@gmail.com>> > Date: Thu, Sep 22, 2011 at 4:35 PM > Subject: Re: [Freesurfer] Fwd: FW: flipped orientation in tksurfer and > tkmedit > To: Ilana Hairston <hairstons...@gmail.com > <mailto:hairstons...@gmail.com>> > > > [chelsea@hypnos ilanagroup]$ recon-all -all -subjid FlippedFS091205dc/ > > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /usr/local/FS51/subjects/ilanagroup > Actual FREESURFER_HOME /usr/local/FS51 > -rw-rw-r-- 1 chelsea ZL 16132 Sep 22 15:37 > /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log > Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 > x86_64 x86_64 GNU/Linux > #-------------------------------------------- > #@# MotionCor Thu Sep 22 16:35:06 EDT 2011 > ERROR: no run data found in > /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri. Make sure to > have a volume called 001.mgz in > /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > Linux hypnos 2.6.18-238.el5 #1 SMP Thu Jan 13 15:51:15 EST 2011 x86_64 > x86_64 x86_64 GNU/Linux > > recon-all -s FlippedFS091205dc exited with ERRORS at Thu Sep 22 > 16:35:06 EDT 2011 > > For more details, see the log file > /usr/local/FS51/subjects/ilanagroup/FlippedFS091205dc/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston > <hairstons...@gmail.com <mailto:hairstons...@gmail.com>> wrote: > > 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.cummif...@gmail.com <mailto:chelsea.cummif...@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.cummif...@gmail.com > <mailto:chelsea.cummif...@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 > <hairstons...@gmail.com <mailto:hairstons...@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.cummif...@gmail.com > <mailto:chelsea.cummif...@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 > <hairstons...@gmail.com > <mailto:hairstons...@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 <tel:734-232-0232>; > Mobile: 650-906-8449 <tel: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 > <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > -- >> ****************************** >> 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 > > > > > > > -- >> ****************************** >> 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
