The control points won't be copied over because they will be wrong (though you can try changing the sign of the first coordinate). I'm surprised that the skull strip edits were lost. Were they edits from the brainmask.final surfs? I've put a new version of xhemireg in the same place as before. The new one will copy over wm.mgz and brainmaks.finalsurfs, so hopefully those edits will be retained. It will also copy over rawavg.mgz, which is all recon-all should need to run (does not really need orig/001.mgz). These copies will be consistent with the other transformations. Sorry, xhemireg was never meant to do this kind of thing. doug
Ilana Hairston wrote: > Hi Doug, > this script resulted in the same problem - recon-all -all didn't run. > It was complaining that there is no 001.mgz. So we created 001.mgz > with recon-all using the RAS orientation flag, and popped it in the > orig folder. > Then the recon ran through w/o errors, but all the fixes were gone > (e.g., skull strip, control points). > Any ideas? > thanks > ilana > > > > On Thu, Sep 22, 2011 at 5:08 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <mailto: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> <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> <mailto: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> > <mailto: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> > <mailto: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> <tel:734-232-0232 <tel:734-232-0232>>; > Mobile: 650-906-8449 > <tel:650-906-8449> <tel: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > > Bugs: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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 > <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 > > > > > > > > -- > > ****************************** > 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 > > > > > > > > > -- > > ****************************** > 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 > > > > > > > > -- > > ****************************** > 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> > > > > > -- >> ****************************** >> 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
