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>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<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.cummiford@**gmail.com <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<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<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.cummiford@**gmail.com<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.cummiford@**gmail.com<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.cummiford@**gmail.com<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<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> >> <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<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<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<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
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