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> 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> [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>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> 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> 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>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> 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> 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 >>>>>>>> >>>>>>>> ******************** >>>>>>>> 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> >>>>>> >>>>>> >>>>>> >>>>>> 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
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