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 greve@nmr.mgh.harvard.eduwrote:
I don't know what that is about. Can you try using this version: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/xhemiregftp://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.cummiford@gmail.com <mailto: chelsea.cummiford@**gmail.com chelsea.cummiford@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 <hairstonster@gmail.com mailto:hairstonster@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/** Conversionhttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Thu, Sep 22, 2011 at 4:32 PM, Ilana Hairston <hairstonster@gmail.commailto: hairstonster@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.cummiford@gmail.com <mailto:chelsea.cummiford@**gmail.comchelsea.cummiford@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.cummiford@gmail.com <mailto:chelsea.cummiford@**gmail.com<chelsea.cummiford@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 <hairstonster@gmail.com <mailto:hairstonster@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.cummiford@gmail.com <mailto:chelsea.cummiford@**gmail.com<chelsea.cummiford@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 <hairstonster@gmail.com <mailto:hairstonster@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. Theorientation 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.** edu/facility/filedrop/index.**htmlhttp://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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html