New subject: Fwd: Fwd: FW: flipped orientation in tksurfer and tkmedit

22 Sep 2011

      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
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
[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 hairstonster@gmail.comwrote:
...
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> 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> 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.comwrote:
...
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> 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> 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
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
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/**compliancelinehttp://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