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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:<mailto:hairstonster@gmail.com> <mailto:hairstonster@gmail.com
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.cummiford@gmail.com
<mailto:chelsea.cummiford@gmail.com>
<mailto:chelsea.cummiford@gmail.com
<mailto: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
<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/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.com <mailto:hairstonster@gmail.com>
<mailto: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.com><mailto:chelsea.cummiford@gmail.com<mailto: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
<mailto:chelsea.cummiford@gmail.com><mailto:chelsea.cummiford@gmail.com<mailto:chelsea.cummiford@gmail.com>>> wrote:<mailto:hairstonster@gmail.com> <mailto:hairstonster@gmail.com
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><mailto:chelsea.cummiford@gmail.com<mailto:chelsea.cummiford@gmail.com>>> wrote:<mailto:hairstonster@gmail.com
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><tel:734-232-0232> <tel:734-232-0232 <tel:734-232-0232>>;
<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. 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
<tel:650-906-8449> <tel:650-906-8449 <tel:650-906-8449>><tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-726-7422 <tel:617-726-7422>>
********************
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>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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The information in this e-mail is intended
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--
******************************
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
greve@nmr.mgh.harvard.edu <mailto: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>
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
greve@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
|