Probably the script was necessary to fix this problem. Look up the
command for mri_convert, it could be that it adjusts the direction
cosines directly.
Best, Martin
On 07/02/2013 02:36 PM, Jonathan Holt wrote:
OK,
so while the structures look normal in tkmedit the orientations are
mixed up. Coronal view shows horizontal, horizontal shows coronal, and
sagittal has been rotated 90 degrees clockwise.
Not entirely sure what to do here! This is the first I've seen of this
issue. keep in mind I processed this subject without an issue using
scripts that essentially pump the nifti through mri_convert and then
recon-all -s
So I'm a bit confused
On Jul 2, 2013, at 2:24 PM, Martin Reuter wrote:
In the meantime you can check how the mri/orig/001.mgz and the
mri/orig.mgz and mri/orig_nu.mgz look.
Best, Martin
On 07/02/2013 02:16 PM, Jonathan Holt wrote:
Thanks Martin,
I have attached recon-all.log. I tried to run the process several
times, I clearly forgot to pass -all that time but I know for
certain the first time I tried I passed -all and it provided the
same issue. I can pass the dicom images but I'll have to wait for my
PI to return in lab.
On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>>
wrote:
Hi Jonathan,
I changed the subject of the thread, to better reflect this
problem, it (so far) has nothing to do with longitudinal processing.
Next time, can you send the log file, it is in
/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log
not the output on the screen.
But first lets check these:
- your command in the email below seems to be missing "-all"?
Probably you passed it?
- and from your screen output it looks like there is a problem
importing the nifit:
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was sufficient information
in the input to assign orientation to the volume...
So you need to check the orientation of your
/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz...
Not sure why your nifti files are incomplete. Can you point -i
to the original dicom?
Best, Martin
On 07/02/2013 01:13 PM, Jonathan Holt wrote:
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt
<whats...@umich.edu <mailto:whats...@umich.edu>> wrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt
<whats...@umich.edu <mailto:whats...@umich.edu>> wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>> wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you
issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time
points appropriately. I have been passing nifti as
opposed to dicom and it's entirely possible that
may be the issue?
jon
On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images?
<tpNid> is a placeholder for the id of your
subject+time point, for example it could be
jon_01 the "path_to_tpN_dcm" needs to specify the
path to the dicom files, point it to the first
file in the MPRAGE series (or multi echo mprage
or what you are using). This is the full path on
your file system to that file.
Best, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were
created in the brief time this string was running
recon-all -all -s <tpNid> -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were
talairach.xfm and talairach.auto.xfm, both were
empty and the tkmedit window was empty.
upon further inspection the log file is
complaining about my nifty.
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be
incorrectly oriented
$Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $
reading from
/net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
WARNING: it does not appear that there was
sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>> wrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt wrote:
I have not and I am not certain how to
do so
On Jul 1, 2013, at 1:03 PM, Bruce Fischl
wrote:
Hi Jon
have you visually inspected the
results of the tal xform?
Bruce
On Mon, 1 Jul 2013, Jonathan Holt wrote:
Log file indicates manual
talairach alignment may be
necessary.
ERROR: talairach_afd: Talairach
Transform:
transforms/talairach.xfm
***FAILED*** (p=0.0079,
pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may
be necessary
Can anyone provide direction.
Alternatively, the error
indicates talairach alignment
can be skipped
with -notal-check flag. Is this
step completely necessary?
jon
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
. 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Email:
mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web :http://reuter.mit.edu <http://reuter.mit.edu/>
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Email:
mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web :http://reuter.mit.edu <http://reuter.mit.edu/>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Email:
mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web :http://reuter.mit.edu <http://reuter.mit.edu/>
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web :http://reuter.mit.edu
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 . 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.
