On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter <mreuter@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 <whatsdac@umich.edu> wrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac@umich.edu> wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter@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 <fischl@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

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-- 
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: 
   mreuter@nmr.mgh.harvard.edu
   reuter@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: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu 
_______________________________________________
Freesurfer mailing list
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
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu 