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
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