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 mailto: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 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.
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