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>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<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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