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 <mreuter@nmr.mgh.harvard.edu mailto: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 <mailto:whatsdac@umich.edu>> wrote: Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac@umich.edu <mailto:whatsdac@umich.edu>> wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto: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 > 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. > > > > > > > > > _______________________________________________ > 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: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@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: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@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: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web :http://reuter.mit.edu
freesurfer@nmr.mgh.harvard.edu
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Martin Reuter