Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote: > Thank you very much for your input. Yes, I did start with analyze format and > also I have visually inspected the images. Almost all my > scans consistently show an extended whole in the prefrontal area (with a few > exception of some scans showing this in posterior > locations). > I am assuming the best is to start with either DICOM or NIFTI and avoid > analyze format. Is this correct? > > Best, > Pablo > > > Date: Tue, 27 Aug 2013 12:08:22 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pablon...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach Failure Detection > > Hi Pablo > > have you visually inspected the talairach xform to see if it is indeed > incorrect? What input format did you start with? Most of these occur > because people start with analyze, which doesn't have the direction > cosines, and so the data is oriented incorrectly > > cheers > Bruce > > > On Tue, 27 Aug 2013, pablo najt wrote: > > > Dear FS experts,I am contacting you to report an error after launching > > recon -all for one of my subjects (see below). I am using a > > macbook pro with snow leopard version 10.6.8. > > > > I would greatly appreciate if you could advise me which step/s should I > > take to correct this. > > Thank you for your attention, > > Pablo > > > > Error:------------------------------------------------------------------------------------------------------------------------------- > - > > ------------------ > > #@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 > > /Users/pablonajt/subjects/tr5713/mri > > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: > > Tue Jun 7 16:33:36 PDT 2011; > > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > > recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013 > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
