Hello experts,
I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse section and the transverse was in the sagital section. I wonder if there is a place where I can send the data for someone to see and tell me how exaclty to flip the orientation of it to suit FreeSurfer.
I would also like to know whether there is a shorter way of processing the data for only mri-stats without running recon-all for all the subjects' data we have.
Thank you
Jan
Hi Jan,
what was your input data?
Bruce On Mon, 3 May 2010, Janani Dhinakaran wrote:
Hello experts,
I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse section and the transverse was in the sagital section. I wonder if there is a place where I can send the data for someone to see and tell me how exaclty to flip the orientation of it to suit FreeSurfer.
I would also like to know whether there is a shorter way of processing the data for only mri-stats without running recon-all for all the subjects' data we have.
Thank you
Jan
I have also been getting error messages, after Talairach correction using tkregister2
*#@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010 /usr/local/freesurfer/subjects/FS060828cr/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6064, pval=0.2817 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/FS060828cr/mri/transforms/talairach_avi.log
TalAviQA: 0.93168 z-score: -10 ERROR: Talairach QA check failed! z-score = -10 <= -6 = threshold 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 Linux venus.mbni.med.umich.edu 2.6.18-128.1.10.el5 #1 SMP Thu May 7 10:35:59 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon May 3 09:57:40 EDT 2010*
On 3 May 2010 10:44, Janani Dhinakaran janinthesky@gmail.com wrote:
Hello experts,
I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse section and the transverse was in the sagital section. I wonder if there is a place where I can send the data for someone to see and tell me how exaclty to flip the orientation of it to suit FreeSurfer.
I would also like to know whether there is a shorter way of processing the data for only mri-stats without running recon-all for all the subjects' data we have.
Thank you
Jan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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what format is your input data in? On Mon, 3 May 2010, Ilana Hairston wrote:
I have also been getting error messages, after Talairach correction using tkregister2
*#@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010 /usr/local/freesurfer/subjects/FS060828cr/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6064, pval=0.2817 >= threshold=0.0050)
awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/FS060828cr/mri/transforms/talairach_avi.log
TalAviQA: 0.93168 z-score: -10 ERROR: Talairach QA check failed! z-score = -10 <= -6 = threshold 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 Linux venus.mbni.med.umich.edu 2.6.18-128.1.10.el5 #1 SMP Thu May 7 10:35:59 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon May 3 09:57:40 EDT 2010*
On 3 May 2010 10:44, Janani Dhinakaran janinthesky@gmail.com wrote:
Hello experts,
I've been having some trouble with the talairach during recon. I followed previous instructions and checked the rawavg image and found that it was in wrongly oriented. The sagittal picture was appearing under coronal but upsidedown, the coronal picture was sideways in the transverse section and the transverse was in the sagital section. I wonder if there is a place where I can send the data for someone to see and tell me how exaclty to flip the orientation of it to suit FreeSurfer.
I would also like to know whether there is a shorter way of processing the data for only mri-stats without running recon-all for all the subjects' data we have.
Thank you
Jan
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Ilana Hairston -
Janani Dhinakaran