[Freesurfer] GLOBAL region of the brain empty! error due to error in intensity normalization?
Hello, I was just running autorecon1 on a subject and I got the mri_watershed Error: GLOBAL region of the brain empty! I am aware that there was a bug in previous versions but I'm using v4.3.1, which I think it's not supposed to have that bug any longer. I tried running -skullstrip with the -no-wsgcaatlas flag, which caused the whole brain and part of the head to be striped out instead of just the skull. Next I tried to compare the output images step by step with images at the same stage for another subject with no error. Regarding the 001.mgz, rawavg.mgz and orig.mgz there were no obvious differences between both subjects, except that the images looked a little darker for the subject that got the error later. However, the nu.mgz image was quite different. The subject with error presented a very dark image, with signal intensities around 40, whereas the subject without error presented normal intensities around 110. The quality of the original images was the same, same sequence, everything. I already ran 20 subjects and this was the first one to show this error. Any help provided with be very much appreciated! Thank you, Ana Catarino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] gaussian and mean curvature in qdec
Hello, I have 2 groups, normal and patients, and was using qdec to compare groups for several measures (thickness, curv, sulc, etc), but couldn't do it for Gaussian (white.K) and mean curvature (white.H). I get the following error: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh How can I create the ?h.white.K.fwhm??.avgsubject.mgh file for every subject? Many Thanks, Ana Catarino ___ 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] gaussian and mean curvature error
Hello, I'm trying to do a gaussian curvature and mean curvature analysis using qdec but I get the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh Can anyone help? Thank you, Ana Catarino ___ 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] Thickness values for every voxel
Hello, Does anyone know if there is a way of getting access to the values of thickness for each voxel / point in the mesh? Thank you, Ana Catarino ___ 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] Thickness values for every vertex
Hello, Does anyone know if there is a way of getting access to the values of thickness for each vertex in the mesh? Thank you, Ana Catarino ___ 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] missing gaussian curvature file
Hello, I was trying to run a qdec analysis on Gaussian curvature and got the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh I get the same error message on mean curvature analysis. Any ideas? Thanks, Ana Catarino ___ 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.
