[Freesurfer] How to measure the cortical thickness in tumor patients?
External Email - Use Caution Dear developers, right now I'm trying to measure the cortical thickness of the right hemisphere in the left side tumor patients. Here I met some problem. Since the complex intensities in the tumor, it makes the 'recon-all -all' command to be very time consuming(3 days per subject). Do you have any experience dealing with the tumor patients? I also tried the '-lh' flag, but there is only one file named 'rh.curv.stats' in stats folder. The command is:recon-all -s 130 -i 130.nii -qcache -3T -hemi rh -all Do you have any idea about where the problem is? Best wishes, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coordinates' annotations question
External Email - Use Caution Hi developers, thank for your amazing program, it’s really helpful. After using it for a short time, I met a question in the middle of my research. I have thousands sets of coordinates in MNI space. And I wanna get the information about where these coordinates locate in Destrieux atlas. Namely, the annotations of these coordinates. As I know, fsl has this command ‘atlasquery’. Do we have something like it?? Thank you very much. Any suggestion would be helpful. best regards, Ziqian Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer]
External Email - Use Caution Hi, I am trying to do connectome to my patient with glioma. But now I’m stuck in parcellation the T1 image. Because the chaotic intensities of tumor totally mess up the outcome. Do you guys have any suggestion to the tumor? Is it any command about mask the tumor or any other method? Any suggestion would be thankful! Best Ziqian ___ 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] Why I have to set the environment every time
External Email - Use Caution Hi, Every time I wanna use the command of freesufer I have to reset the environment again, otherwise it will remind me “not found the command”. Only after I write “export FREESURFER_HOME=/Applications/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.sh” Then I can use it smoothly. But after I close the terminal, I have to rewrite it again. Any suggestion is acceptable. Thanks a lot Ziqian ___ 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.
