Hi Bruce,
Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts?
Thanks,
Adam
Hi Adam
it depends on the source of the bias. If it is fixed in the coordinate system of the scanner you could correct a few, then try using mri_compute_bias and mri_apply_bias to see if it helps (it computes an average bias field in scanner coords, then applies it to a new dataset)
cheers Bruce On Wed, 23 Jul 2014, Adam Mezher wrote:
Hi Bruce,
Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually?
Thanks for clarifying!
Adam Mezher
Hi Adam
I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce
On Tue, 22 Jul 2014, Adam Mezher wrote:
Hi FreeSurfer group, I was wondering if there is a way to include control points in my command line when I run recon-all. We are working with a large dataset and many of the subjects have underestimations in the anterior temporal lobes so it would be beneficial to expand the WM surface slightly on numerous cases rather than doing control point edits on each case individually.
Thank you, Adam Mezher
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Did it help? Try -make all Cheers Bruce
On Jul 30, 2014, at 7:50 PM, Adam Mezher adammezher@gmail.com wrote:
Hi Bruce, Thanks a lot for your help thus far. I've edited, computed, and applied the average bias to the error subjects' orig.mgz files. However, I'm not sure how to re-run all autorecon steps for these cases using the newly created orig.mgz (with bias applied). Thoughts?
Thanks, Adam
Hi Adam
it depends on the source of the bias. If it is fixed in the coordinate system of the scanner you could correct a few, then try using mri_compute_bias and mri_apply_bias to see if it helps (it computes an average bias field in scanner coords, then applies it to a new dataset)
cheers Bruce On Wed, 23 Jul 2014, Adam Mezher wrote:
Hi Bruce,
Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually?
Thanks for clarifying!
Adam Mezher
Hi Adam
I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce
On Tue, 22 Jul 2014, Adam Mezher wrote:
Hi FreeSurfer group, I was wondering if there is a way to include control points in my command line when I run recon-all. We are working with a large dataset and many of the subjects have underestimations in the anterior temporal lobes so it would be beneficial to expand the WM surface slightly on numerous cases rather than doing control point edits on each case individually.
Thank you, Adam Mezher
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
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Bruce Fischl