Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to finish the rest of recon-all for the hemisphere I want. Is there a way to change the order of files created with the recon-all script so all of the volumetric, and all of the wm, and all of broadmann's area, etc. is completed for one hemisphere before being run for the other? Thanks! Lauren Bystrom
There is not an automated way to do this. You might be able to run the steps piecemeal by specifying the flags for each step individually
On 11/18/2015 04:29 PM, Lauren Bystrom wrote:
Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to finish the rest of recon-all for the hemisphere I want. Is there a way to change the order of files created with the recon-all script so all of the volumetric, and all of the wm, and all of broadmann's area, etc. is completed for one hemisphere before being run for the other? Thanks! Lauren Bystrom
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That's what I was thinking. Thank you !
On Wednesday, November 18, 2015, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
There is not an automated way to do this. You might be able to run the steps piecemeal by specifying the flags for each step individually
On 11/18/2015 04:29 PM, Lauren Bystrom wrote:
Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to finish the rest of recon-all for the hemisphere I want. Is there a way to change the order of files created with the recon-all script so all of the volumetric, and all of the wm, and all of broadmann's area, etc. is completed for one hemisphere before being run for the other? Thanks! Lauren Bystrom
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