Hi there,
We are attempting edits on base images and a couple of questions came up when re-running through the pipeline:
1. After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”).
2. When re-running a base, after edits, starting at autorecon2, is it necessary to include all the timepoints in the command like (ie. “-tp subj1 –tp subj2”)? It’d make things simpler if that wasn’t necessary and our reading of the longitudinal processing protocol seems to suggest all the “tp” related stuff happens in autorecon1 when the norm image and transformations are generated. After that, the doc suggests that it simply processes that averaged image per-usual.
Thanks in advance for any help!
*Corrina Fonseca* Staff Research Associate II
Senior Imaging Technician *Center for Imaging of Neurodegenerative Diseases*
*San Francisco VA Medical Center*
*4150 Clement Street (114M)*
*San Francisco, CA 94121*
*http://www.radiology.ucsf.edu/cind http://www.radiology.ucsf.edu/cind*
*(415) 221-4810 x23088*
Hello Corrina,
I believe the answer to your question is Pho.
Best, Stephanie
On Feb 21, 2017, at 5:22 PM, Corrina Fonseca cosfonse@gmail.com wrote:
Hi there,
We are attempting edits on base images and a couple of questions came up when re-running through the pipeline:
After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”).When re-running a base, after edits, starting at autorecon2, is it necessary to include all the timepoints in the command like (ie. “-tp subj1 –tp subj2”)? It’d make things simpler if that wasn’t necessary and our reading of the longitudinal processing protocol seems to suggest all the “tp” related stuff happens in autorecon1 when the norm image and transformations are generated. After that, the doc suggests that it simply processes that averaged image per-usual.Thanks in advance for any help!
Corrina Fonseca Staff Research Associate II
Senior Imaging Technician Center for Imaging of Neurodegenerative Diseases
San Francisco VA Medical Center
4150 Clement Street (114M)
San Francisco, CA 94121
http://www.radiology.ucsf.edu/cind
(415) 221-4810 x23088
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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