Hi Jim,
I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled.
Peace,
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Alexopoulos, Dimitrios" Alexopoulos_D@kids.wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 10, 2016 at 10:56 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] using both T1/T2 and resolutions
Hi,
We¹d like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1
We¹d like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space?
What recon-all command would be best for this process?
Jim
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