Skull stripping? Are you talking about functional or anatomical data? This only applies to FSFAST, not recon-all. You'd run the fsfast preprocessing as normal.
On 10/23/18 12:21 PM, Meisler, Steven Lee wrote:
Thank you! At what point in the processing pipeline should this happen? For example, should this happen before or after skull-stripping?
Best,
Steven
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Tuesday, October 23, 2018 12:12:39 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Physiological Noise Regression from rsMRI
You will just need to create a text file with one or more columns, one for each regressor put this in the run folder (same folder where the raw data are). When you run mkanalysis-sess, add -nuisreg filename N where N is the number of columns you want to include
On 10/18/18 10:34 AM, Meisler, Steven Lee wrote:
Hi all,
I am currently developing a pipeline to remove physiological noise (respiratory and cardiac) from rsMRI images. I am at the point where I have created the regressors using fast_retroicor.m from the physiological data logs. When I add the columns of the regressors up and plot the result, it appears to create pulses at the times when the physiological data peaked. I was wondering if anyone knows how to incorporate the regressor files into FreeSurfer. Please let me know at your earliest convenience.
Thank you,
Steven
--------------
Steven L. Meisler, M.S.E.
Clinical Research Coordinator II
Laboratory for NeuroImaging of Coma and Consciousnesshttps://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605
175 Cambridge Street, Suite 300
Boston, MA 02114
smeisler@mgh.harvard.edumailto:smeisler@mgh.harvard.edu | (617)-726-1884
https://www.linkedin.com/in/steven-meisler
[cid:part4.F599AACC.96853E0E@mgh.harvard.edu]
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