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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, October 23, 2018 12:12:39 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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 Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605> 175 Cambridge Street, Suite 300 Boston, MA 02114 smeis...@mgh.harvard.edu<mailto:smeis...@mgh.harvard.edu> | (617)-726-1884 https://www.linkedin.com/in/steven-meisler [cid:part4.F599AACC.96853E0E@mgh.harvard.edu] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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