Just to comment on this, using the correct conversion factor of 2.355 is critical for the low pass temporal filter sigma. The differences between low pass filters using ‘2’ instead of ‘2.355’ seems to be very noticeable.
--Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: [email protected] > On Apr 13, 2015, at 8:59 AM, Harms, Michael <[email protected]> wrote: > > > Hi, > Just wanted to mention, for purposes of documenting in this thread, that > technically the conversion from FWHM to sigma is: > sigma = FWHM/2.355 > http://en.wikipedia.org/wiki/Full_width_at_half_maximum > > I believe the FEAT just uses "2" rather than "2.355" in the denominator for > the calculation of the sigma for its high pass temporal filter because the > Gaussian filter is very gradual anyway. > > In the HCP pipelines, I believe that we use the technically correct factor of > 1/2.355 for any conversion of FWHM to Sigma. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Kimberly Stachenfeld <[email protected]> > Date: Sunday, April 12, 2015 4:22 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] rsfc preprocessing > > Hi hcp-users, > > I'm new to resting state connectivity analysis (and this list-serve), and I > have a few basic questions about applying it to the HCP data. I'm using the > minimally preprocessed REST1 data. > > 1. The low-pass filtering seems "controversial", though commonly employed -- > is there at this point an agreed-upon way to remove deleterious high > frequency noise? > > In addition, I'm having difficulty with temporally filtering the data in fsl. > To bandpass data from .009 - .08 Hz, I'm running: > > fslmaths nii_in -bptf 77.168.68 nii_out > > where 77.16 = sigma_hipass = 1/(2 * TR * F_hicutoff), for TR = .72 and > F_cutoff = .009 > > and 8.68 = sigma_lopass = 1/(2 * TR * F_locutoff), for TR = .72 and > F_locutoff = .08 > > This seems correct (I at least confirmed with the feat gui that the > conversion from cycle time to sigma is 1/(2*TR)). However, when I look at the > data in the frequency domain, it looks like there is significant response > left for frequencies below .009 Hz (picture attached) and very little between > .01-.08. Does anyone know if I'm doing something incorrectly, or if the > frequency cutoff for a Gaussian filter is just very gradual? > > 2. Any additional preprocessing is recommended, besides temporal filter and > what the minimal pre-processing has already enacted? > > 3. What is an intelligent way to combine correlation matrices? Averaging > (Power et al, 2011)? Binarizing the correlation matrix by setting the top 10% > of voxels to 1 and the rest to 0, and averaging the binarized matrices (Yeo > et al, 2011)? Either? Something fancier? > > Any advice or additional resources would be enormously appreciated -- thanks > very much!! > > Kim > > -- > Kimberly Stachenfeld, BS > Graduate Student > 236A Princeton Neuroscience Institute > Washington Road > Princeton, NJ 08544 > > [email protected] > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
