here are some python routines (for those who live in that ecosystem) :) : http://nipy.org/nitime/examples/filtering_fmri.html https://github.com/nipy/nipype/blob/master/examples/rsfmri_vol_surface_preprocessing_nipy.py#L127
cheers, satra On Tue, Apr 14, 2015 at 10:12 AM, Stephen Smith <[email protected]> wrote: > Well...... I would add that if you want to control the lowpass filtering > with any decent degree of frequency-cutoff specificity I would not use the > Gaussian lowpass filter in fslmaths, but something sharper (eg Butterworth) > eg in matlab. But generally we don't recommend doing lowpass. > > Cheers. > > > > On 14 Apr 2015, at 15:08, Greg Burgess <[email protected]> wrote: > > 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 > > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [email protected] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet <http://smithinks.net> > > > > > _______________________________________________ > 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
