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 <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
