Came across this recently in TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh: AdditionalSigma=`echo "$AdditionalSmoothingFWHM / ( 2 * ( sqrt ( 2 * l ( 2 ) ) ) )" | bc -l`
So even more precise.;-) On Apr 13, 2015, at 8:59 AM, "Harms, Michael" <mha...@wustl.edu> 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: mha...@wustl.edu > > From: Kimberly Stachenfeld <k...@princeton.edu> > Date: Sunday, April 12, 2015 4:22 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > 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 > > k...@princeton.edu > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > 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 > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
