Re: [HCP-Users] rsfc preprocessing

[Harms, Michael]

Ok, correction on myself.  That factor of 1/2.355 (obtained using the formula Donna provided) is what we use for conversion of FWHM to Sigma for *spatial* filtering.  However, it appears that for the *temporal* filtering that we still use the approximation of 1/2 = 0.5 in the relevant HCP pipeline code for setting up the sigma for the high pass temporal filter. e.g., in in TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh: fslmaths ${fake_nifti_file} -bptf `echo "0.5 * $TemporalFilter / $TR_vol" | bc -l` 0 ${fake_nifti_file} and in hcp_fix   hptr=`echo "10 k $hp 2 / $tr / p" | dc -`   ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 ${fmri}_hp$hp Sorry about that. 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 On 4/13/15 9:13 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: 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. 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