[HCP-Users] inhomogeneous signal intensity

2015-04-13 Thread Tianwen Chen
Hi HCP users, When we looked at the resting state fMRI data (minimally preprocessed), we found that there are pretty obvious signal intensity difference between brain areas. For example, the frontal areas have significantly higher signal intensity than other brain areas (see the attached

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Kimberly Stachenfeld
Thanks Matt! This is really helpful. We weren't necessarily going to use a parcellated analysis, since we have the disk space for voxel by voxel -- although it seems like that's what many of the sub graph detection results are for. However, perhaps we should do that if we are going to skip

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Donna Dierker
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

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread 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

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Harms, Michael
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

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Kimberly Stachenfeld
That seems like a good reason -- can you refer me somewhere for the better alternatives? We're on a bit of a timeline so I am hesitant to wait for the HCP version. Thanks again for all the help! On Mon, Apr 13, 2015 at 12:34 PM, Glasser, Matthew glass...@wusm.wustl.edu wrote: Well, I wouldn’t

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Glasser, Matthew
I listed several that are publicly available. Peace, Matt. From: Kimberly Stachenfeld k...@princeton.edu Date: Monday, April 13, 2015 at 11:41 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: rsfc preprocessing

Re: [HCP-Users] rsfc preprocessing

2015-04-13 Thread Glasser, Matthew
Well, I wouldn’t do it that way since there are a variety of better alternatives that deal with the issue in a more targeted way. In any case, we should have a better solution for dense analyses in the future. Peace, Matt. From: Kimberly Stachenfeld k...@princeton.edu Date: Monday,