I have just plotted the timeseries and it seems that my results doesn't really make sense - they look like square oscillations. HCP's results look like real timeseries.
On Fri, Jul 31, 2015 at 10:48 AM, Yizhou Ma <[email protected]> wrote: > Thank you Michael. My system is failing me at this moment and it is hard > to plot. My dual reg results seem normal and I would not have suspected if > I did not compare them with HCP's results. > When I used a brainmask to mask the first 91282 "voxels" I get identical > results as when I did not use a mask. > > Thanks, > Cherry > > > > On Fri, Jul 31, 2015 at 10:25 AM, Harms, Michael <[email protected]> wrote: > >> >> Yes, "_ts2" are dual regression; "_ts3" are the eigentimeseries. See the >> section "Description of released files" in the pdf with the PTN >> distribution. >> >> Steve can comment on the matching issue, but I wonder if the 0's that get >> added to the pseudo-NIFTI file to fill out the matrix dimensions (following >> conversion from CIFTI) are contributing here. You might need to use a mask >> that defines the actual 91282 grayordinates. How different actually are >> your dual regression results vs. the "_ts2" node timeseries in the PTN >> distribution? Perhaps you could create a scatterplot to illustrate the >> difference? >> >> 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: Yizhou Ma <[email protected]> >> Date: Friday, July 31, 2015 10:16 AM >> To: Giles Colclough <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] failure to replicate dual regression 1 results >> (PTN nodetimeseries) >> >> Thank you Steve and Giles. >> >> Giles: I believe the pdf specified that dual regression 1 results are in >> /ts2 and eigentimeseries results are in /ts3, isn't it? >> >> Steve: I am confused here. I am using nifti data converted from cifti, >> which means that the first 91282 "voxels" of my nifti matches the 91282 >> grayordinates in the cifti files. The two methods should be identical >> because they have exactly the same info, only different shapes of matrices. >> Isn't wb_command -cifti-convert -to-nifti the recommended way to use FSL >> commands on cifti data and isn't it supposed to give identical results as >> working with cifti directly? >> >> Best, >> Cherry >> >> On Fri, Jul 31, 2015 at 10:04 AM, Giles Colclough < >> [email protected]> wrote: >> >>> Hi, Cherry, >>> >>> Have a look at the other nodetimeseries data. >>> The ts2 time series are estimated using the eigen-timeseries method. ts1 >>> are calculated using traditional dual regression. >>> >>> A fuller explanation is in the pdf available in the netmats download: >>> >>> >>> Node timeseries (individual subjects) >>> >>> For a given “parcellation” (group-ICA decomposition), the set of ICA >>> spatial maps was mapped onto each subject's rfMRI timeseries data to derive >>> one representative timeseries per ICA component (for these purposes we >>> consider each ICA component as a network "node"). For each subject, these >>> 25 (or 50, 100, 200 or 300) timeseries can then be used in network >>> analyses, as described below. Two distinct methods were used to estimate >>> the node-timeseries: >>> >>> 1. >>> >>> The more traditional "dual-regression stage-1" approach, in which >>> the full set of ICA maps was used as spatial regressors against the full >>> data, estimating one timeseries for each ICA map [Filippini 2009]. >>> 2. >>> >>> A newer approach based on estimating the principal eigen-timeseries >>> within each ICA component; this approach aims to be more robust against >>> component misalignment (between the group-ICA maps and individual >>> subjects' >>> data) and artifacts [O’Reilly 2009, Smith OHBM 2014]. >>> >>> >>> >>> Best, >>> Giles >>> >>> >>> >>> On 31 Jul 2015, at 15:50, Yizhou Ma <[email protected]> wrote: >>> >>> Dear HCP experts, >>> >>> I am trying to run my own dual regression on HCP's rsfMRI data. What I >>> did is use wb_command -cifti-convert -to-nifti to convert group ICA maps >>> and individual rsfMRI scans to NifTI and use FSL's dual_regression command. >>> >>> *dual_regression melodic_IC.nii.gz 1 -1 0 ./test 100307_rsfMRI.nii.gz* >>> >>> I was able to get dual regression results. Yet the dual regression 1 >>> results I get does not match up with the nodetimeseries ts2 results >>> provided in HCP's PTN release. I have opened my group ICA maps and rsfMRI >>> scan in matlab to ensure that the values in them match up with the cifti >>> files. I have tried dual regression with another subject but still the >>> results did not match. >>> >>> Do anyone have an idea what might have gone wrong? >>> >>> Thank you very much, >>> Cherry >>> >>> _______________________________________________ >>> 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 >> >> >> ------------------------------ >> >> 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
