Re: [HCP-Users] failure to replicate dual regression 1 results (PTN nodetimeseries)

[Glasser, Matthew]

Did you demean the timeseries (remove the mean image) before concatenating? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Yizhou Ma <maxxx...@umn.edu> Date: Friday, July 31, 2015 at 11:57 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] failure to replicate dual regression 1 results (PTN nodetimeseries) I have verified again that values in my NIFTI files match with the CIFTI files. I am confused as to why dual_regression is not giving me results that make sense. In the attached files, fig 1 is nodetimeseries for map1, blue for my results and green for HCP results. fig 2 is my results plotted alone. I have no idea if this is something with how dual_regression work with cifti transferred data or if I am doing something wrong. Thanks, Cherry On Fri, Jul 31, 2015 at 11:04 AM, Yizhou Ma <maxxx...@umn.edu> wrote: 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 <maxxx...@umn.edu> 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: Yizhou Ma <maxxx...@umn.edu> Date: Friday, July 31, 2015 10:16 AM To: Giles Colclough <giles.colclo...@gmail.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <giles.colclo...@gmail.com> 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: 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]. 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 <maxxx...@umn.edu> 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 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   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   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