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: >>>> >>>> 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 <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
