Dear Matthew Glasser and Greg Burgess, Many thanks for your replies. It really helped.
I am trying to use the HCP data as controls, while I have another separate disease population data. I need to perform statistical analysis between the HCP controls and my disease population. My data has undergone the DPARSF pipeline, so I felt that it would be better if I pre-processed even the HCP data through the same pipeline. But now I find that there are a multitude of issues in doing that. So I have proceeded with using the ICA-FIX data itself. Thanks again for your responses! Best Regards, Ranga On Thu, Oct 9, 2014 at 11:32 AM, Greg Burgess <[email protected]> wrote: > Hello Ranga, > > There are definitely aspects of the pre-processing that we have done > within HCP, because the specifics are quite tricky to get right. If you > want more on those specifics, you can review the Glasser et al. (2013) > Neuroimage paper and/or the code and scripts that were recently released ( > http://humanconnectome.org/about/pressroom/project-news/hcp-processing-pipelines-released/ > ). > > If you want to do additional preprocessing on your data (e.g., different > temporal filtering or spatial smoothing), you will need to do that on the > NIFTI or CIFTI preproc files. I’m not familiar with DPARSF, but it appears > to want DICOM files as inputs. You might want to migrate to using FSL and > workbench for better compatibility with the HCP data. > > --Greg > > ____________________________________________________________________ > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology > Phone: 314-362-7864 > Email: [email protected] > > On Oct 8, 2014, at 6:53 PM, Glasser, Matthew <[email protected]> > wrote: > > > I wouldn’t recommend trying to redo the preprocessing, as getting that > right is complicated. Why not use the FIX cleaned data and focus on > whatever analysis you are interested in doing? > > > > Peace, > > > > Matt. > > > > From: Ranga Deshpande <[email protected]> > > Date: Wednesday, October 8, 2014 at 6:48 PM > > To: "[email protected]" <[email protected]> > > Subject: [HCP-Users] Reg. DPARSF > > > > Hi, > > > > I am a graduate student at Auburn University MRI Research Center, > Auburn, AL. > > I am currently planning to use some of the HCP 500 data. I am attempting > to use Data Processing Assistant for Resting State fMRI (DPARSF) (see: > http://www.ncbi.nlm.nih.gov/pubmed/20577591 and http://rfmri.org/DPARSF) > to perform pre-processing. > > > > However, I am encountering one error after the other, ranging from > non-detection of data, mal-detection of data (zero-timepoints error), "data > has orientation problems so cannot realign" errors and other non-traceable > errors. I have tried using unprocessed data (pre-processing from scratch), > pre-processed data and even ICA-fix data. In all cases I have issues using > DPARSF. > > > > Has anyone had the same issue of using DPARSF to analyze HCP500 data? > > > > Regards, > > Ranga > > _______________________________________________ > > 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 > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
