Re: [HCP-Users] Reg. DPARSF

[Harms, Michael]

Hi, There are all sorts of reasons that you could get spatially specific results between different scanners/protocol, including differing spatial profiles of the SNR, differing gradient nonlinearities, etc.  So, I don't see how looking for spatial specificity is going to solve of the problem of trying to compare data collected on two different scanners. 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: Ranga Deshpande <rzd0...@auburn.edu> Date: Friday, October 10, 2014 12:07 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: Greg Burgess <gcburg...@gmail.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Reg. DPARSF Dear Michael Harms, Thanks for your reply. I know that such a question is going to arise once I do the processing and get the results, but scanner/protocol effects must be spatially widespread and not specific. If strong specific effects are observed then that will make an interesting result! Regards, Ranga On Fri, Oct 10, 2014 at 8:09 AM, Harms, Michael <mha...@wustl.edu> wrote: Hi Ranga, Separate from the issue of HCP vs. DPARSF processing pipelines, you are going to have a very difficult time comparing HCP data to separate disease population data that was collected on a different scanner and with a different acquisition protocol.  For any differences that you might find, how will you be able to know that it isn't a scanner/protocol effect? 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: Ranga Deshpande <rzd0...@auburn.edu> Date: Friday, October 10, 2014 12:36 AM To: Matt Glasser <glass...@wusm.wustl.edu>, Greg Burgess <gcburg...@gmail.com> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Reg. DPARSF 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 <gcburg...@gmail.com> 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: burge...@pcg.wustl.edu On Oct 8, 2014, at 6:53 PM, Glasser, Matthew <glass...@wusm.wustl.edu> 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 <rzd0...@auburn.edu> > Date: Wednesday, October 8, 2014 at 6:48 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > 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 > 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. 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