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 <[email protected]> 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: [email protected] > > From: Ranga Deshpande <[email protected]> > Date: Friday, October 10, 2014 12:36 AM > To: Matt Glasser <[email protected]>, Greg Burgess < > [email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[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 > > > ------------------------------ > > 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
