Dear Michael Harms, Thanks for your reply. I will consider your suggestion seriously and will think over to see if my study can take an alternate route. Thanks!
Regards, Ranga On Fri, Oct 10, 2014 at 12:13 PM, Harms, Michael <[email protected]> wrote: > > 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: [email protected] > > From: Ranga Deshpande <[email protected]> > Date: Friday, October 10, 2014 12:07 PM > To: "Harms, Michael" <[email protected]> > Cc: Greg Burgess <[email protected]>, "[email protected]" < > [email protected]> > > 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 <[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 > > > ------------------------------ > > 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
