Hello Ben, Since this process has been causing some confusion among multiple users, we’ve decided to put some additional detail in a wiki page. https://wiki.humanconnectome.org/display/PublicData/Advice+for+FEAT+Analysis+of+HCP+task+fMRI+data
Please review this page to determine if it clarifies the process that you should follow to run group-level analyses of task fMRI data. If you have any additional questions, let us know so that we can further clarify this for users. Thanks, --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 Aug 28, 2014, at 9:48 AM, Harms, Michael <[email protected]> wrote: > > Hello Ely, > If you want to run a "Level 3" group analysis, you already have everything > you need if you downloaded the task "analysis" packages, which already > contain the "Level 2" results (combining across runs) for each subject. The > "prepare_level2_feat_analysis.sh" is if you are trying to generate the Level > 2 analysis for each subject yourself, from "Level 1" results (each specific > run). The Level 1 results are not included in the downloadable packages. > > In terms of running the Level 3 analysis, we have a script that helps > automate this, but it needs a little more vetting and clean-up, so I'm not > sure if it will quite make it into the imminent release of the HCP pipelines. > For a volume-based analysis (i.e., using the results in the > tfMRI_<TASK>_hp200_s4_level2vol.feat directory for each subject), I believe > that you can run the Level 3 analysis through the FEAT GUI. (Just tested > that on an simple three-subject group mean model, and it worked). For a > grayordinate-based analysis, you basically have to convert the CIFTI to NIFTI > using 'wb_command -cifti-convert', run the equivalent set of commands > implemented by FEAT on the ensuing NIFTI's, and then convert back to CIFTI. > The aforementioned Level3 analysis script is obviously intended to make this > much simpler, and we will try to get that vetted and ready for release in the > near future. > > 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: <Ely>, Benjamin <[email protected]> > Date: Thursday, August 28, 2014 1:20 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] missing level 1 .feat directories > > Hello all, > > I recently downloaded the preprocessed and analyzed volume data from the 100 > Unrelated Subjects group. My understanding is that to conduct group analyses, > I now need to run the prepare_level2_feat_analysis.sh script for each of the > tasks for each of the subjects. However, when I try to run that script from > the various level 2 task directories for various subjects, I always get the > same error message, e.g.: > > Cannot find > /Volumes/Connectomizer/HCP/Subjects/111312/MNINonLinear/Results/tfMRI_GAMBLING/../tfMRI_GAMBLING_RL/tfMRI_GAMBLING_RL_hp200_s4.feat > Cannot find > /Volumes/Connectomizer/HCP/Subjects/111312/MNINonLinear/Results/tfMRI_GAMBLING/../tfMRI_GAMBLING_LR/tfMRI_GAMBLING_LR_hp200_s4.feat > Cannot find any lower-level .feat directories!!! > > When I look in those lower-level task directories, I only see the level1.fsf > files, so it seems like the level 1 .feat directories are missing. These > level 1 .feat directories are not mentioned in the directory structure > information from the 500 Subjects Release Reference Manual, though. > > Are these level 1 .feat directories necessary, and if so, is there a way to > download them? Or will I need to generate them using FSL? > > Many thanks for your help! > -Ely > > > B. Ely > PhD Student > Icahn School of Medicine at Mount Sinai > _______________________________________________ > 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
