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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.
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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 _______________________________________________ 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] missing level 1 .feat directories Ely, Benjamin
- Re: [HCP-Users] missing level 1 .feat directories Harms, Michael
- Re: [HCP-Users] missing level 1 .feat directories Greg Burgess
- Re: [HCP-Users] missing level 1 .feat director... Ely, Benjamin
