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Hi Josh,
The WU-UMN HCP outputs provide the thickness values already aligned to a common mesh in the *thickness.{32,164}k_fs_LR.dscalar.nii files (both 32k and 164k mesh version available). You should be able to run a nice, permutation-based group analysis on
those using the FSL PALM tool. If you run into problems in that regard, please let us know your experience on the HCP-Users list.
Alternatively, if you want to use FS-specific tools to run the group analysis, the entire FS output, in the standard FS format, is available as part of the “Structural Extended” packages. If you download those, the only small additional step you would
need to do would be to create a “SUBJECTS_DIR” like directory which contains sym-links pointing to the location of the FS data in the HCP file structure.
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: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Josh Gray <jgray7...@gmail.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Date: Friday, May 13, 2016 at 8:25 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] 2 unrelated questions regarding structural data Hello,
1) I am working with the recent release of human connectome data and am trying to run group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want
to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for the pipeline to run properly. Since I did not run recon-all locally, their file arrangement is unique, many files are zipped, etc. Therefore the
scripts (e.g., mris_preproc) do not know where to look, as they do with the typical file structure. Can you tell me what specific files this pipeline needs to generate the GLM? Alternatively, if you have performed this process with the human connectome data
you can tell me which directories/files need to be unzipped and placed in SUBJECTS_DIR. Just need to know what specific files the scripts in the group analysis pipeline are searching for when I run them.-- Graduate Student
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