Hi Mahsa,
For the data in the Q3 release, the prepare_level2_feat_analysis.sh helper
bash script for setting up the registration matrices/directory prior to
running level 2 feat analysis was inadvertently omitted from all the
minimally preprocessed data packages for the tfMRI data, as documented on
the HCP Known Issues and Fixes wiki
<https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Release+Update
s%253A+Known+Issues+and+Planned+fixes> section on the Q3 release. We also
released a data patch in March 2014 which puts this script back in. The
March 2014 Data Patch can be downloaded from the ConnectomeDB splash page.
Also, you may also download task analysis data packages containing the
results of individual subject, cross-run ("level 2") fMRI grayordinates
analysis or volume-based tfMRI processing for each HCP task. If you are
using Connectome In a Box, depending on when you ordered it, you may already
have much of this data.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
<tel:314-362-9387> 314-362-9387
<mailto:[email protected]> [email protected]
<http://www.humanconnectome.org> www.humanconnectome.org
From: [email protected]
[mailto:[email protected]] On Behalf Of Mahsa Alizade
shalchy
Sent: Friday, August 08, 2014 9:21 AM
To: [email protected]
Subject: [HCP-Users] prepare_level2_feat_analysis.sh
Dear HCP users
Hi
I'm trying to perform a 2nd level GLM analysis (using fsl) on the fmri motor
task data.However,I encountered a registeration problem.While I was reading
the data manual I found this:
These directories contain an .fsf file that can be used to run a
higher-level analysis across the two runs of each task. They also contain a
script (prepare_level2_feat_analysis.sh) that must be run first, to set up
appropriate registration matrices in the lower-level outputs.
Unfortunately I can not find "prepare_level2_feat_analysis.sh" in any of
data directories.
Where could I access this file?
Thank you in advance,
Mahsa
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