Dear HCP experts,
I am trying to run first level Gambling task analysis. I copied and pasted
the templates of feat setup files (found in Examples/Scripts) to the
MNINonlinear/Results/fMRI_GAMBLING_LR(
or _RL) respective directory (number of time points were same as the
corresponding scans:253). Next I copied and pasted copy of E-Prime EV files
in the MNINonLinear/Results subdirectory. I am getting the following error
now (highlighted below):
Last login: Sat Apr 11 09:32:36 on ttys002
rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/freesurfer
rmbp:~ Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /Applications/fsl
rmbp:~ Sampada$ cd /Volumes/HCP_Data/Pipelines-3.4.0/Examples/Scripts/
rmbp:Scripts Sampada$ ./TaskfMRIAnalysisBatch.sh
This script must be SOURCED to correctly setup the environment prior to
running any of the other HCP scripts contained here
2
tfMRI_GAMBLING
LS2001
About to use fsl_sub to queue or run
/Volumes/HCP_data/Pipelines-3.4.0/TaskfMRIAnalysis/TaskfMRIAnalysis.sh
This script, TaskfMRILevel1.sh, assumes fslmaths behavior that is available
in version 5.0.6 of FSL. You are using FSL version 5.0.8. Please install
FSL version 5.0.6 before continuing.
This script, TaskfMRILevel1.sh, assumes fslmaths behavior that is available
in version 5.0.6 of FSL. You are using FSL version 5.0.8. Please install
FSL version 5.0.6 before continuing.
cat:
/Volumes/HCP_Data/taskfMRI_Gambling/LS2001/MNINonLinear/Results/tfMRI_GAMBLING/tfMRI_GAMBLING_hp200_s4_level2.fsf:
No such file or directory
Can't find key fmri(level)
set -- --path=/Volumes/HCP_Data/taskfMRI_Gambling --subject=LS2001
--lvl1tasks=tfMRI_GAMBLING_RL@tfMRI_GAMBLING_LR
--lvl1fsfs=tfMRI_GAMBLING_RL@tfMRI_GAMBLING_LR
--lvl2task=tfMRI_GAMBLING --lvl2fsf=tfMRI_GAMBLING
--lowresmesh=32 --grayordinatesres=2 --origsmoothingFWHM=2
--confound=NONE --finalsmoothingFWHM=2
--temporalfilter=200 --vba=NO
. /Volumes/HCP_Data/Pipelines-3.4.0/Examples/Scripts/SetUpHCPPipeline.sh
rmbp:Scripts Sampada$
…... ….. ….. ….. ….. ……..
…..
Do I need to download fsl version 5.0.6 now as well to run the task
analysis?
Can I get any feedback please about the process which I followed from the
HCP site and if I need to put the copied EV files in the respective
subdirectories or LINKED_DATA files into the MNINonlinear/Results/taskfMRI
directory?
Also, if I can get performance score of Gambling task, based upon which we
plan to separate out the regions depending on the score.
Appreciate all your help so far!
Kind regards,
Sampada
P.S.: Sorry about the font last time. I copied and pasted my question from
the notes (which has an artsy font by default!)
--
Sampada Sinha
Post-Doctoral Associate
University of Minnesota (East Bank)
Molecular and neuroimaging laboratory
Department of Psychiatry
Minneapolis-55415
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