Hi
Is in your plans to offer a course/training on the HCP pipelines (OHBM15,
SfN15, may be?)
Thanks!
Oscar Miranda-Dominguez
Postdoctoral Researcher
Fair Neuroimaging Lab
Phone: 503.418.1894 Fax: 503.494.9988
Oregon Health and Science University
Department of Behavioral Neuroscience
3181 SW
We've run into a weird problem when using the GenericfMRIVolume batch script to
process more than 2 tasks at a time. When we setup any more than 2 tasks (we've
tried 3 and 4 tasks), the first 2 run correctly and without error, but any
after that crash in the TopUp section with the following
Hi Oscar,
Your question is quite timely as we are currently formulating plans for an
HCP course that we hope will occur just before OHBM 2015 in Honolulu. Part
of what will be covered will be practicals on using the HCP pipelines. Stay
tuned for more information on the course to be available at
Can you post the text of your launcher script? Only one task is run at a time inside the pipeline, so the issue will be there.
Peace,
Matt.
From: Book, Gregory gregory.b...@hhchealth.org
Date: Tuesday, December 9, 2014 at 12:29 PM
To: hcp-users@humanconnectome.org
You need to expand thePhaseEncodinglistvariable to have the same length as theTasklistvariable (i.e. same number of elements
separated by spaces). This probably should be made clearer in the comments for these variables.
Peace,
Matt.
From: Book, Gregory gregory.b...@hhchealth.org
So the phase encoding list corresponds to the EPI encoding direction, not the
spin echo direction. How does TopUp know the encoding directions of the spin
echos? Does it assume the positive image is the same encoding direction as the
EPI and the negative image is the opposite direction?
From:
Yes it is the EPI phase encoding direction. The positive and negative phase encoding directions are conventional (see the notes next to the variables for the convention). Basically, you want them in the order that produces a field map whose signs look
like a regular field map (as opposed to
Tim,
A patch here to use array instead of space delimited string might be helpful
for error detection:
e.g.
Tasklist=(domino0 domino1 domino2 domino3)
PhaseEncodinglist=(y y- y y-)
nTasklist=${#Tasklist[@]}
nPhaseEncodinglist=${#PhaseEncodinglist[@]}
if [ $nTasklist -ne $nPhaseEncodinglist
After a second thought, maybe convert the list to array specifically for the
comparison purpose so the rest of the pipeline script don’t need to be modified
to use array indexing.
Tasklist=domino0 domino1 domino2 domino3
PhaseEncodinglist=y y- y y-“
TaskArray=($Tasklist)
Thank you Matthew.
Your suggestions were very helpful.
I had to do a few more corrections on selecting the labels for creating
whole brain white matter mask from the ribbon.nii.gz and wmparc.nii.gz
files.
Here what worked at the end:
#_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT
Great to hear!
Matt.
From: Eleftherios Garyfallidis garyfalli...@gmail.com
Date: Tuesday, December 9, 2014 at 7:59 PM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] White matter mask availability in HCP
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