If you search the list you will see a response to this. We hope to get out a
new official version of Connectome Workbench soon so that folks won’t run into
this, but you can either install a development version or comment out that line
for now/
Peace,
Matt.
From:
The output will be named
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean.dtseries.nii.
You will need to look into the logs more deeply than that. I would guess
there is an issue with your installation of R and its package dependencies.
Peace,
Matt.
Dear experts,
I want to use the “hcp_fix" script for clean up of resting state data after HCP
pipelines. I am editing “settings.sh" and wanted to know if I have to edit
these lines copied below:
# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
#
Hello
I wanted to get some further clarification on the ICA+FIX pipeline
Within the fix directory I used the command:
>>hcp_fix
>>/sourcedir/subject/MNINonLinear/Results/rfMRI_REST_AP/rfMRI_REST_AP.nii.gz
>>2000
processing FMRI file rfMRI_REST_AP with highpass 2000
running highpass
running
Hi Nicola,
One more thing, in addition to the duplicated slashes, is that you may want to
consider using a JSESSIONID rather than using your username/password
credentials for your curl calls.
I usually use something like:
read -s -p "ENTER PASSWORD: " PW;JSESSIONID=`curl -s -k -u
I see - ok, great. Will amend that!
Thanks again,
Nicola
On 11/02/2017 06:11 PM, Hodge, Michael wrote:
Hi Nicola,
The archive specification is optional. So it should work with or
without it. I think the problem is likely the duplicate slashes –
“files//MNINonLinear”. I copied your
Hi Nicola,
The archive specification is optional. So it should work with or without it.
I think the problem is likely the duplicate slashes – “files//MNINonLinear”. I
copied your curl command, and worked as-is once I removed the duplicate slash.
Regards,
Mike
From:
oh wait - I have and extra 'archive' in the path... is this what the
problem is?
On 11/02/2017 06:00 PM, Nicola Toschi wrote:
Hi Michael,
I am using:
sub=100206
h=R
curl -u USER:PASS -O
Hi Michael,
I am using:
sub=100206
h=R
curl -u USER:PASS -O
https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST/resources/${sub}_CREST/files//MNINonLinear/Native/${sub}.${h}.sphere.MSMAll.native.surf.gii
so the URL is the same (i think) but
Hi Nicola,
What URL are you using to retrieve the file via CREST/curl? When I do:
curl -s -k --cookie JSESSIONID=$JSESSIONID
Hi Mara,
Tim posted about this about a month ago or so. I'm copying/pasting his
response for your reference:
That is a new option that is not yet in a released version of workbench,
and was probably not intended to be pushed to the pipelines repository.
You can use github to find the version
Dear HCP-users list
I am new to the HCP pipeline and I'm experiencing a problem while running
PostFreeSurferPipelineBatch.s on Mac-Os.
I get the following error message:
While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
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