Dear Sir,
Thanks for your mail, I will recheck everything and try if it works out, I
apologize if my repeated mails are annoying you, since i am new to HCP
workbench, I am facing some problems, earlier i use to work on Neuroimaging
subjects using SPM in Matlab R2013b ( windows 7 OS ), but for my current
work, I have to establish all the study protocols in workbench as part of
my graduate studies. I am totally new to this and i am trying my best to
resolve my issues on my own, If in case some problems arise i will contact
your team, I thank HCP community for being patient enough to respond to my
questions.
Thanks
Vasudev
On 9 February 2016 at 17:18, Timothy B. Brown <tbbr...@wustl.edu> wrote:
> Hi Vasudev,
>
> As Matt points out, if you visit the *Release Notes, Installation, and
> Usage Guide* pointed (see Matt's link provided below), you should find a
> section under the heading *Running the HCP Pipeline on example data. *This,
> hopefully, should be a good starting point for understanding the
> environment variables that must be set correctly in order to run the HCP
> Pipeline Scripts. As is mentioned in the document, we recommend setting
> the values for these environment variables in an "environment script" that
> is sourced before running any of the pipelines.
>
> As Tim Coalson points out, the error message you are getting when you try
> to run the Diffusion Preprocessing pipeline is coming from a line of code
> that expects the environment variable HCPPIPEDIR to be set to contain the
> path to the root directory at which you have installed the HCP Pipeline
> Scripts.
>
> That particular line of code looks like:
>
> source ${HCPPIPEDIR}/global/scripts/log.shlib
>
> The code is written with the expectation that the HCPPIPEDIR environment
> variable is set, and whatever value it is set to will be used in the actual
> command that is run. If the HCPPIPEDIR environment variable is not set,
> then the use of ${HCPPIPEDIR} in the command is replaced by an empty
> string. Thus the source statement is trying to find and use a file at
> the path /global/scripts/log.shlib, which, of course, does not exist. It
> actually should be trying to find and use a file in the global/scripts
> sub-directory of your HCP Pipeline Scripts installation directory.
>
> One other hint, it appears to me from the path to the
> DiffPreprocPipeline_PreEddy.sh script shown in your error message, that
> you may have misunderstood the use of HCPPIPEDIR. You have apparently
> named the directory in which you have installed the HCP Pipeline Scripts
> HCPPIPEDIR with the assumption that naming as such is what is required to
> make the scripts work. This is not the case. As I've noted above,
> HCPPIPEDIR is the name of an environment variable, not (necessarily) the
> name of an actual directory. While it won't prevent things from working if
> the directory happens to be named HCPPIPEDIR, but it may add to some
> confusion and it certainly won't make the parts of the scripts that depend
> upon the HCPPIPDIR *environment variable* work.
>
> Hope that is helpful,
>
> Tim
>
> On Tue, Feb 9, 2016, at 05:25, Glasser, Matthew wrote:
>
> Read the part about environment script:
> https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage
>
>
> Peace,
>
> Matt.
>
> From: Dev vasu <vasudevamurthy.devulapa...@gmail.com>
> Date: Monday, February 8, 2016 at 9:10 PM
> To: Timothy Coalson <tsc...@mst.edu>
> Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] HCP Pipelines :DiffusionPreprocessing
>
> Dear Sir,
>
> If possible could you please provide me some additional documentation on
> how to use efficiently use pre-processing pipelines, I have worked
> previously with SPM, HCP-Workbench is new for me, I have completed working
> on initial tutorials and started establishing DTI clinical data that we
> acquired at Hospital on Workbench, and i am facing several problems most
> of which might be very basic for you but for me ,i am currently stuck at
> this point, I want to study structural connectivity between vestibular
> system and M5 and i would like to use Workbench for my structural
> connectivity analysis . Currently i am doing initial preprocessing with the
> given pipelines .
>
>
> Thanks
> Vasudev
>
> On 9 February 2016 at 01:32, Timothy Coalson <tsc...@mst.edu> wrote:
>
> That looks like the same kind of error - an unset variable that is
> supposed to point to the location of the pipeline scripts.
>
> Tim
>
>
> On Mon, Feb 8, 2016 at 5:52 PM, Dev vasu <
> vasudevamurthy.devulapa...@gmail.com> wrote:
>
> Dear Professor :
>
> I have resolved this issue on my own, but i still couldn't perform
> pre-processing of DTI data , This time i am incurring following error :
>
> "Mo 8. Feb 22:40:00 CET 2016 - DiffPreprocPipeline.sh - Invoking Pre-Eddy
> Steps
> /home/vasudev/Documents/workbench/HCPPIPEDIR/DiffusionPreprocessing/DiffPreprocPipeline_PreEddy.sh:
> line 69: /global/scripts/log.shlib: No such file or directory "
>
>
> Could you please let me know if there is any documentation for DTI
> Preprocessing .
>
>
> Thanks
> Vasudev
>
> On 8 February 2016 at 23:37, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> That looks like you don’t have the pipelines environment script properly
> set up (empty/global/…). Have another look at the set up instructions.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Dev vasu <
> vasudevamurthy.devulapa...@gmail.com>
> Date: Monday, February 8, 2016 at 10:55 AM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] HCP Pipelines :DiffusionPreprocessing
>
> Dear Professor,
>
> I would like to use DiffusionPreprocessing Pipeline for my DTI structural
> connectivity analysis, I have completed the tutorial on how to use HCP
> Pipelines for Preprocessing, I have followed the instruction and i have
> provided the path to study folder and subject, when i run the
> DiffusionPreprocessing.sh, i am incurring following error
>
> "./DiffPreprocPipeline.sh: line 96: /global/scripts/log.shlib: No such
> file or directory
> "
>
> Although the file log.shlib is found in global directory , I am incurring
> the same error.
>
> Could you please clarify me.
>
>
> Thanks
> Vasudev
>
> _______________________________________________
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
>
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> of this information is strictly prohibited. If you have received this email
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> --
> Timothy B. Brown
> Business & Technology Application Analyst III
> Pipeline Developer (Human Connectome Project)
> tbbrown(at)wustl.edu
> ________________________________________
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