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 <[email protected]> Date: Monday,
> February 8, 2016 at 9:10 PM To: Timothy Coalson <[email protected]>
> Cc: Matt Glasser <[email protected]>, "[email protected]"
> <[email protected]> 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 <[email protected]> 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
>> <[email protected]> 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/Dif-
fPreprocPipeline_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 <[email protected]>
>>> 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: <[email protected]> on behalf of Dev vasu
>>>> <[email protected]> Date: Monday, February 8,
>>>> 2016 at 10:55 AM To: "[email protected]" <hcp-
>>>> [email protected]> 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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>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>
>>>>
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>>>> If you are not the intended recipient, be advised that any
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>>>> immediately notify the sender via telephone or return mail.
>>> _______________________________________________
>>>
HCP-Users mailing list
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>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> _______________________________________________
>
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>
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>
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>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
________________________________________
The material in this message is private and may contain Protected Healthcare
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disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited.
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