Dear Sir, When i start running PreFreeSurferPipeline I am incurring an error which says following :
*" vasudev@vasudev-OptiPlex-780:~/Documents/Pipelines-master/Examples/Scripts$ ./PreFreeSurferPipelineBatch.mine.sh <http://PreFreeSurferPipelineBatch.mine.sh> Segmentation fault (core dumped)"* I have not acquired T1w and T2w images, I just have DTI and resting state fMRI data along with Anatomical NIFTI file, could you please let me know why such an error is occurring. I have cross checked everything and i have set up the path accurately for running the Pipeline. Thanks, Vasudev On 9 February 2016 at 17:27, Dev vasu <[email protected]> wrote: > 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 <[email protected]> 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 <[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/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 <[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]" <[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 >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> >> ------------------------------ >> >> 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. >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> >> ------------------------------ >> >> 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. >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> >> ------------------------------ >> >> 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 Information (PHI). >> 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. >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
