Vasudev, Based on a subsequent message that you sent to this mailing list asking for alternatives available when you do not have T1w or T2w images, I'm guessing you may have already figured out what I'm about to write. So please forgive me if I'm simply writing what you already know.
First, there is not enough information in your message below to be able to diagnose why you would be getting a "Segmentation fault". The Segmentation fault could be coming from something happening in your modified batch script (PreFreeSurferPipelineBatch.mine.sh) or from the PreFreeSurferPipeline.sh script that is invoked by the batch script or (most likely) from one of the programs invoked by the PreFreeSurferPipeline.sh script. The most likely reason for the segmentation fault is that, as you indicate, you do not have any structural images for the pipeline to process. Second, based on your indication that you do not have any T1w or T2w images, I would question the need or ability to run the PreFreeSurferPipeline on your data at all. The main functions of this pipeline use the structural (T1w and T2w) images to create a "native space" for the subject by distortion correcting the structural images, rigidly aligning them to the axes of the MNI space, etc. It also does an initial brain extraction based on the structural images. Others on this list are better qualified to provide more details than I, but, in short, the main inputs to the PreFreeSurferPipeline.sh script (and the Structural Preprocessing Pipeline of which the PreFreeSurferPipeline is the initial step) *are the T1w and T2w images*. I am not experienced enough to suggest alternatives for you when structural images are not available. I will defer to others who may have suggestions for alternatives. Tim On Sat, Feb 13, 2016, at 06:21, Dev vasu wrote: > 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 > 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]>, "hcp- >>>> [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]" >>>>>>> <[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. -- 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
