Dear Sir, I have already figured out the the reason for the error and I do have T1w and T2w data at present.
Thanks Vasudev On 15 February 2016 at 14:48, Timothy B. Brown <[email protected]> wrote: > 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]>, "[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. > > -- > 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
