Dear Sir, I will look into the suggestions, i would like to highlight one important aspect, I do not have field map acquisition files , for this reason i did not provide any file path for variable "MagnitudeInputName" in SeimensFieldMapProcessingAll.sh, Can i possibly comment out the necessary sections of code to avoid generating Magnitude_brain and Magnitude_brain_mask images
Thanks Vasudev On 17 March 2016 at 21:37, Timothy B. Brown <tbbr...@wustl.edu> wrote: > Hi Vasudev, > > What you attached was a modified version of the PreFreeSurferPipeline.sh > script. You did not include the command line you actually use to invoke > your changed version of the script. But before you send the command line > you use to invoke your script, I need to point out that the fact that you > modified the PreFreeSurferPipeline.sh script itself seems to indicate > that there is a fairly fundamental misunderstanding about how the HCP > Pipeline Scripts are intended to be used and customized for your situation. > > I would *very strongly* suggest that you should not be modifying any > scripts in the HCP Pipelines Scripts other than those in the > Examples/Scripts directory. The Examples/Scripts directory contains > example "batch" scripts that are intended to illustrate how to invoke the > actual HCP Pipeline Scripts to process your data. For example, the file > PreFreeSurferPipelineBatch.sh provides an example of how to invoke the > PreFreeSurferPipeline.sh script. You should create a copy of the > PreFreeSurferPipelineBatch.sh script (e.g. PreFreeSurferPipeline.Batch. > mine.sh) and make modifications in that file for your situation. > > There is also a file named SetUpHCPPipeline.sh that is an example > environment set up script (a.k.a. "environment script") for running the HCP > Pipeline Scripts. It is in this script (or your own copy of it) that you > should set environment variables to indicate such things as where FSL is > installed on your system (FSLDIR), where FreeSurfer is installed on your > system (FREESURFER_HOME), where the HCP Pipeline Scripts are installed on > your system (HCPPIPEDIR), etc. > > The "batch script" sources the "environment script" to set up all the > environment variables for running the pipeline scripts. > > Modifying the PreFreeSurferPipeline.sh is intended to be done when there > is a need to modify the fundamental behaviors of this particular phase of > the HCP Pipelines. You should not be modifying the > PreFreeSurferPipeline.sh script (or your PreFreeSurferPipeline.mine.sh > script) to set up environment variables or change the values of command > line arguments that are used to specify the files you want the scripts to > work on or the optional mechanisms for doing that work. > > Not that this could not be made to work, but it makes it significantly > harder for anyone to help you to debug things when you are modifying the > core scripts instead of modifying the example scripts that were intended to > be modified or at least used as an example for creating your own scripts > that *call* the core scripts. > > You should not be modifying the parts of the PreFreeSurferPipeline.sh > script that get and set command line arguments (the calls to opts_GetOpt1 > right after the message "Parsing Command Line Options".) This not only > will make helping you more difficult, it should not be necessary at all. > Every one of those options is specifiable from the command line used to > invoke the PreFreeSurferPipeline.sh script as is shown in the > PreFreeSurferPipelineBatch.sh script. > > Please have a look at the "batch" scripts and the "environment script" in > the Examples/Scripts directory and read the documentation comments in > those files. There is definitely room for improvement in those comments, > and I'm open to suggested improvements and revisions in the comments. But > I hope that they at least form a pretty good starting point. > > Also, if you visit the following web page > http://www.humanconnectome.org/courses/2015/exploring-the-human-connectome.php, > scroll down to the section labelled "Course Schedule and Resources", then > find and select the link for Practical 2 on Day 1 > (Day1_Practical2_wb_command&PipelinesI.pdf), you'll get a PDF document that > I hope will be helpful. In particular, within that PDF document, start > reading on Page 6 in the section titled "Part2. HCP Pipelines I". > > Tim > > On Thu, Mar 17, 2016, at 13:06, Dev vasu wrote: > > Dear Sir, > > I am sending the file with command line options along with paths that i > allocated in PreFreesurferPipeline.sh. I am reviewing the file again and > checking the options that i have set . If you could recognize some thing > which i cannot could you please correct me > > Thanks > Vasudev > > On 17 March 2016 at 18:38, Timothy B. Brown <tbbr...@wustl.edu> wrote: > > Vasudev, > > On 14 Mar 2016 at 12:13, Dev vasu <vasudevamurthy.devulapa...@gmail.com> > wrote: > > When i run Prefreesurfer pipeline, the execution fails at the start of > :Field Map Preprocessing and Gradient Unwarping in > > T2WToT1wDistortionCorrectAndReg.sh following is the error that i > > am getting > > > > " START: T2WToT1wDistortionCorrectAndReg.sh > > > > START: Field Map Preprocessing and Gradient Unwarping > > > > Cannot open volume -Tmean for reading! > > > > Could you please clarify me about this error message. > > Based on the error messages you are showing above, it is very likely that > there is a malformed or missing command line argument somewhere in your > call to the PreFreeSurferPipeline.sh script. > > For example, the PreFreeSurferPipeline.sh script calls the > T2wToT1wDistortionCorrectAndReg.sh script which in turn *might* call the > SiemensFieldMapPreprocessingAll.sh script (depending upon the exact > version of the HCP Pipeline Scripts you are using and the command line > input parameters that you give it). In the > SiemensFieldMapPreprocessingAll.sh script, there is a message output that > looks like: > > echo " START: Field Map Preprocessing and Gradient Unwarping" > > This appears to be the last message you get before the error. > > Shortly after the output of the "START: ..." message, there is a call to > fslmaths that looks like: > > ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude > > Upon reaching that call to fslmaths, if the variable MagnitudeInputName > is empty, then the actual command that will issued will look something like: > > ${FSLDIR}/bin/fslmaths -Tmean ${WD}/Magnitude > > Note that fslmaths is expecting as its first argument the name of an > input volume file. In the above case, it has been given -Tmean as its > first argument. So fslmaths will try to open a volume file named "-Tmean". > Which is, of course, wrong. There will not be a file named -Tmean. Thus, > you get the error message: Cannot open volume -Tmean for reading! > > In fact, you can duplicate the error message by issuing an fslmaths > command with -Tmean as its first argument. > > [~]$ fslmaths -Tmean > Cannot open volume -Tmean for reading! > [~]$ > > So, as Matt Glasser indicated in a previous reply, you will need to post > the exact text of your call to the PreFreeSurferPipeline.sh script in > order for anyone to be able to provide any more information other than the > guess that I've made above. You will also need to include the > specification of the exact version of the HCP Pipeline Scripts you are > using (e.g. v3.4.0, v3.6.1, v3.9.0, etc.) because there may be differences > in what scripts are invoked by the PreFreeSurferPipeline.sh script based > on the version of the HCP Pipeline Scripts in use. > > Sorry for the long winded nature of this reply, but I am hoping that it > will: > > 1. Help you and others on the HCP-Users list further along the path of > being able to diagnose and debug such problems, and > 2. Help you understand why Matt was requesting that you post your call > to the PreFreeSurfer pipeline. > > Regards, > > Tim > > -- > 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. > > Email had 1 attachment: > > - PreFreeSurferPipeline.mine.sh > 38k (application/x-sh) > > -- > 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
