In this case, it would be *much better* to use the command line options that are already available for the case in which you do not have field map files rather than making any modifications (including commenting out code) in the core scripts. I think things will go much smoother for you if you follow this intended path. I apologize if the fact that this was the intended path wasn't as clear as it should have been. Thank you for bringing this up on the HCP-Users list. I hope that by going through this question and answer process openly, we have saved a number of others from similar frustrations. Tim On Thu, Mar 17, 2016, at 15:47, Dev vasu wrote: > 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 <[email protected]> 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 <[email protected]> wrote: >>>> Vasudev, >>>> >>>> On 14 Mar 2016 at 12:13, Dev vasu <[email protected]> >>>> 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. -- 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
