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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
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