Vasudev,
Please look at the comments in the PreFreeSurferPipelineBatch.sh script in the
Examples/Scripts directory. In particular, look at the comments that are headed
with "Readout Distortion Correction:" If you do not have field maps to use to
do readout distortion correction, then you need to make sure the
--avgrdcmethod= option used on the command line to invoke the
PreFreeSurferPipeline.sh script is set to --avgrdcmethod=NONE.
In the modified version of PreFreeSurferPipeline.sh that you previously
sent, you have set things up so that the --avgrdcmethod= option is
completely ignored and set the AvgrdcSTRING variable to indicate that
you want to use Siemens field maps for readout distortion correction
AvgrdcSTRING=${FIELDMAP_METHOD_OPT}
When the AvgrdcSTRING value is set this way, the
PreFreeSurferPipeline.sh script will try to do readout distortion
correction using the specified Magnitude (--fmapmag=) and Phase (--
fmapphase=) field map files.
You've left the code that retrieves these two options alone.
MagnitudeInputName=`opts_GetOpt1 "--fmapmag" $@`
PhaseInputName=`opts_GetOpt1 "--fmapphase" $@`
and since you say you do not have field map files, I would expect that
you are not specifying those options on the command line when you invoke
your script.
Therefore, the MagnitudeInputName and PhaseInputName variables are
getting empty string values.
Having MagnitudeInputName be an empty string and having the options set
to use Siemens field maps would cause that empty string value to get
passed all the way down to the SiemensFieldMapPreprocessingAll.sh
script. This would cause the MagnitudeInputName variable in the
SiemensFieldMapPreprocessingAll.sh script to be an empty string and
cause the problem with fslmaths trying to open up a file named -Tmean.
Hope this is helpful.
Please consider making your modifications to the "batch" script instead
of a script that provides core functionality of the HCP Pipelines.
Tim
On Thu, Mar 17, 2016, at 13:32, Dev vasu wrote:
> Dear Sir,
>
> For the subjects that i use , We have not done any Field map
> acquisition.
>
>
> Thanks,
> Vasudev
>
>
>
> On 17 March 2016 at 19:01, Timothy B. Brown <tbbr...@wustl.edu> wrote:
>> Vasudev,
>>
>> Yes, that is very likely to be the problem.
>>
>> In general, if a part of the pipeline fails, it is very likely that
>> it will not generate the necessary files for the next step.
>>
>> If you have not been able to successfully run all of the Pre-
>> FreeSurfer pipeline, I would not expect the necessary files to be
>> available in order to run the next major step which is the FreeSurfer
>> pipeline.
>>
>> Tim
>>
>> On Thu, Mar 17, 2016, at 12:47, Dev vasu wrote:
>>> Dear Sir,
>>>
>>>
>>> After running Prefreesuferpipeline.sh my script does not generate
>>> "acpc_dc2standard" and "acpc_dc_restore" is it because my
>>> PreFreesurferpipeline.sh got terminated in middle, since i could not
>>> do gradient unwarping ?.
>>>
>>>
>>> Thanks
>>> Vasudev
>>>
>>>
>>> On 17 March 2016 at 18:41, Timothy B. Brown <tbbr...@wustl.edu> wrote:
>>>> Vasudev,
>>>>
>>>> > I would like to know if the "acpc_dc2standard" and
>>>> > "standard2acpc_dc" atlas was provided by HCP, or whether they are
>>>> > output generated from Freesurfer.sh script,
>>>>
>>>> The file acpc_dc2standard.nii.gz is generated in the
>>>> AtlasRegistrationToMNI152_FLIRTandFNIRT.sh script which is invoked
>>>> by the PreFreeSurferPipeline.sh script.
>>>> It is subsequently used in the PostFreeSurferPipeline.sh script and
>>>> in the GenericfMRIVolumeProcessingPipeline.sh script.
>>>>
>>>> If you search in your pipelines directory for acpc_dc2standard in all
>>>> files, you should see something like:
>>>>
>>>> [HCPpipeline@login01 Pipelines-3.6.0]$ find . -exec grep --with-
>>>> filename "acpc_dc2standard" {} \;
>>>>
./PreFreeSurfer/PreFreeSurferPipeline.sh: --
owarp=${AtlasSpaceFolder}/xfms/acpc_dc2standard.nii.gz \
>>>>
./PostFreeSurfer/PostFreeSurferPipeline.sh:AtlasTransform="acpc_dc-
2standard"
>>>>
./fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh:AtlasTransform="acp-
c_dc2standard"
>>>>
[HCPpipeline@login01 Pipelines-3.6.0]$
>>>>
>>>> The file standard2acpc_dc.nii.gz file is similarly generated in the
>>>> AtlasRegistrationToMNI152_FLIRTandFNIRT.sh script and subsequently
>>>> used in the PostFreeSurferPipeline.sh script.
>>>>
>>>> > also could you please let
>>>> > me know if the "acpc_dc_restore" files which is used as naming
>>>> > convention in Postfreesurfer script are outputs generated by
>>>> > freesurfer.sh ?.
>>>>
>>>> The files named *acpc_dc_restore* are generated and used by the
>>>> PreFreeSurferPipeline.sh script. They are also used as inputs to
>>>> several subsequent pipelines including FreeSurferPipeline.sh,
>>>> PostFreeSurferPipeline.sh, and
>>>> GenericfMRIVolumeProcessingPipeline.sh.
>>>>
>>>> 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.
>> --
>> 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
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