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=${AtlasSpaceFolder}/xfms/acpc_dc2standard.nii.gz \
>
> ./PostFreeSurfer/PostFreeSurferPipeline.sh:AtlasTransform="acpc_dc2standard"
>
> ./fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh:AtlasTransform="acpc_dc2standard"
> [HCPpipeline@login01 Pipelines-3.6.0]$
>
> 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
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