Thanks for the reply. I've made some edits to the PreFreeSurfer pipeline
that allow me to run it without the T2 or the field map, and I'm wondering
whether they're sensible. Specifically, I've
1) Set AvgrdcSTRING to "NONE" in PreFreeSurferPipelineBatch.sh.
2) Set Modalities to "T1w" in PreFreeSurferPipeline.sh.
3) Removed the call to T2wToT1wReg.sh from PreFreeSurferPipeline.sh.
4) Removed the call to BiasFieldCorrection_sqrtT1wXT1w.sh from
PreFreeSurferPipeline.sh. (Side note: I believe this script is mis-named
and should be . . ._sqrtT1wXT2w.sh.)
5) In the call to AtlasRegistrationToMNI152_FLIRTandFNIRT.sh, set --t1rest
to ${T1wFolder}/${T1wImage}_acpc and --t1restbrain to
${T1wFolder}/${T1wImage}_acpc_brain.
6) Removed the first call to applywarp from
AtlasRegistrationToMNI152_FLIRTandFNIRT.sh, as well as all the calls to
applywarp and fslmaths that involve T2w images.
(My reason for making these changes is that I'd like to apply the HCP
pipeline to non-HCP data that do not include T2 scans or field maps.)
Best,
Dan
On Thu, Jul 9, 2015 at 3:30 PM, Harms, Michael <[email protected]> wrote:
>
> Sorry, but no -- not currently. The T2w is a fundamental component of
> HCP acquisitions and pipelines, so stuff related to it is embedded into the
> pipelines.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [email protected]
>
> From: "Daniel P. Bliss" <[email protected]>
> Date: Thursday, July 9, 2015 4:24 PM
> To: "[email protected]" <[email protected]>
> Subject: [HCP-Users] Easy way to have PreFreeSurferBatch.sh not process
> the T2w?
>
> Hi all,
>
> Is there an easy way to set PreFreeSurferBatch.sh to perform full
> preprocessing on the T1w scan, but skip all preprocessing steps that
> involve the T2w?
>
> Thanks,
> Dan
>
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