Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

I don't know; Anastasia is the author. She's busy today and tomorrow, I was just trying to push it forward. Does it work with the given config file in 7.2?

On 7/25/2022 5:46 PM, kingwai.chu@gmail.com wrote:

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I added it to the config file, then it complains

interreg: Undefined variable.

When I added interreg = 5, then it complains

subj: Undefined variable.

Should I continue fixing it until no more Undefined variable?

*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, July 25, 2022 5:42 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

I think the wiki is wrong. Try setting it to 3 in the config

On 7/25/2022 5:30 PM, kingwai.chu@gmail.com wrote:

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Hi Douglas,

According to

TRACULA tutorial

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https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
<https://secure-web.cisco.com/1YmZsfNNF2-hIwlP4SVMeWmro3S6_ShXDaAbTt2crsEmdQne-MX5QsRlMCMbLBZ4XGjAhQKXN80Ro3gRtSgISkplOshl8Jl9RHNDCdsv_xIhyqjYmDejPNpbxxPXWicOzB32_El09nIHPiVNjsakDv5K-Vm7TuGe1_KRyKDOs4LcQNgZjekQ12oNoOGOGjRrrHXUePaAnan4hRAYvDCG4qnZ6i98TicZFC2XhfswWCkw90-ynses9onW4e5LLnSwJZrKtsXXmWTMKtxDuhBP1yIOC2hDf8LlSWmmSubzclnlh9I4h_VVVRQToywBLfcGR1QIAdleURvGUR8e9UqoMzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTracula>

A very simple configuration file, where only the absolutely
necessary inputs are specified, intrareg is not there.

and it works on v7.2.0. w/o it explicitly specified.

From the same site above,

Step 12: Specify the intra-subject registration method

“The options are 1 (FLIRT with a correlation ratio cost), 2 (FLIRT
with a mutual information cost), and 3 (bbregister, which uses a
boundary-based cost). The default is option 3 (bbregister).”

If I don’t specify it in the config file, it should automatically
use the default setting which is intrareg = 3.

I will add it to the config file and try again.

Thanks,

King-Wai

*From:*freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu>
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of
*Douglas N. Greve
*Sent:* Monday, July 25, 2022 5:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

are you sure the config file is right? it should be defining the
intrareg variable

On 7/25/2022 2:11 PM, kingwai.chu@gmail.com wrote:

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    Hi Douglas,

    Thank you for looking into this.

    It gives the following error.

    trac-preproc.sh -c config.file

    intrareg: Undefined variable.

    Thanks,

    King-Wai

    *From:*freesurfer-bounces@nmr.mgh.harvard.edu
    <freesurfer-bounces@nmr.mgh.harvard.edu>
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of
    *Douglas N. Greve
    *Sent:* Monday, July 25, 2022 1:55 PM
    *To:* freesurfer@nmr.mgh.harvard.edu
    *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

    Can you copy the attached trac-preproc into $FREESURFER/bin
    and try again (after removing the link)?

    On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:

        *        External Email - Use Caution *

        Hi Anastasia,

        Just downloaded FreeSurfer version 7.3 and trying out TRACULA.

        Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3

        However trac-all -prep is looking for
        ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  from
        segmentThalamicNuclei.sh which doesn’t exist.

        Because in v7.3, segmentThalamicNuclei.sh output a new
        version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz).

        I worked around this problem by linking
        ThalamicNuclei.v12.T1.FSvoxelSpace.mgz  to
        ThalamicNuclei.v13.T1.FSvoxelSpace.mgz

        ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
        ThalamicNuclei.v12.T1.FSvoxelSpace.mgz

        trac-all finished w/o problem.

        trac-all -version

        trac-all 7.3.0

        I seems trac-all in v7.3 forgets to update the fact that
        segmentThalamicNuclei.sh output v13 of the file.

        Or it is looking for v12 for a reason?

        Is my fix correct?

        Thanks,

        King-Wai





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