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I added it to the config file, then it complains
interreg: Undefined variable.
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When I added interreg = 5, then it complains
subj: Undefined variable.
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Should I continue fixing it until no more Undefined variable?
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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
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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 mailto:kingwai.chu@gmail.com wrote:
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Hi Douglas,
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According to
TRACULA tutorial
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Wawa7n82Ac-dxyJdbIRzWGaYawZoqFkIMlb_ww0U2WwkYe...
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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.
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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).”
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If I don’t specify it in the config file, it should automatically use the default setting which is intrareg = 3.
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I will add it to the config file and try again.
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Thanks,
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King-Wai
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From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu 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 mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
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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 mailto:kingwai.chu@gmail.com wrote:
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Hi Douglas,
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Thank you for looking into this.
It gives the following error.
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trac-preproc.sh -c config.file
intrareg: Undefined variable.
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Thanks,
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King-Wai
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From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu 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 mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
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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 mailto:kingwai.chu@gmail.com wrote:
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Hi Anastasia,
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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
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trac-all finished w/o problem.
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trac-all -version
trac-all 7.3.0
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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?
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Is my fix correct?
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Thanks,
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King-Wai