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This page will take you through the steps of processing your longitudinal data: first with running the cross sectionals and creating the longitudinals, and then with editing the data and rerunning the different streams with the new edits.  This page will take you through the steps of processing your longitudinal data: first with running the cross sectionals and creating the longitudinals, and then with editing the data and rerunning the different streams with the new edits.
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== Creating the Longitudinal Data == == Creating Longitudinal Data ==
Remember to set your SUBJECTS_DIR to the directory where your cross sectionals (the different time points collected) are saved, and to source FREESURFER.
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Remember to set your SUBJECTS_DIR to the directory where your cross sectionals (the different time points collected) are saved, and to source FREESURFER.
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First, run all your cross sectionals. Run recon-all -all for all tpNs (i.e. all time points for all subjects):
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First, run all your cross sectionals. Run recon-all -all for all tpNs (i.e. all time points for all subjects):
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Second, create your template/base from the tpNs. Here you can choose a name for teh templateID, e.g. 'bert' or 'bert_base' if 'bert' is already used for the first time point of this subject:
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Second, create your template/base from the tpNs. Here you can choose a name for teh templateID, e.g. 'bert' or 'bert_base' if 'bert' is already used for the first time point of this subject:
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Finally, create the longitudinals using the template and tpNs. Repeat the following steps for all tpNs. The resulting directories will be in the format of tp1id.long.templateID
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Finally, create the longitudinals using the template and tpNs. Repeat the following steps for all tpNs. The resulting directories will be in the format of tp1id.long.templateID
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Processing your Longitudinal Data

This page will take you through the steps of processing your longitudinal data: first with running the cross sectionals and creating the longitudinals, and then with editing the data and rerunning the different streams with the new edits.

Contents

  1. Processing your Longitudinal Data
    1. Creating Longitudinal Data
    2. Inspecting Longitudinal Data
    3. Post-Processing Longitudinal Data
    4. Editing Longitudinal Data

Creating Longitudinal Data

Remember to set your SUBJECTS_DIR to the directory where your cross sectionals (the different time points collected) are saved, and to source FREESURFER. 

cd /path/to/your/data
setenv SUBJECTS_DIR $PWD
source $FREESURFER_HOME

First, run all your cross sectionals. Run recon-all -all for all tpNs (i.e. all time points for all subjects): 

recon-all -all -subjid <tpNid>

Second, create your template/base from the tpNs. Here you can choose a name for teh templateID, e.g. 'bert' or 'bert_base' if 'bert' is already used for the first time point of this subject: 

recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all

Finally, create the longitudinals using the template and tpNs. Repeat the following steps for all tpNs. The resulting directories will be in the format of tp1id.long.templateID 

recon-all -long <tpNid> <templateID> -all

Inspecting Longitudinal Data

Post-Processing Longitudinal Data

Editing Longitudinal Data

FsTutorial/LongitudinalTutorial_tktools (last edited 2013-11-01 14:33:07 by MaritzaEbling)