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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 source the FREESURFER. 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. 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 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 steps for all tpNs. The resulting directories will be in the format of tp1id.long.templateID 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

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 the Longitudinal Data
    2. Editing your Data

Creating the 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

Editing your Data

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