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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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| recon-all -all -subjid tpN | 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 |
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| == Inspecting Longitudinal Data == | |
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| == Editing your Data == | == Post-Processing Longitudinal Data == == Editing Longitudinal Data == |
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.
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
Inspecting Longitudinal Data
Post-Processing Longitudinal Data