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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. |
[[FsTutorial|top]] | [[FsTutorial/TroubleshootingData|previous]] = Longitudinal Processing - Tutorial = This page will take you through the steps of processing your longitudinal data: first with running the cross sectionals and creating the unbiased within-subject base and longitudinals. Then we will take a look at the results, learn how to do some post-processing and about editing the data and rerunning the different streams with the new edits. You can read more about the longitudinal stream at [[LongitudinalProcessing]] and about edits at [[LongitudinalEdits]]. |
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| == Creating the Longitudinal Data == | == Preparations == |
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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. | * If you are taking one of the formally organized courses, the tutorial data is already installed on the computer provided to you so please skip ahead to the '''Viewing Volumes with Tkmedit''' section. If not, then to follow this exercise exactly be sure you've downloaded the [[FsTutorial/Data|tutorial data set]] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. If you are using the tutorial data please set the environmental variable {{{TUTORIAL_DATA}}} to the location that you have downloaded the data to (here, it has been copied to $FREESURFER_HOME/subjects): {{{ tcsh setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs }}} * Notice the command to open tcsh. If you are already running the tcsh command shell, then the 'tcsh' command is not necessary. First you need to set your SUBJECTS_DIR to the appropriate place: {{{ setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR }}} * this will set your {{{SUBJECTS_DIR}}} to the location where your tutorial data is if you have defined the variable {{{TUTORIAL_DATA}}} as indicated at the top of this tutorial. If you are not using the tutorial data you should set your {{{SUBJECTS_DIR}}} to the directory in which the subject you will use for this tutorial is located. |
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| == 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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| ---- 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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== Editing your Data == |
== Inspecting Longitudinal Data == == Post-Processing Longitudinal Data == == Editing Longitudinal Data == |
Longitudinal Processing - Tutorial
This page will take you through the steps of processing your longitudinal data: first with running the cross sectionals and creating the unbiased within-subject base and longitudinals. Then we will take a look at the results, learn how to do some post-processing and about editing the data and rerunning the different streams with the new edits. You can read more about the longitudinal stream at LongitudinalProcessing and about edits at LongitudinalEdits.
Preparations
If you are taking one of the formally organized courses, the tutorial data is already installed on the computer provided to you so please skip ahead to the Viewing Volumes with Tkmedit section. If not, then to follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. If you are using the tutorial data please set the environmental variable TUTORIAL_DATA to the location that you have downloaded the data to (here, it has been copied to $FREESURFER_HOME/subjects):
tcsh setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
- Notice the command to open tcsh. If you are already running the tcsh command shell, then the 'tcsh' command is not necessary.
First you need to set your SUBJECTS_DIR to the appropriate place:
setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR
this will set your SUBJECTS_DIR to the location where your tutorial data is if you have defined the variable TUTORIAL_DATA as indicated at the top of this tutorial. If you are not using the tutorial data you should set your SUBJECTS_DIR to the directory in which the subject you will use for this tutorial is located.
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