cortical_thickness
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cortical_thickness [2017/08/03 18:18] mpenrod |
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| Freesurfer is a useful tool for segmenting a T1-weighted image and building a cortical mesh. To segment the subject's T1-weighted image using freesurfer from the command line type: | Freesurfer is a useful tool for segmenting a T1-weighted image and building a cortical mesh. To segment the subject's T1-weighted image using freesurfer from the command line type: | ||
| <code>recon-all -i /home/projects/MRI/[subjid]/[YYYYMMDD]/[subjid]_WIP_MEMP_VBM_SENSE_13_1_MSE.nii.gz -subjid [subid] -all</code> | <code>recon-all -i /home/projects/MRI/[subjid]/[YYYYMMDD]/[subjid]_WIP_MEMP_VBM_SENSE_13_1_MSE.nii.gz -subjid [subid] -all</code> | ||
| - | The MATLAB script **parallel_recon.m** has been written to (with slight adjustments in order to specify file input and output) automate and parallelize the process, which typically takes 6-10 hours per file. | + | The MATLAB script **parallel_recon.m** has been written to (with slight adjustments in order to specify file input and output) automate and parallelize the process, which typically takes 6-10 hours per file. It is also recommended that the process be executed on multiple servers in order to further parallelize the process. |
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| + | ====Longitudinal Analysis==== | ||
| + | ===Pre-processing=== | ||
| + | Following the segmentation of the T1-weighted image, two further pre-processing steps are necessary to proceed with longitudinal analysis of the data. Firstly, an unbiased template must be created for each subject, taking into account all time-points/sessions. Secondly, each time-point must be processed again using these templates in order to standardize subject data across time-points. | ||
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| + | The command to create the unbiased template is: | ||
| + | <code>recon-all -base [output file name] -tp [time-point 1 file] -tp [time-point 2 file] ... -tp [time-point n file] -all</code> | ||
| + | Next, the command to process each time-point using this template is: | ||
| + | <code>recon-all -long [template file] [time_point file] -all</code> | ||
| + | The **recon-all -base** command will take about as long as the original FreeSurfer segmentation, however each iteration of the **recon-all -long** command will take approximately half the time. Using helper functions, the **paralell_recon.m** script will also generate and execute these commands. | ||
| We will follow the steps outlined in the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Freesurfer Wiki]] for analyzing cortical thickness. The first steps are described [[https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing|here]]. | We will follow the steps outlined in the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Freesurfer Wiki]] for analyzing cortical thickness. The first steps are described [[https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing|here]]. | ||
cortical_thickness.txt · Last modified: 2017/08/04 18:58 by mpenrod
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