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--- cortical_thickness [2016/08/17 19:37]
bdelab created
+++ cortical_thickness [2017/08/03 18:48]
mpenrod
@@ Line 13: / Line 13: @@
 <code>cd /mnt/diskArray/projects/MRI/[subid]
 parrec2nii -c -b *.PAR</code>
-Step 2: In MATLAB compute the root mean squared (RMS) image. Once again this might have already been done in the [[Anatomy_Pipeline|Anatomy Pipeline]] so you can re-use that RMS image
+Step 2: In MATLAB compute the root mean squared (RMS) image. Once again this might have already been done in the [[anatomy|Anatomy Pipeline]] so you can re-use that RMS image
 <code>T1path = 'Path to t1 weighted image';
 T1path = mri_rms(T1path); % Root mean squared image</code>
@@ Line 20: / Line 20: @@
 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>
+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.
+====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.
+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]].

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