====== DTI processing ======

  * [[http://www.fmrib.ox.ac.uk/fsl/fdt/index.html|FSL's Diffusion Toolbox]]

  * convert the raw DTI data into nifti format
  * skull strip the DTI
  * run eddy current correction
  * run dtifit to calculate FA,eigenvalues,etc
     * these steps are handled through the [[mirecc:mireccanat:make_dti]] script
  * run bedpostx on the cluster to estimate crossing fibers
     * running bedpost requires copying the dtifit results to a temporary directory within the MIRECC.03/Analysis/dti_temp folder and running each slice individually through the cluster.  If you do not run the slices individually they are run sequentially, which can take 1 week to finish.
     * [[mirecc:runBEDPOST_PRE.sh]] -- sets up the bedpostx directory
     * [[mirecc:submit_CROSS.sh]] -- submits the individual slices through [[mirecc:runBEDPOST_CROSS.sh]] (this does not need to be run)
     * once all 60+ slices are completed, they need to be combined into one volume and moved back to the individual subject's directory.
     * navigate to the subject's folder (on Selye) and run:
<code>bedpostx_postproc.sh dti</code>
     * copy the dti.bedpostx folder to the subject's folder on Cohen
     * now dti can be normalized and dyads can be masked: [[mirecc:post_dti_steps.sh]]
     * navigate to /data/code and run it as bash -x post_dti_steps.sh SUBJNUM








====== First, FreeSurfer, Manual Comparison ======

  * Convert the raw anatomicals into nifti, and flip them from the default orientation into LAS (FSL's preferred orientation) - [[mirecc:mireccanat:makeFirst_anat|script]]
  * Run the FIRST subcortical segmentation - [[mirecc:mireccanat:first_seg|FIRST Methods]] - [[http://www.fmrib.ox.ac.uk/fsl/first/index.html|FSL FIRST Documentation]]
  * Run FreeSurfer segmentation on the same T1 as FIRST - [[mirecc:mireccanat:free_surfer|FreeSurfer Methods]] - [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MorphAndRecon|FreeSurfer Documentation]]
  * Calculate Overlap using fslstats - [[mirecc:mireccanat:overlap|Overlap Methods]] 


====== flowchart showing steps of getting first/freesurfer volumes into the same space ======

{{:mirecc:mireccanat:mirecc_free_first_chart1.jpg|:mirecc:mireccanat:mirecc_free_first_chart1.jpg}}