Freesurfer Abridged

2018-04-04T14:34:33Z

Rebecca: /* Functional */

== Setting Up ==
*Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject

This is an <i>abridged</i> version of the more detailed list provided elsewhere in the wiki.

== Structural ==

# Slicer
#* In terminal, <code>Slicer &</code>
#* Load data brainmask.nii
#* Save data as brainmask.mgz
#* Results: creates brainmask.mgz file
# Autorecon 1
#* In terminal, <code>autorecon1_SC.sh FS_0184</code>
#* Don't bother editing after this step; skip to autorecon 2
#* Result: populates mri folder (includes "T1.mgz")
# Autorecon 2
#* In terminal, <code>autorecon2_SC.sh FS_0184</code>
#* Editing
#** One terminal, <code>tksurfer FS_0184 lh inflated</code>
#** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
#** Look for any noticable spikes in the tksurfer brain and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.
#* Results: creates lh.cortex.label and rh.cortex.label in label folder
# Autorecon 3
#* In terminal, <code>autorecon3_SC.sh FS_0184</code>
#* Editing
#** In terminal, <code>tksurfer -annot aparc FS_0184 lh pial</code>
#** If needed, reference <code>tksurfer -annot aparc fsaverage lh pial</code>
#** Repeat with right hemi
#** Make sure to EXPORT ANNOTATION! Do not "save overlay!"
#** Again, be sure to see the autorecon3 page
#*Result: populates label folder (includes "lh.aparc.annot" and "rh.aparc.annot")

== Functional ==

# Bold file preparation
#* Semcat processing
#** In terminal, <code> matlab &</code>
#** In matlab, <code>startup_smp12</code>
#** **Check with your local Principle Investigator™ or Graduate Work Horse™ for more details about Semcat bold files**
#* LDT processing
#** In terminal, <code>matlab &</code>
#** nii_4D_drop_vols('f.nii', [# vols to drop])
#** set_TR(2.047, [1 2 3 4 5 6], 'f.nii')
#** d=datenum('DD-Mmm-YYYY') (e.g. '05-Oct-1997')
#** subj_ID='0183'
#** FSTSExtractor('prefix', 'LDT_', 'subject', subj_ID, 'run', i, 'tr', 2.047, 'volumes_dropped', <initial # drop vols>, 'date', d)
#*** This step must be completed for each f.nii file in each bold folder
#*** IT IS VERY IMPORTANT to look at what volumes to drop. It will likely not be the same for each bold file, unless it is a newer LDT participant. You can find more information [[http://ccnlab.psy.buffalo.edu/wiki/index.php/Freesurfer_BOLD_files]] here.
# Analysis
#* cd to subject folder
#* mkanalysis.sh
# Contrasts
#* cd to subject folder
#* Run <code>mkcontrast.sh</code>
# Pre-processing
#* Run <code>preproc-sess -per-run -fwhm 6 -surface self lhrh -fsd bold -s FS_<subj_ID></code>
# Selxavg
#* Run <code>selxavg3-sess -s <subjectname> -analysis <analysis path></code>
#* Analysis path is where your LDT.?h.sm6 folders are.
# (Optional) Clut and Subparcellation
#* Run <code>clut.sh FS_<subj_ID></code>
#* Run <code>subpar.py FS_<subj_ID></code>
# Blobs

== Timeseries Analysis ==

CCN Wiki - User contributions [en]

Freesurfer Abridged