{"id":354,"date":"2014-02-06T16:27:15","date_gmt":"2014-02-06T21:27:15","guid":{"rendered":"https:\/\/sites.bu.edu\/cnrlab\/?page_id=354"},"modified":"2014-02-06T16:47:31","modified_gmt":"2014-02-06T21:47:31","slug":"freesurfer-quality-control-step-1-fix-pial-surface","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/cnrlab\/lab-resources\/freesurfer-quality-control-guide\/freesurfer-quality-control-step-1-fix-pial-surface\/","title":{"rendered":"FreeSurfer Quality Control: Step 1: Fix Pial Surface"},"content":{"rendered":"

Freesurfer Quality Control Guide<\/h1>\n

Step 1: Correct the Pial Surfaces to remove<\/span> any non-brain tissue<\/h2>\n

Step 1a: Load the target subject into FreeView using the terminal:<\/h3>\n

You can also open FreeView with all the appropriate files preloaded using the following commands:<\/p>\n

export SUBJ=YourSubjectName<\/strong>\r\nfreeview \\\r\n-v $SUBJECTS_DIR\/$SUBJ\/mri\/orig.mgz \\\r\n-v $SUBJECTS_DIR\/$SUBJ\/mri\/brainmask.mgz:colormap=jet:colorscale=0,1:opacity=0.3 \\\r\n-f $SUBJECTS_DIR\/$SUBJ\/surf\/lh.pial:edgecolor='255,0,0' \\\r\n-f $SUBJECTS_DIR\/$SUBJ\/surf\/rh.pial:edgecolor='255,0,0' &<\/pre>\n
Step 1b: -OR- Load the target subject into FreeView using the GUI:<\/h3>\n
In your terminal, open FreeView:<\/p>\n
freeview &<\/pre>\n
Load the following volume files for the subject you are editing:<\/p>\n
<\/p>\n