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Freesurfer notes

28 Nov 2018

The .mgz file format is used to store high-resolution structural data and other data which are to be overlaid on the high-resolution structural volume.

  • Freeview

With one Freeview command line, you can load several output volumes.

  • Subcortical Segmentation

    • In automatic subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels

    • The automatic subcortical segmentation can take many (11+) hours to complete.

Freesurfer Tutorial

source: link

Parameters

  • Input : T1 Weighted image
  • T1 Contrast: white matter brighter than gray matter
  • ~ 1 \(mm^3\)
  • Higher resolution may be worse
  • Full brain
  • Usually one acquisition is ok
  • More if high acceleration
  • Siemens —> MPRAGE or GE —> SPGR
  • 1,5T or 3T
  • 7T might have problems
  • Subject age > 5 years old
  • Brain has no major problems (i.e. Tumours, Parts missing)
  • Non-human primates possible

Command Lines

recon-all

Fully automated reconstruction, reconstruction here refers to cortical reconstruction.

  • 1 T1 image —> 180 slice of image. We call it series. recon-all use only one of those series, and it will find the other 179

-i

recon-all -i file1.dcm -i file2.dcm

  • file.dcm is a single DICOM file
  • you can use NIFTI as well with -i file.nii

-subject bert

“bert” is the name of the subject, also called subject ID. Freesurfer will create a folder and it will do all of its analysis inside of this folder. And it will go into great detail about what’s inside of the folder. Create a folder in $SUBJECTS_DIR

-all

means to do everything can take 10-20 hours

inside the $SUBJECTS_DIR bert folder, there are 5 folders:

  • scripts recon-all.log recon-all.done
  • mri : all the volume results
  • surf : all the surface statistics
  • label : all the surface statistics
  • stats : table fits stats

.mgz > freesurfer specific format. lh.orig: left hemisphere surface base file rh.orig: right hemisphere surface base file

Intensity Bias correction

When scan somebody, the brightness is not uniform across the image

Skull skip

Remove all non-brain structure, –> brainmask.mgz

White Matter Segmentation

wm.mgz

  • Separates white matter from everything else
  • Uses aseg to “fill in” subcortical structure
  • Cerebellum removed, brain stem still there