Is FreeSurfer in MNI space?

FreeSurfer also reports “Talairach MNI” coordinates. These are MNI305 space.

What is the RAS coordinate system?

RAS Coordinate space is centered in the voxel whose Volume Index is (128, 128, 128). One voxel has dimensions 1 x 1 x 1 in RAS space. Because the RAS axes are not all in the same direction as Volume Index axes, the axis extents in RAS have different ranges: either -127.5 to + 128.5, or -128.5 to +127.5.

What is QDEC FreeSurfer?

QDEC is an acronym for Query, Design, Estimate, Contrast. It is intended to aid researchers in performing inter-subject / group averaging and inference on the morphometry data (cortical surface and volume) produced by the FreeSurfer processing stream.

What does recon all do FreeSurfer?

Overview: Reconstructing the Cortical Surface FreeSurfer contains a large suite of programs which can take several hours to process a single subject, and days to process an entire dataset. Recon-all stands for reconstruction, as in reconstructing a two-dimensional cortical surface from a three-dimensional volume.

Is Fsaverage in MNI space?

Within the world of Freesurfer, the fsaverage space has been roughly / approximately coregistered to MNI space (for more details see here, thanks to Denise Ruprai) but is based on different subjects (as far as I know based on the Buckner40 dataset which has become part of the genomics superstruct repository).

What is TkMedit?

TkMedit is the main volume viewer and editor for FreeSurfer. Use it to view volumes, overlay surfaces onto them in 2D, edit reconstruction defects, view functional overlays and time courses, view segmentations, and draw or edit labels.

What are the four coordinate system that relate to the CT scanner?

In Slicer, the axial, sagittal, and coronal views each have their own XYS coordinate system. In each window, each voxel on each image slice has its own (X, Y) screen coordinates and the slice number in which it lies.

What is Qform and Sform?

The qform transformation (as stored in a NIfTI header) relates the voxel co-ordinates (in mm) to scanner space (aka some frame of reference on the scanner), and is a rigid transform. The sform transformation relates the voxel co-ordinates to some standard space (eg. MNI space), is an affine transform.

How long does it take to run FreeSurfer?

around sixteen to twenty-four hours
As you will soon find out, FreeSurfer takes a long time to process an individual subject – around sixteen to twenty-four hours on a typical iMac, with some variation due to factors such as the quality of the input data.

What is the size of the FreeSurfer mni152 1mm template?

FSL_MNI152_FreeSurferConformed_1mm.nii.gz is the FSL MNI152 1mm template interpolated and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume (obtained by putting the FSL MNI152 1mm template through recon-all using FreeSurfer 4.5.0) 2.

Where can I find the FreeSurfer subjects?

These subjects are also currently in the developmental version of FreeSurfer which can be accessed from the Martinos center network (/autofs/cluster/freesurfer/centos4.0_x86_64/dev/subjects/). These subjects will be officially included in some future FreeSurfer release.

How to convert surface Roi to volumetric space in FreeSurfer?

First, create a registration file called register.dat with FreeSurfer’s tkregister2 command: Where “beta_0001.nii” is a beta map created in the subject’s native space, and “subject” is the name of the subject that has been preprocessed with recon-all. We then use the command mri_label2vol to convert the surface ROI to volumetric space:

What coordinates does FreeSurfer report for Talairach?

Note on Talairach: FreeSurfer does not report true “Talairach” coordinates. The coordinates listed unter “Talairach” are actually based on Matthew Brett’s 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html ). FreeSurfer also reports “Talairach MNI” coordinates. These are MNI305 space.