NITRC SRI24 Atlas: Normal Adult Brain Anatomy Forum: open-discussion

SRI24 atlas

farisa_fathima — Thu, 06 Mar 2025 7:44:54 GMT

How many regions are  there in SRI24 atlas and which .nii file to use from the directory?

RE: MNI space?

Torsten Rohlfing — Wed, 12 Mar 2014 18:37:10 GMT

Hi Matthew -

Sorry I ignored you for so long. Apparently I wasn't monitoring this forum.

To answer your suggestion - we think of SRI24 as a standard space ;)

Regarding MNI - putting our template into MNI space (I assume MNI152?) would not be valid. Or rather, using its ROIs to quantify individual brains mapped into MNI space wouldn't be valid.

That's because the MNI152 template is a fuzzy mess of affine-aligned brains, so when you normalize an individual brain to it, then you really cannot rely on stuff (especially in the cortex) going in the right place.

Hope this makes sense.

Best,
Torsten

MNI space?

Matthew Kempton — Mon, 25 Feb 2013 15:38:56 GMT

Hello - great template.

It would be really useful if you could povide a version of your template in MNI space. From what I understand from the paper the atlas is not in a standard space. Having a version transformed to MNI space would allow you to sample regions from brains that have been normalised in SPM

RE: inconsistent laterality

Torsten Rohlfing — Thu, 12 Jul 2012 17:20:52 GMT

Yarik: you already know this, but just to make sure there aren't any loose ends in the forum, let me mention here again that this issue was fixed in the 2.0 release of the SRI24 atlas in March 2012.

dti data

Torsten Rohlfing — Thu, 12 Jul 2012 17:19:40 GMT

The FA file is indeed "fractional anisotropy", but in order to
store the values as integers, not floats, we multiplied all values
by 1000. So 943 is really FA=0.943.

The md, l1, and lt values are exactly what you are saying.

Now for the meaning of the eigenvalues, l1 through l3 - these do
NOT define any coordinate system. The eigen*vectors* define such
coordinate system for each tensor, but you can not derive these
from the eigenvalues.

You can get the eigenvector data for the dominant eigenvalue from
two additional, archives that we put for download on the NITRC
download page, [url=../frs/?group_id=214]http://www.nitrc.org/frs/?group_id=214[/url]

[url=../frs/download.php/2467/sri24_tensors_nifti.zip]sri24_tensors_nifti.zip[/url]

[url=../frs/download.php/3948/sri24_tensors_nrrd.zip]sri24_tensors_nrrd.zip[/url]

The first has the data in NIFTI format, the second in NRRD.

For the remaining two eigenvectors, I currently do not have
the files ready. I can probably put these together also, but
it will take a little while.

Hope this helps.

Torsten

[quote]
On 07/12/2012 05:08 AM, wrote:

The file "fa" contains the data of the fractional anisotropy and I
would expect the values of "fa" to be in the range [0,1]. When I
opened the file I figured out that the values ranged from 0 to
943. Does "fa" denote something else and not fractional
anisotropy?

According to your paper published in Human Brain Mapping, "md" is
the average of the eigenvalues of the diffusion tensor and "l1" is
the largest of the eigenvalues. Is "lt" the average of the other
two eigenvalues, i.e., (l2+l3)/2 ?

Do the eigenvalues l1, l2 and l3 are the values in the x, y, and z
co-ordinates of a global Cartesian system, or every set of (l1,
l2, l3) corresponds to a local orthogonal system of the
eigenvectors of the diffusion tensor? If they correspond to a
local orthogonal system is it possible for me to get the
eigenvectors for each eigenvalue?

[/quote]

inconsistent laterality

Yaroslav Halchenko — Thu, 08 Mar 2012 21:43:21 GMT

It seems that lpba40 labels (didn't check all -- just selected randomly 1) has incorrect laterality (L vs R), e.g. see
http://www.onerussian.com/tmp/sri24-inconsistent-laterality.png
for both lpba40 and tzo116 (where it seems to be alright)

or am I missing something? (volumes for both atlases have the same qform/sform... also qform has L-R orientation while sform R-L... intentional?)

License clarification: Derived data

Torsten Rohlfing — Thu, 17 Dec 2009 18:50:32 GMT

This post is intended to clarify some aspects of licensing for the SRI24 atlas related to the "derived data" concept.

a) Newly created label maps are NOT considered derived data.

If you use the SRI24 atlas to create new label maps, e.g., segmentations of new anatomical structures, then we shall not consider this derived data. You are free to distribute these label maps as you see fit. We would appreciate citations to the SRI24 HBM paper in any publications using such maps. We would also prefer if new label maps were distributed primarily through the NITRC/SRI24 project. However, this is not strictly required.

b) Modified/edited images and/or label maps provided by us ARE considered derived data.

Please do not distribute modified SRI24 images or label maps. You are free to use any derived data locally in your laboratory. If you would like to distribute edited data, please contact Torsten Rohlfing (torsten@synapse.sri.com) to arrange for these data to be incorporated in the official SRI24 distribution. We will be more than happy to accommodate such requests.