Hi,

I am new to MRIcroGL, and I wanted to know how can I add a new atlas.

Thanks :D

Atlases are stored in the /Resources/atlas folder (for MacOS, right click on the application and choose "Show Package Contents"). The "Intention" of the NIfTI image should be set to Labels (to see the Header, select the image in the MRIcroGL Layers menu and click the "Show Header" from the "Options" button - the intention is shon on the "Statistics" tab).

Hi, 

I tried to change the Intention to Labels, but it doesn't save, do you know what can I do?


Thanks

If the NIfTI file is compressed, uncompress it (e.g. myatlas.nii.gz -> myatlas.nii). After modifying the header, choose File/SaveHeader menu item to save your changes.

This is super helpful & I'm able to add a new atlas from FSL. I can't get the labels to show up though. In FSL these are stored in a separate xml file - how would I port these over into MRIcroGL? 

Thanks for a super useful tool!

You can include a text file with the name filename.txt (or filename.nii.txt if your atlas is filename.nii.gz). Alternatively, you can embed this text file into the NIfTI header after the first 352 bytes and before the image data (just make sure your Vox_offset includes this).

I would suggest Unix style line endings (0x0A) and each row lists a region, with each line starting with the intensity index, a space and then the name of the region:

1 Precentral_L 2001
2 Precentral_R 2002
3 Frontal_Sup_L 2101
4 Frontal_Sup_R 2102
5 Frontal_Sup_Orb_L 2111
6 Frontal_Sup_Orb_R 2112
7 Frontal_Mid_L 2201
8 Frontal_Mid_R 2202
9 Frontal_Mid_Orb_L 2211
10 Frontal_Mid_Orb_R 2212
11 Frontal_Inf_Oper_L 2301
12 Frontal_Inf_Oper_R 2302
13 Frontal_Inf_Tri_L 2311
14 Frontal_Inf_Tri_R 2312
15 Frontal_Inf_Orb_L 2321
16 Frontal_Inf_Orb_R 2322
17 Rolandic_Oper_L 2331
18 Rolandic_Oper_R 2332
19 Supp_Motor_Area_L 2401
20 Supp_Motor_Area_R 2402
...

Hello dear expert,
I'm a novice user of MRIcroGL and intend to see labels of a new added atlas as well.

I created a text file with the same name as the atlas file I added ("MNI152NLin2009cSym_CerebrA.txt" & "MNI152NLin2009cSym_CerebrA.nii").
This text file contains only 2 columns, no headers, separated by spaces, and uses Unix-style line endings. The first column is the serial number (intensity index) and the second column is the corresponding label name (replace spaces with underscores):

1 Rostral_Middle_Frontal_R
2 Vermal_lobules_VI-VII_R
3 Inferior_temporal_R
4 Accumbens_Area_R
5 Inferior_Lateral_Ventricle_R
6 Pericalcarine_R
7 Lateral_Orbitofrontal_R
8 Rostral_Anterior_Cingulate_R
9 Superior_Parietal_R
10 Inferior_Parietal_R
...

I put this text file under the "atlas" folder. However, when I open the atlas, the label names are not showing up automatically. I'd tried to drag it on the user interface and failed to achieve too.
Where did I go wrong and what should I do?

Many thanks.

The first column (index number) is separated from the second column (name) with a tab. This allows names to have spaces. Make sure your NIfTI header sets the 'Intention' as 'Labels'

.

Hi, 

I follow you advice but unfortunately when saving the new nifti file with 'intention' set to 'Labels' I cannot open the image because the following error came out 'This image file is smaller than described in header'. 
Could you help me? 
Thank you 

Eleonora