NITRC IIT Human Brain Atlas (v.5.0) Forum: open-discussion

RE: To find out which pairs of gray matter labels have connections through a user-defined ROI

Wang Fengting — Tue, 27 Sep 2022 8:02:08 GMT

[i]Originally posted by Wang Fengting:[/i][quote]Dear exports,

Thank you very much for the timely reply. I have registered the individual T1 to the IITmean_t1.nii.gz and drew my ROI based on the IITmean_t1 template by both MRIcron and ITK-SNAP. However, the result.txt still said that 0.00% of the selected ROI is used in this analysis and 100.00%of the ROI is located outside of the white matter. Nevertheless, it gave me the analysis results of most possible connections which were consistent with the literature reports. Can I still use these results? What is the problem?

Thanks again for the excellent work.

Best regards,
Frances.[/quote]
It seems that it only accepts ROI in one layer but does not accept VOI in several layers. Is there an approach to work it out?

RE: To find out which pairs of gray matter labels have connections through a user-defined ROI

Wang Fengting — Sun, 25 Sep 2022 10:45:02 GMT

Dear exports,

Thank you very much for the timely reply. I have registered the individual T1 to the IITmean_t1.nii.gz and drew my ROI based on the IITmean_t1 template by both MRIcron and ITK-SNAP. However, the result.txt still said that 0.00% of the selected ROI is used in this analysis and 100.00%of the ROI is located outside of the white matter. Nevertheless, it gave me the analysis results of most possible connections which were consistent with the literature reports. Can I still use these results? What is the problem?

Thanks again for the excellent work.

Best regards,
Frances.

RE: To find out which pairs of gray matter labels have connections through a user-defined ROI

Konstantinos Arfanakis — Tue, 20 Sep 2022 14:44:12 GMT

Hi Frances,

It sounds like your ROI is not in IIT space. To make sure the ROI is in IIT space, you can open the mean FA template (IITmean_FA.nii.gz), or the mean T1 template (IITmean_t1.nii.gz), or any other template of the IIT atlas as reference and draw the ROI based on the template you see in the background. Just make sure you use the matrix size you are interested in. The IIT atlas is available in 182x218x182 or 256x256x256; the latter templates have filenames that end with _256. Make sure you pick the matrix size you want. An ROI defined in one matrix size will not work in the other. By using an IIT template as background, you ensure that the generated ROI is located in IIT space. Please let us know if you continue having problems.

Regards,
Konstantinos

To find out which pairs of gray matter labels have connections through a user-defined ROI

Wang Fengting — Tue, 20 Sep 2022 3:19:12 GMT

Hi experts,

I defined my ROIs as ablation regions located in the anterior limb of internal capsule, and tried to find pairs of gray matter labels that have connections through these regions. However, the results.txt said that 0.00%of the selected ROI is used in this analysis. Can anyone tell me what is the problem?

Many thanks,
Frances.

RE: Using IIT Atlas with DTITK and JHU

Konstantinos Arfanakis — Wed, 17 Feb 2021 14:38:45 GMT

Hi Darius,

I am afraid I don't understand which step you can't get to work.
Are you trying to bring the JHU labels in IIT space? And how exactly are you trying to do that?
Please provide more details about your steps.

K.

RE: Using IIT Atlas with DTITK and JHU

Darius Mewes — Mon, 15 Feb 2021 0:05:05 GMT

Hey Konstantinos,

thanks for your comprehensive answer. I understand that I have to do a registration. Do I also have to flip the image in case my preferred atlas is in a different layout (not in 256 IIT LPI)? I've tried around with image transformations and header changes for over an hour now but I'm still a bit confused whether this is just something memory related or actual alteration of the interpreted data.

Thanks for your help
Darius

RE: Using IIT Atlas with DTITK and JHU

Konstantinos Arfanakis — Thu, 04 Feb 2021 5:11:44 GMT

Hi Darius,

First, a few notes that may or may not apply to your project.

Note 1: I am not sure how committed you are to using JHU regions. If you want to conduct ROI analysis in white matter, you may want to use connectivity-based ROIs instead of the anatomically-defined JHU ROIs that may contain very different connections. The track-density images corresponding to the different edges of the connectome can be converted to masks (one mask per edge), transformed to the space of individual subjects, and used to extract average values of different MRI properties per edge.

Note 2: You mentioned you want to perform tractography on the IIT atlas. Note that the tractogram is already provided. Of course you can redo tractography on the HARDI template using your preferred approach and parameters.

Now to your questions:
The space of the IIT atlas and the ICBM152 space do not perfectly match. You should register one space to the other. If you do that, can't you apply the resulting transformation to the JHU regions to bring them to IIT 256x256 space?
Also, how did you apply the linear transformation?
Finally, if the above do not spark any ideas that lead to solutions, can you share a screen shot so that we get a feeling of the kinds of problems you have encountered?

Take care,
Konstantinos

Using IIT Atlas with DTITK and JHU

Darius Mewes — Wed, 03 Feb 2021 10:35:38 GMT

Hello IIT forum,

thanks to the developers for providing this great atlas. When trying to use it with DTI-TK and the JHU atlas I've encountered the following challenge:

I want to use tensor based registration techniques by DTI-TK and register subject images to the IIT Atlas. Then I want to perform tractography on the IIT Atlas with the provided FOD data. Afterwards I would like to extract fiber bundles through JHU ROIs.

My understanding at the moment is as follows:

- DTI-TK requires the 256 voxel version of IIT. In this version, the origin is set to 0 and the orientation is LPI.
- The JHU atlas is, like the IITAtlas, in ICBM152 space. The transform of the non 256 voxel versions of the IITAtlas is:

1 0 0 -91
-0 1 0 -126
-0 0 1 -72

Therefore, I want to linearly transform the JHU atlas by this transformation (and probably also flip the x-axis ?) in order to be in the DTI-TK compatible space. Unfortunately neither just a linear transform (or the inverse) or a transform and a flip on the x axis has yielded good results.

What am I doing wrong?

Thanks for your help,
Darius

RE: IIT Human Brain Atlas

Konstantinos Arfanakis — Thu, 14 Jan 2021 3:26:54 GMT

Hello,

The 256x256x256 version of the mean DTI template of the IIT Human Brain Atlas (i.e. the IITmean_*_256.nii files) is directly compatible with DTI-TK tools (no pre-processing needed). The mask you are referring to was made exclusively for use in the non-linear registration step of DTI-TK.

Regards,
Konstantinos

IIT Human Brain Atlas

Jean de Dieu Uwisengeyimana — Wed, 13 Jan 2021 19:56:12 GMT

Hello all,

Why there is IITmean_tensor_mask_256.nii.gz but no [b]IITmean_tensor_mask.nii.gz[/b]. Anyone knows where I can find it or generate it? I tried to the TVtool but it couldn't generate the mask