NITRC IIT Human Brain Atlas (v.5.0) Forum: help

Warping T1 (LeadDBS MNI) to IITmean_t1

Adriana Jorge — Fri, 14 Apr 2023 15:39:49 GMT

Hello,

I'm fairly new to the neuroscience world, so I apologize in advance for any stupid question.

I'm trying to obtain a warp matrix to use in mrtrix that warps a T1 from MNI space (LeadDBS) to the IITmean_t1. The objective is to latter apply the inverse warp to co-register VTAs (estimate in LeadDBS MNI space) onto the HARDI template. Does anyone have any suggestions on how I should go about that? Is ANTs a good way to obtain that warp matrix? And if so, which parameters should I be using?

Thank you,
Adriana

White matter tract lengths?

canislupus — Mon, 02 Nov 2020 3:52:52 GMT

Dear experts,

I was delighted to come across this atlas but I'm missing a type of information that's critical to my analyses. This information is tract length, and now I'm wondering if it was part of this dataset. If not, can you provide some advice on how I could quantify it? Ideally, I'd like to assign an average tract length to every edge in the structural connectome, besides weight.

Thank you very much,
Canis

RE: WM LUT labels

Sarah Gimbel — Fri, 04 Sep 2020 21:22:25 GMT

That is exactly what I was looking for! Thank you very much!!!
Sarah

RE: WM LUT labels

Konstantinos Arfanakis — Fri, 04 Sep 2020 21:01:47 GMT

Hi again,

Please check now. We have uploaded new LUT_WM_0to1.txt and LUT_WM_0to255.txt. We have also updated the manual. This should be what you were looking for. Thank you for pointing this out and please let us know if you find anything else that we could improve.

Thanks,
Konstantinos

RE: WM LUT labels

Sarah Gimbel — Fri, 04 Sep 2020 18:12:51 GMT

Thank you so much!!!
Sarah

WM LUT labels

Konstantinos Arfanakis — Fri, 04 Sep 2020 17:38:06 GMT

Hi Sarah,

You are correct. The labels are currently displaying as Label#### and there is no alternative that displays the full names. For now, you can decode these names using the information in page 42 of the manual. And since you asked, we will go ahead and generate more user-friendly LUTs. Please check back in a few days.

Konstantinos

WM LUT labels

Sarah Gimbel — Fri, 04 Sep 2020 17:06:07 GMT

Hello,
I am trying to use the WM LUT downloaded from the documents page, but the labels are displaying as "Label###" instead of the name. Is there a way to fix this or find a LUT that has the name of the WM tract on it?
Many thanks,
Sarah

RE: Welcome to Help

Konstantinos Arfanakis — Tue, 10 Nov 2015 13:33:24 GMT

Dear Norbert,

To download files of the atlas just go to the Download link (left bar of https://www.nitrc.org/projects/iit/ ).
The Contents_of_IIT_atlas file describes all the files of the atlas. The HOWTO files give step by step instructions on how to accomplish different tasks. If you need more guidance let us know what you are trying to achieve and we can help you further.

Regards,
Konstantinos

RE: Welcome to Help

Norbert Franke — Tue, 10 Nov 2015 11:44:40 GMT

Dear Collegues,

I was asked to tell others about my experiences with IIT Human Brain Atlas (v.4.1). But to be honest I could not download it. Can anybody give me an advice how to download and use it?

Norbert

nfranke@uni-bonn.de

RE: bvals and bvecs?

Konstantinos Arfanakis — Sun, 29 Mar 2015 0:06:32 GMT

Hi Bal Ram,

Thank you for your kind words.
To answer your question, the diffusion gradient file is different for each voxel. For more information on why that is, please see Varentsova et al. http://www.ncbi.nlm.nih.gov/pubmed/24440528
This means that if we have N voxels we have N bvecs files. These will not be compatible with bedpostx.
For that reason, we have already reconstructed FODs and provide them in the "HARDI" template. You can use these FODs with mrtrix.

Please let us know if you have additional questions.

Konstantinos