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

RE: All HOW TOs moved to the Manual

Konstantinos Arfanakis — Sat, 20 Jul 2019 7:14:40 GMT

Hi Julio,

The names have now been added. Please download the new version of the manual.

Regards,
Konstantinos

RE: All HOW TOs moved to the Manual

Julio Villalon Reina — Thu, 18 Jul 2019 1:36:01 GMT

Hi, Prof. Arfanankis, I started using V 5.0 of the atlas. I could not find in the documentation the full names that define the acronyms of the "List of White Matter Bundles". Would it be possible to provide those as well? Thank you.

All HOW TOs moved to the Manual

Konstantinos Arfanakis — Mon, 24 Jun 2019 20:47:15 GMT

In version 5.0, all HOW TOs were updated and moved to the Manual of the IIT Human Brain Atlas.

RE: HOW TO use the DTI template for registration

magan — Thu, 15 Feb 2018 10:48:12 GMT

Thanks. I was running it on linux and my colleague has pointed out that linux does not recognise \r so the end of line marker had to be changed from "\n\r" to "\n"

RE: HOW TO use the DTI template for registration

Konstantinos Arfanakis — Wed, 14 Feb 2018 15:56:31 GMT

This is strange. It seems that there was a problem with lines 2 and 70 of the script. If you open the script in a text editor you will see that both of these lines have only the "return key" in them, and no commands. This tells me that there may be a problem with the way your operating system and shell (bash, cshell etc.) handle that part of the script. One thing I would suggest is to remove those empty lines from the script and rerun. Also, if you have access to a different computer (different operating system or different shell) you may want to try the scripts there.
I am curious to know what you find.

Konstantinos

RE: HOW TO use the DTI template for registration

magan — Tue, 13 Feb 2018 12:53:05 GMT

Hello!

I am following the steps in the documentation How to use the IIT Human Brain Atlas in TBSS but when I try to run ./tbss_4_prestats_iit 0.25, I encounter the following errors:

./tbss_4_prestats_iit: line 2: $'\r': command not found
./tbss_4_prestats_iit: line 70: $'\r': command not found
./tbss_4_prestats_iit: line 71: syntax error near unexpected token '$'{\r''
'/tbss_4_prestats_iit: line 71: 'Usage() {

What went wrong there and what's the solution to this?

Many thanks!

RE: HOW TO use the DTI template for registration

Konstantinos Arfanakis — Thu, 21 Jan 2016 5:36:16 GMT

>
Hi Rowena,

DTI-TK registration only works for a number of slices that is a power of 2. So it probably won't work.

Konstantinos

RE: HOW TO use the DTI template for registration

Rowena C — Wed, 20 Jan 2016 5:31:21 GMT

[color=#000000]Hi Konstantinos,[/color]

Just curious: will the registration not work if I did the steps but register to the 182 space template?

Best,
Rowena

[i]Originally posted by Konstantinos Arfanakis:[/i][quote]Hi Rowena,

I think the jhu labels are in 182 space (not 256). As a result, the output of DTI-TK using our 256 atlas will most likely not work with the jhu labels. I should mention here that you may want to take a look into the "HOW-TO-use-the-WM-atlas". The IIT white matter atlas contains four-dimensional (4D) white matter labels. This means that each white matter voxel is assigned a list of gray matter label-pairs with the most probable connections through that voxel. The reason behind the 4D labels is that multiple fiber populations often share the same voxels, and therefore white matter voxels must be given the chance to have multiple labels. If you still prefer the winner-takes-all approach (similar to the jhu approach) then you can simply use the top label in each voxel of our atlas, which means you can simply use the first volume of our 4D atlas and ignore the rest of the volumes (less likely labels). However, I recommend avoiding "winner-takes-all" white matter atlases, for the reason explained above. It is best to embrace the truth i.e. multiple connections can share the same white matter voxels, so each white matter voxel should have multiple labels.

Please let me know if you have more questions.

Regards,
Konstantinos[/quote]

RE: HOW TO use the atlas in TBSS

Konstantinos Arfanakis — Thu, 05 Nov 2015 3:17:30 GMT

November 4th 2015. A minor bug was discovered and fixed in the following files:
tbss_4_prestats_iit
tbss_4_prestats_iit_256
tbss_non_FA_iit
tbss_non_FA_iit_256
In the previous versions, the tbss_skeleton command (at the end of these scripts) was run without the -s option. This means that the IIT skeleton provided was not used and was actually recalculated from the IITmean_FA. This has now been fixed in the new version of the scripts.

RE: HOW TO use the DTI template for registration

Konstantinos Arfanakis — Thu, 22 Oct 2015 0:33:35 GMT

Hi Rowena,

I think the jhu labels are in 182 space (not 256). As a result, the output of DTI-TK using our 256 atlas will most likely not work with the jhu labels. I should mention here that you may want to take a look into the "HOW-TO-use-the-WM-atlas". The IIT white matter atlas contains four-dimensional (4D) white matter labels. This means that each white matter voxel is assigned a list of gray matter label-pairs with the most probable connections through that voxel. The reason behind the 4D labels is that multiple fiber populations often share the same voxels, and therefore white matter voxels must be given the chance to have multiple labels. If you still prefer the winner-takes-all approach (similar to the jhu approach) then you can simply use the top label in each voxel of our atlas, which means you can simply use the first volume of our 4D atlas and ignore the rest of the volumes (less likely labels). However, I recommend avoiding "winner-takes-all" white matter atlases, for the reason explained above. It is best to embrace the truth i.e. multiple connections can share the same white matter voxels, so each white matter voxel should have multiple labels.

Please let me know if you have more questions.

Regards,
Konstantinos