NITRC IBSR Forum: open-discussion

Problem facing Ground truth volume reading

Madhumita Ray — Tue, 23 May 2023 10:32:46 GMT

Hi Andy,

As Ground truth image is storing the value as 0,1, 2, 3, I am just printing out the voxels with value 1. It shows that the CSF is in the centre only, whereas it is present at boundary also. The image is attached here for your reference.

Regards
Madhumita

RE: Couldn't able to read ground truth image volume properly

Madhumita Ray — Mon, 22 May 2023 6:24:56 GMT

Is it the actual README file?

RE: Couldn't able to read ground truth image volume properly

Madhumita Ray — Mon, 22 May 2023 6:17:01 GMT

Hi Andy,

I am working with .nii files. The header of the files cannot be able to read properly. Kindly help me to read the header of the image voluve as well as the mask volume. Which README file storing the header of the .nii volume.

I can find out two README file in the .zip file.

one README file showing

Torsten Rohlfing has released these images into the public domain. Any use of them should reference this paper:

T. Rohlfing, "Image similarity and tissue overlaps as surrogates for image registration accuracy: Widely used but unreliable," IEEE Transactions on Medical Imaging, vol. 31, no. 2, pp. 153-163, 2012.

Another file is showing
Mac OS X 2 y « ATTR7Šø « œ œ com.apple.TextEncoding utf-8;134217984

Where is the actual README file for .nii image volume.

please help me as early as possible.

RE: Couldn't able to read ground truth image volume properly

Andrew Worth — Wed, 17 May 2023 13:40:08 GMT

You'll have to provide more details.

Andy.

Couldn't able to read ground truth image volume properly

Madhumita Ray — Wed, 17 May 2023 8:07:38 GMT

Hi,

I am reading the image volume and the ground truth image volume at the same way but I am facing the problem to identify the CSF region at the groundtruth image volume. My Groundtruth images showed that there is no CSF at the boundary region only at the centre but at the original images there are CSF at the boundary region, though I am reading the two volumes at the same way. Please help me regarding this issue.

Thank you.

Regards
Madhumita Ray

RE: how work with IBSR

Andrew Worth — Tue, 15 Feb 2022 1:26:45 GMT

[i]Originally posted by gholamzade:[/i][quote]Hi
I download opening IBSR, but I can't understand how to "combine all of the slice images into one "raw" file like this in unix (all one line):"
would you more explain about it?
Thanks alot.
elham.[/quote][color=#000000] Hi gholamzade,[/color]

[color=#000000]Sorry for the slow response. In unix you can just use "cat". I hope that makes sense.[/color]

[color=#000000]Kind regards,[/color]

[color=#000000]Andy.[/color]

RE: Inconsistent spatial information in IBSR v2.0

Andrew Worth — Tue, 15 Feb 2022 1:25:27 GMT

[i]Originally posted by Christian Haselgrove:[/i][quote]It appears that the spatial information in the IBSR 2.0 is inconsistent within subjects. IBSR_01_segTRI_ana.img, for instance, has an translation in its transformation matrix that doesn't appear in IBSR_01_ana.img or IBSR_01_seg_ana.img. Some subjects also have a difference in voxel size. The voxel-by-voxel correspondence in the .img files appears okay, so a workaround is to use each subject's anatomical .hdr and .mat for the segmentation and tri-segmentation. (Andy, can you verify this workaround is sound?)[/quote]
[color=#000000]Sorry for the slow response, Christian! Yes, that sounds good to me. Let me know if you want me to look into this further.[/color]

[color=#000000]Kind regards,[/color]

[color=#000000]Andy.[/color]

RE: Problem finding the spacial coordinates of IBSR ROIs

Andrew Worth — Tue, 15 Feb 2022 1:21:51 GMT

[i]Originally posted by Jacinta Silva:[/i][quote]Hello,
I need the .node file of the IBSR atlas to make an image in Brainnet Viewer software. However I can't find it anywhere. Can you help me urgently.
Thank you![/quote]
[color=#000000]Hello Jacinta Silva,[/color]

[color=#000000]I'm not familiar with such a thing. Perhaps you could contact Brainnet Viewer for answers.[/color]

[color=#000000]Best wishes,[/color]

[color=#000000]Andy.[/color]

Problem finding the spacial coordinates of IBSR ROIs

Jacinta Silva — Tue, 15 Feb 2022 0:42:55 GMT

Hello,
I need the .node file of the IBSR atlas to make an image in Brainnet Viewer software. However I can't find it anywhere. Can you help me urgently.
Thank you!

Inconsistent spatial information in IBSR v2.0

Christian Haselgrove — Wed, 14 Apr 2021 21:43:59 GMT

It appears that the spatial information in the IBSR 2.0 is inconsistent within subjects. IBSR_01_segTRI_ana.img, for instance, has an translation in its transformation matrix that doesn't appear in IBSR_01_ana.img or IBSR_01_seg_ana.img. Some subjects also have a difference in voxel size. The voxel-by-voxel correspondence in the .img files appears okay, so a workaround is to use each subject's anatomical .hdr and .mat for the segmentation and tri-segmentation. (Andy, can you verify this workaround is sound?)