NITRC IBSR Forum: help

RE: How to use .buchar and .hdr files? Whata are .buchar and .hdr files?

Andrew Worth — Sun, 01 May 2022 16:43:13 GMT

Hi Aimen,

See the README files that come with the data for a description of the format of the files. The "OpeningIBSR.imgFiles.pdf" file you can find in the downloads may also help you find a way to open them.

Best wishes,
Andy.

[i]Originally posted by Aimen Mushtaq:[/i][quote]Hi, I have downloaded the dataset on windows for 20 normal MRI images with segmentation masks. I have unzipped the files and have got .buchar and .hdr files as a result. I am unable to read the data on windows. Kindly help me in this regard. Thank you.[/quote]

How to use .buchar and .hdr files? Whata are .buchar and .hdr files?

Aimen Mushtaq — Sat, 26 Mar 2022 14:42:16 GMT

Hi, I have downloaded the dataset on windows for 20 normal MRI images with segmentation masks. I have unzipped the files and have got .buchar and .hdr files as a result. I am unable to read the data on windows. Kindly help me in this regard. Thank you.

Preprocessing Code

M. Fatih TALU — Sat, 10 Oct 2020 21:20:18 GMT

I am looking for a code where I can get the IBSR_nifti_stripped output using the IBSR_ana.zip data. Can you share a document or code containing these preprocessing steps?

Thank you

RE: problem with IBSR image

parastu95 — Sat, 29 Aug 2020 16:37:32 GMT

Hello,

I have been reading a paper, Fluid Vector Flow and Applications in Brain Tumor Segmentation, and I noticed grund truth segmentation for IBSR Tomur datasets. I wonder if there is actually any ground truth provided for these datasets

RE: Segmentation Results in IBSR Data

Merve Tan — Sat, 06 Jul 2019 23:30:29 GMT

[i]Originally posted by Andrew Worth:[/i][quote]Hello Merve,

Sorry, there is no such file that provides the volumes. As you probably know, the way to do it is to count the voxels for each tissue and multiply by the voxel volume for that scan.

Andy.[/quote]

[color=#000000]Hello Andrew,[/color]

[color=#000000]Thank you very much for your response. I keep that in mind. Sorry about my late response.[/color]

[color=#000000]Best regards,[/color]
[color=#000000]Merve[/color]

RE: Segmentation Results in IBSR Data

Andrew Worth — Tue, 25 Jun 2019 15:54:40 GMT

Hello Merve,

Sorry, there is no such file that provides the volumes. As you probably know, the way to do it is to count the voxels for each tissue and multiply by the voxel volume for that scan.

Andy.

Segmentation Results in IBSR Data

Merve Tan — Mon, 24 Jun 2019 23:07:13 GMT

Dear NITRC users,

I am using a pipeline to measure the volumes of cortex GM, WM, ventricular CSF and extra-ventricular (sulcal) CSF. To do so, I do segmentation on T1W brain MRI. I would like to use the ground truth data to evaluate the accuracy of this pipeline.

What I need is [u]not[/u] a comparison to other software (e.g. Freesurfer), but instead to check if the pipeline provides accurate and consistent volumetric calculations of these structures. Therefore, I need volumetric results of the ground truth data for each of these structures.

I downloaded the IBSR 2.0 skull-stripped NIFTI, IBSR_V2.0, 20 Normals. When I open these files, I can see the segmentations very well (as attached). However, I cannot find a file that directly gives the volumetric results as cm^3 or number of voxels corresponding to each segmented structure. (e.g. Left ventricle --- cm^3, R WM --- cm^3).

I read the README file and saw that UnZip may cause an artifact. But, I am using "the Unarchiver" for Mac and "7Zip" for Windows. Also, the otl file is empty.

Is there a file that gives the direct volumetric results of these segmented structures? Thank you.

Best,
Merve

RE: Regarding IBSR_V2.0 dataset

Andrew Worth — Thu, 16 May 2019 14:26:51 GMT

Hello,

The "CMA" files like IBSR_01_CMA.tgz are basically useless because they are in a format that is hard to open. That must be why they were deleted.

The ANALYZE files are an old imaging format. See [url=https://en.wikipedia.org/wiki/Analyze_(imaging_software)]https://en.wikipedia.org/wiki/Analyze_(imaging_software)[/url]. This has been superseded by the NIfTI format, see [url=https://nifti.nimh.nih.gov/]https://nifti.nimh.nih.gov/[/url].

There are various applications that can open the ANALYZE format such as MIPAV ([url=https://mipav.cit.nih.gov/]https://mipav.cit.nih.gov/[/url]).

Or you can convert them into NIfTI using:

<span style="white-space: pre;"> nifti_tool -infiles</span><span style="white-space: pre;"> IBSR_01_ana.img -prefix IBSR_01.nii -copy_im</span>

See [url=https://sourceforge.net/projects/niftilib/]https://sourceforge.net/projects/niftilib/[/url].

Andy.
[i]Originally posted by dalvinder kaur:[/i][quote]I have download IBSR_V2.0, which contains 18 subjects of IBSR_01_ANALYZE.tgz and IBSR_01parc_ANALYZE.tgz to IBSR_18_ANALYZE.tgz and IBSR_18parc_ANALYZE.tgz. Each IBSR_01_ANALYZE.tgz folder contains two subfolders that are images and segmentation. But, I am unable to open the disc image files, and also couldn't find where is the corresponding ground truth images of IBSR dataset. Please also provide the information about IBSR_01parc_ANALYZE.tgz folder. I couldn't find IBSR_01_CMA.tgz file that is explained in the readme file.[/quote]

Regarding IBSR_V2.0 dataset

dalvinder kaur — Thu, 16 May 2019 6:44:57 GMT

I have download IBSR_V2.0, which contains 18 subjects of IBSR_01_ANALYZE.tgz and IBSR_01parc_ANALYZE.tgz to IBSR_18_ANALYZE.tgz and IBSR_18parc_ANALYZE.tgz. Each IBSR_01_ANALYZE.tgz folder contains two subfolders that are images and segmentation. But, I am unable to open the disc image files, and also couldn't find where is the corresponding ground truth images of IBSR dataset. Please also provide the information about IBSR_01parc_ANALYZE.tgz folder. I couldn't find IBSR_01_CMA.tgz file that is explained in the readme file.

RE: Welcome to Help

dalvinder kaur — Thu, 16 May 2019 5:30:28 GMT

[i]Originally posted by Hoang Anh Dau:[/i][quote]Hello,

I am a first-year PhD student at RMIT University in Melbourne.

I would like to run some experiments on the images from IBSR.
However, I am having difficulty viewing these images as they are in .img format.
I have sought for help on the website, readme file and the Internet but have not had any luck. Other people seem to not have this problem I guess.
I hope you can help me out.
I am sorry if the question sounds silly. Thank you.

Sincerely,
Anh[/quote]