About the dimension of labels, T1 and T2 images

[CaelynCheung1996]

Recently I am trying to use the dataset to test my network. However, I found that the size of the images of the hippocampal subfields labels, T1 and T2 images are totally different. How can I overlay the labels on the original atlases if I don't know where exactly the manual segmentation is(I'm not sure from which slice the labels are defined). I am quite bothering with this problem. Hope that someone can explain.

[mallarchak]

Hi Caelyn,

Glad your using out work. To help you further we’re going to need more details. What file format are you working in am which files did you pull down?

Thanks.

Mallar

Sent from my iPhone

On Apr 13, 2018, at 10:21 PM, Caelyn notifications@github.com wrote:

Recently I am trying to use the dataset to test my network. However, I found that the size of the images of the hippocampal subfields labels, T1 and T2 images are totally different. How can I overlay the labels on the original atlases if I don't know where exactly the manual segmentation is(I'm not sure from which slice the labels are defined). I am quite bothering with this problem. Hope that someone can explain.

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[CaelynCheung1996]

Hi,

So first I downloaded the MNC formates atlases of T1,T2 brain and hippocampal subfields label. However, the dimension of all these images are consistent. My work need to use all these images. Today I found a previous answer of the previous issue posted here and it provides the new images of T1 and labels images in NIFTI format and their dimension size match in each patient case, which are what I need exactly. However, the T2 NIFTI format is not available and I just have a original MNC format ones. I tries mant methods but could't find a good way to make the dimension size of T2 set as same as the NIFTI T1 and labels,which rally bothers me for almost a week. Could you please also uploaded the T2 NIFTI format as those provided in the previous issue? That would be a great help for our users. Thanks so much!

[CaelynCheung1996]

@mallarchak Hi,

So first I downloaded the MNC formates atlases of T1,T2 brain and hippocampal subfields label. However, the dimension of all these images are consistent. My work need to use all these images. Today I found a previous answer of the previous issue posted here and it provides the new images of T1 and labels images in NIFTI format and their dimension size match in each patient case, which are what I need exactly. However, the T2 NIFTI format is not available and I just have a original MNC format ones. I tries mant methods but could't find a good way to make the dimension size of T2 set as same as the NIFTI T1 and labels,which rally bothers me for almost a week. Could you please also uploaded the T2 NIFTI format as those provided in the previous issue? That would be a great help for our users. Thanks so much!

[gdevenyi]

Hi,

The standard official releases of all atlases and labels are MINC. These files are all corrected oriented and sized.

If you are having trouble with NIFTI files the first thing to check is with another NIFTI tool. NIFTI has no standardized dimension information so each tool does whatever it wants.

Unofficial NIFTI files are available at: http://cobralab.net/files/atlases-nifti.zip http://cobralab.net/files/brains_t1_nifti.tar.bz2 http://cobralab.net/files/brains_t2_nifti.tar.bz2

[mallarchak]

I would suggest perhaps making the conversion with a tool of choice? I believe ITK-snap will import minc files and support export to nifti. But, again, it's tough to guarantee the behaviour of nifti across software packages as the rules are not consistent (as Gabe mentioned).

mallar

On Mon, Apr 16, 2018 at 10:37 AM, Gabriel A. Devenyi < notifications@github.com> wrote:

Hi,

The standard official releases of all atlases and labels are MINC. These files are all corrected oriented and sized.

If you are having trouble with NIFTI files the first thing to check is with another NIFTI tool. NIFTI has no standardized dimension information so each tool does whatever it wants.

Unofficial NIFTI files are available at: http://cobralab.net/files/atlases-nifti.zip http://cobralab.net/files/brains_t1_nifti.tar.bz2 http://cobralab.net/files/brains_t2_nifti.tar.bz2

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[CaelynCheung1996]

Thanks so much for the detailed answer!

I did use the itk-snap in MacOS and Linux to convert the minc files to nifti ones. However, either minc or nifti shows the same dimension. For example, for case1, the dimension for T1 image is 489734503, while for T2 and hippocampal label are 523631540 and 489734734, which are not consistent with each other. So when I used itk-snap to overlay the labels on T1 and T2, it failed because the coordinate information cannot be detected and they just cannot match with each other because various dimension.

However, when I did this on 3D Slicer as mentioned in the previous post, it works. The point is that I have to make these three minc file into same dimension, probably adding some dark empty slices. However, I was unable to do this because I didn't know from which slice the label was drawn on T1 and what is the corresponding slice for labels in T2 images. The format actually is fine for me and I can work this out. It's the different dimension that bothers me. Conversely, the unofficial nifti files released are all in same dimension, (T1&T2&Label: 489734503), which is a great help for me. So I don't know what caused this problem exactly or if there's any explanation that can help me understand this better.

[mallarchak]

Hi - Not what dimensions you are referring to. ARe the number you are providing the total # of voxels?

mallar

On Tue, Apr 17, 2018 at 1:34 AM, Caelyn notifications@github.com wrote:

Thanks so much for the detailed answer!

I did use the itk-snap in MacOS and Linux to convert the minc files to nifti ones. However, either minc or nifti shows the same dimension. For example, for case1, the dimension for T1 image is 489734503, while for T2 and hippocampal label are 523631540 and 489734734, which are not consistent with each other. So when I used itk-snap to overlay the labels on T1 and T2, it failed because the coordinate information cannot be detected and they just cannot match with each other because various dimension.

However, when I did this on 3D Slicer as mentioned in the previous post, it works. The point is that I have to make these three minc file into same dimension, probably adding some dark empty slices. However, I was unable to do this because I didn't know from which slice the label was drawn on T1 and what is the corresponding slice for labels in T2 images. The format actually is fine for me and I can work this out. It's the different dimension that bothers me. Conversely, the unofficial nifti files released are all in same dimension, (T1&T2&Label: 489734503), which is a great help for me. So I don't know what caused this problem exactly or if there's any explanation that can help me understand this better.

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[CaelynCheung1996]

@mallarchak voxel numbers in each dimension are different with T1, T2 and labels of same case.

[mallarchak]

we're going to try regridding everything to a common size in minc, converting to nifti, and then we'll send this to you shortly.

On Tue, Apr 17, 2018 at 10:27 PM, Caelyn notifications@github.com wrote:

@mallarchak https://github.com/mallarchak voxel numbers in each dimension are different with T1, T2 and labels of same case.

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[CaelynCheung1996]

Thanks so much. I think this would be a great help to us researchers working on imaging processing task instead of that we need to do the registration and revamping based on different method.

On Wed, Apr 18, 2018 at 10:44 PM mallarchak notifications@github.com wrote:

we're going to try regridding everything to a common size in minc, converting to nifti, and then we'll send this to you shortly.

On Tue, Apr 17, 2018 at 10:27 PM, Caelyn notifications@github.com wrote:

@mallarchak https://github.com/mallarchak voxel numbers in each dimension are different with T1, T2 and labels of same case.

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Xiaohui Zhang Junior Student Beihang University, Department of Biomedical Engineering No.37 Xueyuan Road Haidian, Beijing, China Phone: +86 13020023358 Email: caelyncheung1996@gmail.com

[gdevenyi]

https://www.dropbox.com/s/5ny2jopbtdi5vsz/test.zip?dl=0

[mallarchak]

This is after regridding?

On Fri, Apr 20, 2018 at 10:54 AM, Gabriel A. Devenyi < notifications@github.com> wrote:

https://www.dropbox.com/s/5ny2jopbtdi5vsz/test.zip?dl=0

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[gdevenyi]

The T2 niftis are resampled to be like the T1.

[mallarchak]

thanks!

On Fri, Apr 20, 2018 at 10:57 AM, Gabriel A. Devenyi < notifications@github.com> wrote:

The T2 niftis are resampled to be like the T1.

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[CaelynCheung1996]

So now the T1, T2 and labels are in same size?

On Fri, Apr 20, 2018 at 10:59 PM mallarchak notifications@github.com wrote:

thanks!

On Fri, Apr 20, 2018 at 10:57 AM, Gabriel A. Devenyi < notifications@github.com> wrote:

The T2 niftis are resampled to be like the T1.

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Xiaohui Zhang Junior Student Beihang University, Department of Biomedical Engineering No.37 Xueyuan Road Haidian, Beijing, China Phone: +86 13020023358 Email: caelyncheung1996@gmail.com

[mallarchak]

yes.

On Fri, Apr 20, 2018 at 11:00 AM, Caelyn notifications@github.com wrote:

So now the T1, T2 and labels are in same size?

On Fri, Apr 20, 2018 at 10:59 PM mallarchak notifications@github.com wrote:

thanks!

On Fri, Apr 20, 2018 at 10:57 AM, Gabriel A. Devenyi < notifications@github.com> wrote:

The T2 niftis are resampled to be like the T1.

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