# Neonatal WM atlas
**URL:** https://community.mrtrix.org/t/neonatal-wm-atlas/3244
**Category:** Uncategorized
**Created:** [January 28, 2020, 9:18am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244 "2020-01-28T09:18:46Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 28, 2020, 9:18am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/1 "2020-01-28T09:18:46Z")
I would like to define ROIs of WM tracts in a neonatal image of brain. I have 3dT1 and DKI scan. I should use 3dT1 as an anatomical reference. Do you suggest any existing neonatal atlas to do so?
thank you.
Here you find attached my data
[https://onedrive.live.com/?id=B0C0561E34E9D76F!613&cid=B0C0561E34E9D76F](https://onedrive.live.com/?id=B0C0561E34E9D76F%21613&cid=B0C0561E34E9D76F)
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 28, 2020, 12:23pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/2 "2020-01-28T12:23:59Z")
Hi,
There are two neonatal parcellations of WM that I’m aware:
> **[Multi-contrast human neonatal brain atlas: Application to normal neonate...](https://www.sciencedirect.com/science/article/abs/pii/S1053811911000875?via=ihub)**
>
> MRI is a sensitive method for detecting subtle anatomic abnormalities in the neonatal brain. To optimize the usefulness for neonatal and pediatric car…
This one contains: T2w,T1w and FA and can be found here:
[http://cmrm.med.jhmi.edu/cmrm/Data\_neonate\_atlas/atlas\_neonate.htm](http://cmrm.med.jhmi.edu/cmrm/Data_neonate_atlas/atlas_neonate.htm)
And the second one is based on the M-CRIB atlas, but I don’t know if it is available:
> **[White Matter Extension of the Melbourne Children’s Regional Infant Brain...](https://www.biorxiv.org/content/10.1101/590596v1)**
>
> Background Understanding typically developing infant brain structure is crucial in investigating neurological disorders of early childhood. Brain atlases providing standardised identification of neonatal brain regions are key in such investigations....
The rest of the atlas I’m aware of, don’t have WM parcellation to use without T2w. I hope this helps.
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 28, 2020, 1:47pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/3 "2020-01-28T13:47:57Z")
Thank you. Do you just know how to open .dat file ?
thank you
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 28, 2020, 2:02pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/4 "2020-01-28T14:02:15Z")
Hi,
I don’t know that format, I think is an extension to be used in their own software. In the past I used with the analyze version.
Best regards,
Manuel
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### Author:  [@jdtournier](https://community.mrtrix.org/u/jdtournier)
#### Post date: [January 29, 2020, 10:02am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/6 "2020-01-29T10:02:22Z")
I think this might help:
[https://www.nitrc.org/forum/forum.php?thread\_id=2118&forum\_id=2](https://www.nitrc.org/forum/forum.php?thread_id=2118&forum_id=2)
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 29, 2020, 10:03am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/7 "2020-01-29T10:03:40Z")
yes,
thank you I have just seen that post.
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 29, 2020, 10:23am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/8 "2020-01-29T10:23:28Z")
Hi @ros,
I am curious about this, is there any difference if you convert the .dat to nifti or the analyze to nifti? Are the same images?
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 29, 2020, 10:26am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/9 "2020-01-29T10:26:05Z")
I think they are the same images! However, some images are there just in .dat format as far as I can see.
Rosella
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 30, 2020, 9:27am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/10 "2020-01-30T09:27:14Z")
Hi. Do you know if JHU neonate atlas is integrated with FSL?
thanks
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 30, 2020, 9:51am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/11 "2020-01-30T09:51:47Z")
Hi,
> Do you know if JHU neonate atlas is integrated with FSL?
I don’t think so, I think they have the adult atlas only.
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 30, 2020, 10:02am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/12 "2020-01-30T10:02:21Z")
Ok because I would need to calculate some DTI metrics over each of the 122 ROis contained in the atlas parcellation , but I have to find a quick way to extract each ROI separately and use it as a mask .
thanks,
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 30, 2020, 10:41am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/13 "2020-01-30T10:41:39Z")
Hi,
You could do that from the command line, for example for the label 2:
> fslmaths ID\_LABELS\_B0space.nii.gz -thr 2 -uthr 2 -bin ID\_label\_2.nii.gz
> fslstats ID\_FA.nii.gz -k ID\_label\_2.nii.gz -m
or with mrtrix:
> mrstats -output mean -mask ID\_label\_2.nii.gz ID\_FA.nii.gz
Then you just need to do it in a for loop (this is how I do it). I hope this helps.
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 30, 2020, 10:43am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/14 "2020-01-30T10:43:13Z")
Yes, for your atlas this is ok and I use it too but for the JHU atlas I do not have separate image corresponding to each ROI.
Thanks
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 30, 2020, 10:51am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/15 "2020-01-30T10:51:21Z")
HI,
The firs command I wrote, generates an independent image for each ROI (you just need to replace the 2 for the ID of the other ROIs).
> fslmaths ID\_LABELS\_B0space.nii.gz -thr 2 -uthr 2 -bin ID\_label\_2.nii.gz
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 30, 2020, 11:03am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/16 "2020-01-30T11:03:31Z")
Ah ok thank you! And ID\_label\_B0\_space.nii.gz is the parcellation map image, isn’t it?
many thanks
Rosella
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 30, 2020, 11:17am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/17 "2020-01-30T11:17:28Z")
Hi,
Yes, registered to your diffusion image.
Best regards,
Manuel
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [January 30, 2020, 2:26pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/18 "2020-01-30T14:26:30Z")
Thank you very much!
Rosella
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### Author:  [@ros](https://community.mrtrix.org/u/ros)
#### Post date: [February 19, 2020, 1:43pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/19 "2020-02-19T13:43:52Z")
Because I have found a .hdr file in the neonate atlas page
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### Author:  [@tuwanhanjing](https://community.mrtrix.org/u/tuwanhanjing)
#### Post date: [December 24, 2024, 11:38pm UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/20 "2024-12-24T23:38:27Z")
Hi,
I am currently working on neonatal image registration using the JHU\_neonate\_SS atlas. Could you please share it with me? I am unable to access the download website: [http://cmrm.med.jhmi.edu/cmrm/Data\_neonate\_atlas/atlas\_neonate.htm](http://cmrm.med.jhmi.edu/cmrm/Data_neonate_atlas/atlas_neonate.htm)
Thank you!
Best regards,
Hanjing
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### Author:  [@mblesac](https://community.mrtrix.org/u/mblesac)
#### Post date: [January 6, 2025, 9:52am UTC](https://community.mrtrix.org/t/neonatal-wm-atlas/3244/21 "2025-01-06T09:52:55Z")
Hi,
You are right, the link doesn’t seem to work. However, the authors have a new tool that they recommend to use (still beta version and being tested):
> **[GitHub - OishiLab/OpenMAP-Di: DTI Infant Brain Parcellation Using OpenMAP-Di](https://github.com/OishiLab/OpenMAP-Di)**
>
> DTI Infant Brain Parcellation Using OpenMAP-Di
The main method for adult brain is published [here](https://pmc.ncbi.nlm.nih.gov/articles/PMC11551626/)
If you still want the atlas, I should have it in my computer from previous experiments, please drop me an email ([manuel.blesa@ed.ac.uk](mailto:manuel.blesa@ed.ac.uk)) and I’ll send it to you.
Best regards,
Manuel
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