How do I use SCT on the separated sagittal/axial/coronal sections generated by `dcm2bids`?

alialvi92 · February 12, 2024, 10:36pm

Hello @jcohenadad and @joshuacwnewton , thank you for responses above. I am a beginner myself. I have a similar question and I realize that this may be too basic. I used dcm2bids converter to convert my dicom files to nifti format with BIDS sidecars. This is what the “ls” of my target output directory for an example MRI looks like:

Directory: E:\Alvi\Thesis\tmp_dcm2bids\helper

Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a----        2024-02-12   3:46 PM            911 002_TOH1002_COR_LOC.json
-a----        2024-02-12   3:46 PM        1493545 002_TOH1002_COR_LOC.nii.gz
-a----        2024-02-12   3:46 PM           1001 003_TOH1002_SAG_T2_FSE_16_PSAT.json
-a----        2024-02-12   3:46 PM        3736351 003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz
-a----        2024-02-12   3:46 PM            973 004_TOH1002_SAG_T1_FSE_2_PSAT.json
-a----        2024-02-12   3:46 PM        3784015 004_TOH1002_SAG_T1_FSE_2_PSAT.nii.gz
-a----        2024-02-12   3:46 PM            995 005_TOH1002_AXIAL_T2_FST_VOL_MTC_PSAT.json
-a----        2024-02-12   3:46 PM        6321888 005_TOH1002_AXIAL_T2_FST_VOL_MTC_PSAT.nii.gz
-a----        2024-02-12   3:46 PM            939 006_TOH1002_AXIAL_T2_FSE_16.json
-a----        2024-02-12   3:46 PM        1893630 006_TOH1002_AXIAL_T2_FSE_16.nii.gz

As you can, see converting the whole DICOM folder to NIFTI generates these individual sequences. How can I use these files to then input into sct_deepseg_sc?

Again, I apologize if this is too basic or if this is not the right place to ask this?

joshuacwnewton · February 12, 2024, 10:37pm

Hi @alialvi92,

I am just going to move your message into a separate forum post (to help make the forum more searchable for future readers). Then I will answer your message.

alialvi92 · February 12, 2024, 10:38pm

Sounds good, thank you so much and again, apologies for the inconvenience!

joshuacwnewton · February 12, 2024, 10:53pm

Hi @alialvi92,

For basic usage of sct_deepseg_sc, you can find a tutorial for spinal cord segmentation here: Segmentation - Spinal Cord Toolbox documentation

The hands-on portion of the tutorial is here: Hands-on: Using sct_deepseg_sc on T2 data - Spinal Cord Toolbox documentation

If you want to run sct_deepseg_sc many times (e.g. multiple scans/contrasts per subject, and multiple subjects in a dataset), then we recommend using sct_run_batch. We have a tutorial for this here: Analysis pipelines with SCT - Spinal Cord Toolbox documentation

Please let me know if you have any further questions or concerns.

Kind regards,
Joshua

alialvi92 · February 12, 2024, 11:01pm

Thanks @joshuacwnewton , yes I have been through the tutorials for both sct_deepseg_sc as well as sct_run_batch. I guess my main concern is the difference in nifti files that I am looking at vs what we see in the hands-on section for sct_deepseg_sc. When I open the t2.nii.gz in MRIcroGL for instance, I can see all the 3 views since its a 3D MRI. However, when I am using my own files and converting the entire DICOM MRI to nifti using dcm2bids, I am only able to generate the axial and sagittal and coronal sections as separate nii.gz files. So I am able to open ONLY ONE OF THE SEQUENCES at a time in MRIcroGL.
So I am not sure how to use sct_deepseg_sc for these files? Is there a way I can manually generate a 3D MRI nii.gz from these files?

joshuacwnewton · February 12, 2024, 11:08pm

Ahh, thank you so much for the additional explanation. Your question is much clearer now.

Personally, I am not too familiar with the dcm2bids conversion process. (I have personally used dcm2niix only a few times, and I haven’t come across separated output such as this.) So, I will ask my colleagues to see if they have any insight into how to approach your situation.

Kind regards,
Joshua

alialvi92 · February 12, 2024, 11:11pm

Perfect, thanks so much! If this helps your colleagues, the MRIs that I am using are pretty old, early 2010s late 2000s, not sure if that matters but just wanted to mention that. Thanks again!

valosekj · February 13, 2024, 12:39pm

Hello @alialvi92!

Yes, this is expected. You can also notice that the example t2.nii.gz image has the same resolution in all three planes (axial, sagittal, coronal). This is because the image is a so-called isotropic scan, meaning that voxels have the same size in all three planes. In this case, it is 0.8 x 0.8 x 0.8 mm. You can verify this by running sct_image and looking for tag pixdim:

sct_image -i t2.nii.gz -header
...
pixdim		[1.0, 0.8, 0.8, 0.8, 1.5, 0.0, 0.0, 0.0]
...

At the same time, sct_image can be used to show the number of slices for individual planes (axial, sagittal, coronal); see tag dim:

sct_image -i t2.nii.gz -header
...
dim		[3, 64, 320, 320, 1, 0, 0, 0]
...

You can notice that the t2.nii.gz image has 64, 320, and 320 slices making it “3D”.

Can you please run the sct_image command for your images to see their pixdim and dim? For example sct_image -i 003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz -header.

Thank you!
Jan

alialvi92 · February 13, 2024, 2:46pm

Thank you so much @valosekj for taking the time to explain.

sct_image -i 003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz -header

–

dim [3, 512, 512, 12, 1, 1, 1, 1]

pixdim [-1.0, 0.429688, 0.429688, 3.5, 3.5, 0.0, 0.0, 0.0]

I also ran it for the axial scan
sct_image -i 003_TOH1002_AXIAL_T2_FSE_16.nii.gz -header

dim [3, 256, 256, 32, 1, 1, 1, 1]

pixdim [-1.0, 0.78125, 0.78125, 3.500037, 6.0, 0.0, 0.0, 0.0]

What would you recommend? Thanks again!

valosekj · February 13, 2024, 2:58pm

Thank you for the provided details @alialvi92!

Based on the sct_image output, both your images seem to be 3D:

003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz has dimensions 512 x 512 x 12.
003_TOH1002_AXIAL_T2_FSE_16.nii.gz has dimensions 256 x 256 x 32.

So, you should be able to run sct_deepseg_sc using the following commands (one command for each image):

sct_deepseg_sc -i 003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz -c t2
sct_deepseg_sc -i 003_TOH1002_AXIAL_T2_FSE_16.nii.gz -c t2

jcohenadad · February 13, 2024, 3:18pm

Also please note that segmenting the spinal cord on sagittal slices of 3.5mm is not optimal. I recommend to either run the segmentation on axial scans, or on scans with ‘good’ isotropic resolution (eg. 1mm iso)

alialvi92 · February 13, 2024, 3:30pm

Thank you so much @valosekj and @jcohenadad . I was able to run sct_deepseg_sc on both of them separately. My concern is that how reliable would be, for instance, something like measuring CSA across different levels? I remember from the course videos from Dec 2023 that proper segmentation is critical for obtaining accurate CSA values.
I have attached the FSL eyes output as well as the QC report for both sagittal and axial image. I am aware that I can manually correct the segmentation on FSL eyes but given that I will be doing for sagittal and axial separately, would this be appropriate and would it generate reliable quantitative metrics like CSA?

valosekj · February 13, 2024, 3:52pm

Great!

As mentioned by @jcohenadad, the sagittal sequence (003_TOH1002_SAG_T2_FSE_16_PSAT.nii.gz) with highly anisotropic sagittal slices (0.429688 x 0.429688 x 3.5) is suboptimal for computing CSA. Therefore, I would go with the axial sequence (003_TOH1002_AXIAL_T2_FSE_16.nii.gz) to measure CSA.

PS: based on the provided screenshots, I can see you work with a compressed cord. Note that in SCT v6.2 (which will be released in the following days), we will release a new model (sct_deepseg -task seg_sc_lesion_t2w_sci), which might work even in highly compressed cords. Thus potentially minimizing the amount of manual corrections. More details about this new model can be found in this preprint.

alialvi92 · February 13, 2024, 3:57pm

Oh that is fantastic! Thanks so much. @valosekj , so looking forward to this release! Kudos to all of you!
Alvi