Dhcp structural pipeline measure docker only T2

1

Hello,

I am trying to use the dhcp docker for the pipeline measures but I am not sure if it will work with only T2 images. I do not have enough usable T1 images for this data set. When I run it I get ‘no T1 for session-1’. Thanks!

Best,
Alex

2

Hi @ajdneuro,

Yes, you can run the structural pipeline without T1 images. However, this means you won’t get myelin maps for your subjects (T1w/T2w ratio). What command are you using for the structural pipeline?

Best wishes,

Logan

3

Hi Logan,

Thanks! I ran the pipeline, just the script (docked) for calculating the measures is not working without the T1s.

Best,
Alex

4

Hi Alex,

If you are using the command as per the BioMedIA GitHub here:

$ docker run --rm -t \
    -u $(id -u):$(id -g) \
    -v $PWD/data:/data \
    biomedia/dhcp-structural-pipeline:latest subject1 session1 44 \
            -T1 data/T1w.nii.gz -T2 data/T2w.nii.gz -t 8

You just need to remove the -T1 flag. Let me know if that doesn’t work :slight_smile:

Logan

5

Sorry I mean these scripts:

6

At what point in the pipeline are you getting this error?

7

When I run the docker image and point it to the derivates it gives this error:
pa0639 no T1 for session session-1

9

Hi Logan,

I am using only T2-w image using the following command:

docker run --rm -t
-u (id -u):(id -g)
-v $PWD/data:/data
biomedia/dhcp-structural-pipeline:latest sub-NYS1553 ses-001 43
-T2 data/sub-NYS1553_ses-001_T2w.nii.gz -t 8

but I am getting Surface, Segmentation and additional errors.
I have attached the log and error files.

sub-NYS1553-ses-001.additional_log.txt (3.6 KB)
sub-NYS1553-ses-001.segmentation_err.txt (12.2 KB)
sub-NYS1553-ses-001.segmentation_log.txt (120.7 KB)
sub-NYS1553-ses-001.surface_err.txt (2.6 KB)
sub-NYS1553-ses-001.surface_log.txt (1.2 KB)

Your help is highly appreciated,
Parinaz.