The length of *dscalar structural data

1

Hi everyone,

I am planing to use .*dscalar data from the dHCP 3rd release.
But when I checked the dimensions of those data from different neonates using the Matlab function “cifti_read”, I found that variable cdata has a different length, such as the following two data.

sub-CC00660XX09_ses-215900_desc-corr_thickness.dscalar.nii
sub-CC00703XX10_ses-206101_desc-corr_thickness.dscalar.nii

And I am aware that all surfaces have already aligned to the template with MSM. I am curious about whether the different data length (the number of vertex) was caused by the fact that different age templates were used during the MSM alignment. If the answer is yes, could I resample (cifti_resampe from workbench) those data to the same number of vertex?

Thank you very much.

Best,
Lin

2

Hi @Bertram,

To my knowledge, the 3rd release dHCP neonatal data is released in native space, which would account for the difference in the number of vertices/length of the cdata variable. We do provide the transforms to get from native to template space ( xfm/sub-{subid}_ses-{sesid}_hemi-{hemi}_from-native_to-dhcpSym40_dens-32k_mode-sphere.surf.gii), and the script to do this is located here: dHCP_template_alignment/align_to_template_3rd_release.sh at master · ecr05/dHCP_template_alignment · GitHub

All the template spaces for the 3rd release cortical surface atlas have the same number of vertices (32,492 per hemisphere).

Best wishes,

Logan

4

Hi Logan,

Thank you very much for answering my questions.
I have checked the scripts you suggested, but I still have some questions on these scripts.

(1) align_to_template_3rd_release.sh (Line 63-68) seems need *rot.surf.gii files that are not provided by the downloaded data.

(2) Regarding rotational_transforms, can I use “rotational_transforms/week40_toFS_LR_rot.%hemi%.txt” for all ages (e.g., 28 weeks, 30 weeks, etc.)

(3) Actually, I found there are no Native folders in downloaded 3rd release data, so files in anat folder are all in the native space, right?

Best wishes,

Lin

5

@lzjwilliams i am kind of new to the dHCP surface analysis.
with the “xfm/sub-{subid}_ses-{sesid}_hemi-{hemi}_from-native_to-dhcpSym40_dens-32k_mode-sphere.surf.gii”, how can I register the cortical thickness in naive space to the template surface space ?
when i use web_command -surface-apply-affine, it gave me error reading the transform file. Any suggestions ? Thank you very much.

Yun

6

Hi @Yun_Wang,

You will need to use wb_command -metric-resample where:

  • metric in is the cortical thickness in native space
  • current sphere is the native to template registered sphere
  • new sphere is the standard 32k sphere
    -metric out is the resampled sphere
  • you should use ADAP_BARY_AREA as the resample method where you need to provide native and template space midthickness surfaces

Best wishes,

Logan

7

Thank you very much! It works perfectly.