Hi Jay,
To add to Donna's comments, did you also download the structural
preprocessed (not extended) package for the subjects you are interested in?
The structural extended package only has FreeSurfer outputs that are
intermediates from the HCP structural pipeline. If you have data from both
of the packages, it works (I just tried it) to open both these files in
Workbench and setup the first as an underlay and the second as the overlay:
{Subject_ID}/T1w/{Subject_ID}/mri/T1w_hires.nii.gz
{Subject_ID}/T1w/aparc.a2009s+aseg.nii.gz
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
[email protected]
www.humanconnectome.org
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of
[email protected]
Sent: Thursday, September 17, 2015 10:33 AM
To: Jihoon Choi
Cc: [email protected]
Subject: Re: [HCP-Users] Obtaining hires version of aparc.a2009s+aseg.mgz
Hi Jay,
You might not have this file/package, but it looks to me like there is a
file of the same voxel dimensions, etc. as the T1w_hires.nii.gz:
Structural_preproc/T1w/991267/mri/aparc.a2009s+aseg.mgz
wb_command -nifti-information -print-header
Structural_preproc/T1w/aparc.a2009s+aseg.nii.gz
native endian: true
sizeof_hdr: 348
magic: n+1
datatype: 16
bitpix: 32
dim[0]: 3
dim[1]: 260
dim[2]: 311
dim[3]: 260
pixdim[0]: -1
pixdim[1]: 0.7
pixdim[2]: 0.7
pixdim[3]: 0.7
vox_offset: 25376
scl_slope: 1
scl_inter: 0
sform_code: 1
srow_x: -0.7 0 0 90
srow_y: 0 0.7 0 -126
srow_z: 0 0 0.7 -72
qform_code: 1
quatern_b: 0
quatern_c: 1
quatern_d: 0
qoffset_x: 90
qoffset_y: -126
qoffset_z: -72
xyzt_units: 10
intent_code: 0
intent_name:
1 extension:
If you don't want to download that package, you might be able to grab just
that file via XNAT.
If you just want to view the parcellation as an overlay, though, you can
already do so without resampling the parcellation, e.g.:
tkmedit -f T1w_hires.nii.gz -aparc+aseg
(assuming you have freesurfer installed)
If you want to use aparc.a2009s+aseg.mgz, then you need software that reads
mgz (e.g., freesurfer, 3D Slicer). But there are also NIFTI versions of the
parcellation that will work with viewers like AFNI, fslview, and wb_view.
Generally these don't require the overlay and underlay to be in the same
grid (e.g., structural underlay may be higher res than functional overlay).
Provided the headers are good, they view fine together.
Donna
> Dear HCP team,
>
> We are currently using the S500 preprocessed extended dataset and we
> were wondering if we can obtain a hires version of
'aparc.a2009s+aseg.nii.gz'
> file (So that it would have compatible overlay with 'T1_hires.nii.gz').
> Are there any methods (ex. Freesurfer commands) that you could suggest
> for us?
>
> Thank you,
>
> Jay
>
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