AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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November 01, 2019 04:47PM
I'm trying to convert a ROI mask i've downloaded to MNI space but am having a lot of difficulty.

The file is an .hdr file and this is the output from 3dinfo:

Dataset File: superior_temporal_sulcus_posterior_branch_R.img
Identifier Code: ANZ_Y-maODBW7WtxIxcckBBIGA Creation Date: Fri Nov 1 16:43:40 2019
Template Space:
Dataset Type: MRI Anatomy (-anat)
Byte Order: MSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: ANALYZE
Storage Space: 4,145,776 (4.1 million) bytes
Geometry String: "MATRIX(-1,0,0,-0.5,0,-1,0,-0.5,0,0,1.,0.5):149,188,148"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -148.500 [R] -to- -0.500 [R] -step- 1.000 mm [149 voxels]
A-to-P extent: -187.500 [A] -to- -0.500 [A] -step- 1.000 mm [188 voxels]
I-to-S extent: 0.500 [S] -to- 147.500 [S] -step- 1.000 mm [148 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is byte

As you can see there is no template space. My question is how can I get this into MNI space correctly?

I have tried converting into .nii.gz using `3dcalc -a file.hdr -expr 'a' -prefix R_STS.nii.gz`

This then gives me a .nii file in ORIG space:

Dataset File: R_STS.nii.gz
Identifier Code: AFN_au7mMHyj7hD_rjS04Yhxag Creation Date: Fri Nov 1 16:37:40 2019
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 4,145,776 (4.1 million) bytes
Geometry String: "MATRIX(-1,0,0,-0.5,0,-1,0,-0.5,0,0,1.,0.5):149,188,148"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -148.500 [R] -to- -0.500 [R] -step- 1.000 mm [149 voxels]
A-to-P extent: -187.500 [A] -to- -0.500 [A] -step- 1.000 mm [188 voxels]
I-to-S extent: 0.500 [S] -to- 147.500 [S] -step- 1.000 mm [148 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is byte: 0 to 255

How can I then transform this into MNI? I have tried using 3dfractionalize to no avail.

Thanks for your help!
Subject Author Posted

converting 'No template space' .hdr to MNI .nii

bb2958 November 01, 2019 04:47PM

Re: converting 'No template space' .hdr to MNI .nii

Daniel Glen November 05, 2019 03:06PM

Re: converting 'No template space' .hdr to MNI .nii

ptaylor November 07, 2019 09:28AM