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  

Previous Message Next Message
Message List New Topic Print View
|
maitra
February 06, 2018 04:48PM
Hi,

I am a statistician: please pardon the naivette in asking this question but I am trying to use AFNI to massage my functional data in anatomic space.

I have an anatomic mask in registered space of the following dimensions, according to 3dinfo: 

$ 3dinfo highres001_brain_mask.nii.gz 
++ 3dinfo: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]

Dataset File:    highres001_brain_mask.nii.gz
Identifier Code: NII_leRqPU-x38xngCWArCInPg  Creation Date: Tue Feb  6 15:42:38 2018
Template Space:  ORIG
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   21,233,664 (21 million [mega]) bytes
Geometry String: "MATRIX(1.2,0,-4.44089e-16,-87.57317,1.110223e-16,-1.197917,1.785035e-08,86.66275,2.220446e-16,-4.15611e-18,1.197917,-113.6052):144,192,192"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Right-to-Left
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient RPI]
R-to-L extent:   -87.573 [R] -to-    84.027 [L] -step-     1.200 mm [144 voxels]
A-to-P extent:  -142.139 [A] -to-    86.663 [P] -step-     1.198 mm [192 voxels]
I-to-S extent:  -113.605  -to-   115.197 [S] -step-     1.198 mm [192 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float



I would like to use the mask on the functional image which has the following dimensions: 

$ 3dinfo  bold.nii.gz 
++ 3dinfo: AFNI version=AFNI_16.2.18 (Sep 19 2016) [64-bit]
*+ WARNING: NO spatial transform (neither qform nor sform), in NIfTI file 'bold.nii.gz'

Dataset File:    bold.nii.gz
Identifier Code: NII_JyK_cBH0zg63lAZEiCCJPw  Creation Date: Tue Feb  6 15:43:46 2018
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   66,811,392 (67 million [mega]) bytes
Geometry String: "MATRIX(1,0,0,0,0,1,0,0,0,0,1,0):72,72,36"
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:   -71.000 [R] -to-     0.000     -step-     1.000 mm [ 72 voxels]
A-to-P extent:   -71.000 [A] -to-     0.000     -step-     1.000 mm [ 72 voxels]
I-to-S extent:     0.000     -to-    35.000 [S] -step-     1.000 mm [ 36 voxels]
Number of time steps = 358  Time step = 1.00000s  Origin = 0.00000s
  -- At sub-brick #0 '?' datum type is byte
  -- At sub-brick #1 '?' datum type is byte
  -- At sub-brick #2 '?' datum type is byte
** For info on all 358 sub-bricks, use '3dinfo -verb' **

Is there a way to essentially refit the mask to match the dimensions in the BOLD space?

Feel free to let me know if my question is unclear.

Many thanks again for any help, and best wishes,
Ranjan
Reply Quote
RSS
Subject Author Posted

extract mask for BOLD images from anatomic image mask

maitra February 06, 2018 04:48PM

Re: extract mask for BOLD images from anatomic image mask

Daniel Glen February 06, 2018 06:02PM

Re: extract mask for BOLD images from anatomic image mask

RWCox February 06, 2018 09:51PM

Re: extract mask for BOLD images from anatomic image mask

maitra February 07, 2018 01:43PM

Re: extract mask for BOLD images from anatomic image mask

Bob Cox February 07, 2018 02:02PM

Re: extract mask for BOLD images from anatomic image mask

maitra February 07, 2018 04:56PM

Re: extract mask for BOLD images from anatomic image mask

Daniel Glen February 07, 2018 05:04PM