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  

|
July 09, 2009 12:12PM
Hi,

An AFNI 3d volume of brain data appears correct when viewed in the AFNI window.
But 3dcalc with the volume as input states that every voxel contains a bad float.
And float_scan on the volume reports that every voxel contains an infinite value.
The same tests using an older (2007) version of AFNI did not detect any bad floats.
What could be the reasons?

Here are the errors:
float_scan dataset+orig.BRIK
+++ Found 360448 Infinite values in dataset+orig.BRIK
3dcalc -prefix dataset_3dcalc_a -a dataset+orig -expr "a"
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Jul 9 2009) [32-bit]
++ Authored by: A cast of thousands
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./dataset+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./dataset+orig.BRIK is 27.210194 degrees from plumb.
*+ WARNING: 360448 bad floats replaced by 0 in sub-brick 0

++ Output dataset ./dataset_3dcalc_a+orig.BRIK


Here is the info on the brain volume
3dinfo dataset
++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Jul 9 2009) [32-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./dataset+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./dataset+orig.BRIK is 27.210194 degrees from plumb.

Dataset File: dataset+orig
Identifier Code: XYZ_euu1jADSktkczus4lKI9vQ Creation Date: Thu Jul 9 10:03:47 2009
Dataset Type: Intensity (-fim)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 1441792 (1.4 million) bytes
Geometry String: "MATRIX(1.7188,0,0,-106.214,0,0.785932,1.77867,-35.0446,0,-1.528589,0.914512,114.972):128,128,22"
Data Axes Tilt: Oblique (27.210 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Superior-to-Inferior
third (z) = Anterior-to-Posterior [-orient RSA]
R-to-L extent: -106.214 [R] -to- 112.074 [L] -step- 1.719 mm [128 voxels]
A-to-P extent: -35.045 [A] -to- 2.306 [P] -step- 1.779 mm [ 22 voxels]
I-to-S extent: -103.316 -to- 114.972 [S] -step- 1.719 mm [128 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is float: 0 to 1


Thank you,
Kathleen

Subject Author Posted

float_scan

Kathleen Hansen July 09, 2009 12:12PM

Re: float_scan

rick reynolds July 09, 2009 01:09PM

Re: float_scan

Kathleen Hansen July 09, 2009 02:00PM

Re: float_scan

rick reynolds July 09, 2009 04:26PM

Re: float_scan

Kathleen Hansen July 10, 2009 09:44AM

Re: float_scan

rick reynolds July 10, 2009 09:47AM

Re: float_scan

Kathleen Hansen July 10, 2009 09:48AM

Re: float_scan

rick reynolds July 10, 2009 10:00AM

Re: float_scan

Kathleen Hansen July 10, 2009 10:10AM

Re: float_scan

rick reynolds July 10, 2009 02:16PM

Re: float_scan

rick reynolds July 10, 2009 07:04PM