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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May 07, 2015 08:00AM
I have created a nifti file in my own fMRI program. If I look at it with 3dinfo it says that there are 160 volumes. If I look at it with fslinfo it says that there is only one volume. How do I change the nifti header such that AFNI understands that there is only one volume?

This is what I have changed so far

nifti_image *outputNiftiStatisticsEPI = nifti_copy_nim_info(inputfMRI);
outputNiftiStatisticsEPI->nt = 1;
outputNiftiStatisticsEPI->dim[4] = 1;
outputNiftiStatisticsEPI->nvox = EPI_DATA_W * EPI_DATA_H * EPI_DATA_D;





3dinfo bold_pvalues_contrast1_EPI.nii.gz
++ 3dinfo: AFNI version=AFNI_2011_12_21_1014 (Aug 13 2014) [64-bit]

** WARNING: NIfTI file bold_pvalues_contrast1_EPI.nii.gz dimensions altered since AFNI extension was added

Dataset File: bold_pvalues_contrast1_EPI.nii.gz
Identifier Code: NII__wFvfILlbwjznQCEILpaJQ Creation Date: Wed Apr 29 14:38:11 2015
Template Space: TLRC
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 540,672 (541 thousand [kilo]) bytes
Geometry String: "MATRIX(-3.125,0,0,0,0,-3.125,0,0,0,0,4,0):64,64,33"
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: -196.875 [R] -to- 0.000 -step- 3.125 mm [ 64 voxels]
A-to-P extent: -196.875 [A] -to- 0.000 -step- 3.125 mm [ 64 voxels]
I-to-S extent: 0.000 -to- 128.000 [S] -step- 4.000 mm [ 33 voxels]
Number of time steps = 160 Time step = 2.00000s Origin = 0.00000s
-- At sub-brick #0 '?' datum type is float: 0 to 1127


fslinfo bold_pvalues_contrast1_EPI.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 33
dim4 1
datatype 16
pixdim1 3.125000
pixdim2 3.125000
pixdim3 4.000000
pixdim4 2.000000
cal_max 1.0000
cal_min 0.0000
file_type NIFTI-1+
Subject Author Posted

Different header information in FSL and AFNI

kickan May 07, 2015 08:00AM

Re: Different header information in FSL and AFNI

rick reynolds May 07, 2015 08:25AM

Re: Different header information in FSL and AFNI

kickan May 07, 2015 08:38AM

Re: Different header information in FSL and AFNI

rick reynolds May 07, 2015 08:51AM

Re: Different header information in FSL and AFNI

kickan May 07, 2015 08:55AM