One further thought on this. Apparently the ANALYZE 7.5 format does not
define the scl_slope and scl_intercept values; these apparently were first
used by SPM and became part of the NIFTI definition. Perhaps when fsl
utils are using *.hdr/*.img files defined as ANALYZE files, it ignores
these. I have found the fslmaths will use the scl_slope and scl_intercept
if the file is a nii.gz file.
Is this the reason?
John
On 1/16/13 7:15 PM, "RICHARDS, JOHN" <[log in to unmask]> wrote:
>I have ANALYZE MRI volumes from CURRY that have current density, which are
>values < 1. The HDR has "calibration scaling" set. When I use fslhd, or
>fslmaths, or fslmerge, with these files, it appears to not read the
>calibration scaling. ANALYZE/NIFTII has a calibration intercept and
>scale that is supposed to be applied to the store values. MRICRON reads
>these files correctly, shows the calibration scaling, and has voxel values
>with the scaling. If I use:
>
>Fslmaths inputfile.hdr -add 0 outputfile.nii.gz, then the scaling factor
>is not read; the fslstats -M reports a value that appears to be about
>x*scale, and when I view this in MRICron the individual voxels in the
>input file, * scale, are what are shown in the output file.
>
>So it appears the fsl utils are not reading the calibration scale.
>
>Any help?
>
>John
>
>***********************************************
>John E. Richards
>Carolina Distinguished Professor
>Department of Psychology
>University of South Carolina
>Columbia, SC 29208
>Dept Phone: 803 777 2079
>Fax: 803 777 9558
>Email: [log in to unmask]
><applewebdata:[log in to unmask]>
>HTTP: jerlab.psych.sc.edu
>*************************************************
>
>
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