range of nifti volumes

[pbellec]

I just downloaded the nifti volume from the "MCI" query, and the range is weird (max is something like 50000). I may not understand what this map represents, but I thought it was a simple average of binary volumes (full of spheres). Is the range right ? Is so, what does it represent ?

[r03ert0]

what are you using to read the .nii files?
the .nii maps are the sum of locations mapping each voxel.
I downloaded the one for MCI, which was made out of 63 articles, and the
maximum was 74 (remember that there are sometimes >1 experiment per
article). For Alzheimer, the max I get 140.

On Mon, Oct 20, 2014 at 9:45 PM, Pierre Bellec notifications@github.com
wrote:

I just downloaded the nifti volume from the "MCI" query, and the range is
weird (max is something like 50000). I may not understand what this map
represents, but I thought it was a simple average of binary volumes (full
of spheres). Is the range right ? Is so, what does it represent ?

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Reply to this email directly or view it on GitHub
#2.

[pbellec]

I use MRIcron. The max gets set at around 50000.

Pierre Bellec
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
Telephone (1) 514 713 5596
SIMEXP lab http://simexp-lab.org

On Mon, Oct 20, 2014 at 4:43 PM, Roberto Toro notifications@github.com
wrote:

what are you using to read the .nii files?
the .nii maps are the sum of locations mapping each voxel.
I downloaded the one for MCI, which was made out of 63 articles, and the
maximum was 74 (remember that there are sometimes >1 experiment per
article). For Alzheimer, the max I get 140.

On Mon, Oct 20, 2014 at 9:45 PM, Pierre Bellec notifications@github.com
wrote:

I just downloaded the nifti volume from the "MCI" query, and the range
is
weird (max is something like 50000). I may not understand what this map
represents, but I thought it was a simple average of binary volumes
(full
of spheres). Is the range right ? Is so, what does it represent ?

—
Reply to this email directly or view it on GitHub
#2.

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https://github.com/r03ert0/brainspell/issues/2#issuecomment-59836399.[image:
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[r03ert0]

Hmm. I just checked with MRIcron, and the max was at 54979.109, which I
thought was curious because the volume is encoded using shorts (int16
integers) and values can't have decimals. I found that MRICron is changing
the 'slope' value for the image intensity to 3118 (I didn't find how to
change it). It would be possible that brainspell is writing a bogus slope.
To rule out that out, I used fslhd to print the mci.brainspell.nii file,
and the slope value is not set. Here's the complete header

sizeof_hdr 348
data_type INT16
dim0 4
dim1 45
dim2 54
dim3 45
dim4 1
dim5 0
dim6 0
dim7 0
vox_units Unknown
time_units Unknown
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 4.0000000000
pixdim2 4.0000000000
pixdim3 4.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Unknown
qform_code 0
qto_xyz:1 4.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 4.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 4.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip generated by rto
aux_file none

On Mon, Oct 20, 2014 at 10:51 PM, Pierre Bellec notifications@github.com
wrote:

I use MRIcron. The max gets set at around 50000.