[Pkg-exppsy-pynifti] PyNIfTI 0.20090303.1

[Yaroslav Halchenko]

on behalf of Matthias I am posting his reply ;)
BTW, adding a header line such as
In-Reply-To: <20090329162141.GG20315 at washoe.rutgers.edu>
should be sufficient to continue the thread (substitute actual ID with
the ID of email you are replying to)... not sure if gmail allows you to
do all that in its WUI though...

I will comment on in a follow up email

On Sun, 29 Mar 2009, Matthias Ekman wrote:

Hi Yaroslav,

(may be you can bring this mail bag to the list. Our admin disabled
some functions, so I cant use my gmail account properly from work and
I want to avoid to start a new thread each time.)

Thanks for your suggestion with nifti_tool. But it shows nothing,
which i assume means 'no' difference. Comparison with some arbitrary
niftis shows some difference; so I think I used it the right way.
Nevertheless I show you what fslhd (FSL Tool) says to my tmp.nii.gz
(created with Pynifti on win/os x).

Going through the output there is no difference to bold.nii.gz in
$pymvpa_dataroot


> also, may be I missed, what tool was used to render the image after all?
> how does rendering of original bold.nii.gz look like?

sorry, don't got you here. What exactly do you mean by 'rendering' ?
Do you mean the attached screenshot? I opened the nifti in fslview
and printed a screenshot (nothing "fancy" with matplotlib/gnuplot).

Cheers,
Matthias



sizeof_hdr     348
data_type      INT16
dim0           4
dim1           40
dim2           20
dim3           1
dim4           1452
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       4
nbyper         2
bitpix         16
pixdim0        0.0000000000
pixdim1        3.0999999046
pixdim2        3.7500000000
pixdim3        3.7500000000
pixdim4        2.5000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     352
cal_max        2623.0000
cal_min        0.0000
scl_slope      1.000000
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      3.100000  0.000000  0.000000  0.000000
qto_xyz:2      0.000000  3.750000  0.000000  0.000000
qto_xyz:3      0.000000  0.000000  3.750000  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        FSL4.0
aux_file

-- 
Yaroslav Halchenko
Research Assistant, Psychology Department, Rutgers-Newark
Student  Ph.D. @ CS Dept. NJIT
Office: (973) 353-1412 | FWD: 82823 | Fax: (973) 353-1171
        101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102
WWW:     http://www.linkedin.com/in/yarik