Look at the scl_slope and scl_intercept in the NIfTI headers, which should
(for these data) have values of 1 and 0. The mnc2nii software used to
convert these images seems to have put random tiny values in them. .
The header contents are below:
sizeof_hdr: 348
data_type: ' '
db_name: ' '
extents: 0
session_error: 0
regular: 'r'
dim_info: 0
dim: [3 197 233 189 0 0 0 0]
intent_p1: 0
intent_p2: 0
intent_p3: 0
intent_code: 0
datatype: 16
bitpix: 32
slice_start: 0
pixdim: [0 1 1 1 0 1 0 0]
vox_offset: 348
scl_slope: 1.5259e-05
scl_inter: -2.7413e-18
slice_end: 0
slice_code: 0
xyzt_units: 10
cal_max: 0
cal_min: 0
slice_duration: 0
toffset: 0
glmax: 0
glmin: 0
descrip: 'mnc2nii nihpd_sym_04.5-08.5_gm.mnc
nihpd_sym_04.5-08.5_gm.nii '
aux_file: ' '
qform_code: 0
sform_code: 1
quatern_b: 0
quatern_c: 0
quatern_d: 0
qoffset_x: 0
qoffset_y: 0
qoffset_z: 0
srow_x: [1 0 0 -98]
srow_y: [0 1 0 -134]
srow_z: [0 0 1 -72]
intent_name: ' '
magic: 'n+1 '
Best regards,
-John
On Wed, 20 Jun 2018 at 23:05, avantika mathur <[log in to unmask]> wrote:
> Dear SPM users,
>
> I am working on fMRI data from 5-6 year old children. I wanted to use a
> pediatric template for normalization. I downloaded the *4.5–8.5 y.o*
> (prepuberty) NIHPD template from (http://nist.mni.mcgill.ca/?p=974).
> Thereafter, I converted the files to .nii format. Visualization of nii
> files reveal perfectly ffine images (Attached is the template).
> nihpd_sym_04.5-08.5_csf.nii
> <https://drive.google.com/file/d/1VImQKu0EFWMwwyTzAYA3FHULUdFHEV5J/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_gm.nii
> <https://drive.google.com/file/d/1EcRkVuDAa05yUjpjNnuBvUxfzkcG8EZA/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_mask.nii
> <https://drive.google.com/file/d/1UUmRnL6A_tk2hu6mj-CHoA97E0m4H_ba/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_pdw.nii
> <https://drive.google.com/file/d/1D7HGV6MdJ-p_eM2R77aGAw6cS_F61Dh2/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_t1w.nii
> <https://drive.google.com/file/d/1FgB6YWYdKGBJwYaEvOQXI7xjVr1X2vWo/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_t2w.nii
> <https://drive.google.com/file/d/1jnBevSS_FTn1eMkPigYgqKppDfspVQfn/view?usp=drive_web>
>
> nihpd_sym_04.5-08.5_wm.nii
> <https://drive.google.com/file/d/1Yjkshq9wnWTGMMcLkLe0I1i0a3ttrCke/view?usp=drive_web>
>
>
> I am using old segment in SPM12. I enter the subject data T1 image (Data)
> and tissue probability maps from the template (grey matter, white matter
> and csf ). Once I run segment the output files c1 (grey matter), c2 (white
> matter) and c3 (csf) are empty. The segmentation fails giving me null
> images.
>
> Does anyone know why this happens?
>
> What tissue probability maps should I use for segmentation (old segment)
> in pediatric population? Then how do I use the output in normalization?
>
> Please let me know if anyone has faced the same issue before.
>
> Thanks
>
> --
> Avantika Mathur
>
--
Prof John Ashburner
Professor of Imaging Science
UCL Institute of Neurology
Queen Square
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square, London, WC1N 3BG
E: [log in to unmask] T: +44 (0)20 3448 4365
http://www.fil.ion.ucl.ac.uk/
