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

​​​​

 nihpd_sym_04.5-08.5_gm.nii

​​​​

 nihpd_sym_04.5-08.5_mask.nii

​​​​

 nihpd_sym_04.5-08.5_pdw.nii

​​​​

 nihpd_sym_04.5-08.5_t1w.nii

​​​​

 nihpd_sym_04.5-08.5_t2w.nii

​​​​

 nihpd_sym_04.5-08.5_wm.nii

​

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/