This is very useful tool to present our research results and it is very easy to use. But I have tried so many times for uploading my nii file and all fail. 
Can anyone provide a more detail process for making the nii file for neuropub.

thanks a lot

lichih

Hi,
At what stage is it failing and which procedure are you using? Are you uploading it by using another app (e.g. Dropbox or Mail) or are you uploading it through iTunes on your computer?

My guess is that your nii file does not fulfil the requirements. The requirements are:

1. Images you upload must have the same resolution as the 2x2x2 mm^3 MNI template that comes with SPM and FSL. This means the dimension has to be 91x109x91 voxels.
2. The images need to be in 32-bit float format.
3. The transformation matrix (sform-matrix) has to be the same as the MNI template.
4. It has to be a 3D file. 4D files are not supported.

The file can either be a .nii file or a .nii.gz. The latest version (v1.1) supports compressed files.

Only images satisfying these demands will be listed in the image list, otherwise they will be deleted to save space.

You can easily check if your image fulfils these demands with the fslhd program if you are using FSL. This program will list the header information in your nii file. The interesting parts that must be the same are:

data_type FLOAT32
dim0 3
dim1 91
dim2 109
dim3 91

sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000

I hope this helps.

So many thanks, finally I success.
But here is another question about the Min/Max threshold levels.
Is there any relationship between the p-value and the threshold number?

thanks again

lichih

This all depends on what kind of image you have loaded. The threshold levels will represent t-values if you have loaded a student-t image. Any student-t value below or above the min/max t-values given will then be invisible. You need to convert the image from student-t to p-values if you want the threshold levels to threshold on p-values. Some tools, like FSL's randomise, will give you p-valued images and then you will threshold on the p-values.