NITRC NeuroPub Visualizer Forum: neuropub

RE: Is there any tutorial for making the nii file

Lars Forsberg — Mon, 25 Feb 2013 19:10:09 GMT

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.

RE: Is there any tutorial for making the nii file

lichih ho — Fri, 22 Feb 2013 15:22:49 GMT

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

RE: Is there any tutorial for making the nii file

Lars Forsberg — Fri, 22 Feb 2013 7:00:25 GMT

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.

Is there any tutorial for making the nii file

lichih ho — Fri, 22 Feb 2013 1:41:56 GMT

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

RE: Sensitivity - what do you think?

Lars Forsberg — Fri, 03 Dec 2010 15:30:59 GMT

Only problem is space. I would like to keep as much space as possible to the viewer. I was thinking if it would work to just decrease the sensitivity a bit, but that will make it slower when you want to browse quickly through the brain. I will keep your ideas in mind. Perhaps there's some easy way of implementing it.

RE: Sensitivity - what do you think?

Dianne Patterson — Fri, 03 Dec 2010 4:56:29 GMT

[userquote=Lars Forsberg#larsef]I found the app's cursor to be too sensitive when moving the finger over the screen, so I've been thinking about making it less sensitive. It's difficult to move the cursor to a specific coordinate. What do you think? [/userquote]

How about an alternative means of selecting coordinates...I liked scrolling around with my finger...but you could have x,y,z boxes...o those cylindrical slot machine like things...those are fast and slick.

Sensitivity - what do you think?

Lars Forsberg — Thu, 02 Dec 2010 21:03:59 GMT

I found the app's cursor to be too sensitive when moving the finger over the screen, so I've been thinking about making it less sensitive. It's difficult to move the cursor to a specific coordinate. What do you think?

Welcome to neuropub

Lars Forsberg — Thu, 02 Dec 2010 20:44:37 GMT

Welcome to neuropub