Hi,

That's odd; SPM should be able to read/write .nii files pretty easily. Two suggestions:

1. Use SPM12 instead of SPM8 (probably better to do so anyway, no matter what you want to do).

2. Try and convert the files with MRIcron (http://www.mccauslandcenter.sc.edu/mricro/mricron/) which is pretty powerful at reading/writing formats.

Hope that helps,

M.

It would be helpful to see the exact error message of SPM8 and know with which spm function you tried to load the files...

cheers,

martin

i would make sure if those nifti files are zipped (are they actually .nii.gz files?) if that is the case, decompress them first. 

Hi

Dear all

I try all of aforementioned things, no one of them  worked.

http://www.humanconnectome.org/

Dear Martin

This is the SPM error when i load one of these files

Can you remove the semi-colon at the end of the first line, so we can see the HeaderInfo? Also try:

spm_type(HeaderInfo.dt(1))

By the way, as a sanity check, can you read other NIfTI format files, e.g. does the following work properly?

spm_check_registration(fullfile(spm('dir'), 'canonical', 'avg152T1.nii'))

As a wild guess, I'm wondering if the Connectome files are NIfTI-2 format... The release notes for SPM12b mention that there's preliminary support for that, so I'd second Matthew's suggestion to try SPM12b.

http://www.fil.ion.ucl.ac.uk/spm/software/spm12/SPM12_Release_Notes.pdf

Hi

Dear Gerard i also try the functions and follow your advises the function

spm_check_registration(fullfile(spm('dir'), 'canonical', 'avg152T1.nii'))

worked well but it still give this error for Connectome files

Cheers

Previously you just used spm_vol, and didn't get an error when reading the headers, so I would try that again, rather than using spm_vol_nifti, which seems to give you an error immediately. You should then be able to use spm_type as I mentioned before.

Another thing to try would be (again without semi-colon, so we can see output)

N = nifti('your_filename.nii')

I still have error

This is a sample of these files in the attachment.

Please could you attach the examples as .tgz or .zip rather than .rar? Sorry for being lazy!

Here my zip file, you are welcome.

Hi Osama, sorry for the slow reply. These files do indeed appear to be NIfTI-2 (the header size is 540, as described here http://nifti.nimh.nih.gov/pub/dist/doc/nifti2.h, which you can check with f=fopen('file'); fread(f,1,'int') in matlab).

SPM12b can read them, though it warns that "code 4 is not an option for units". It seems that the files are one-dimensional (i.e. not images, but perhaps individual time-series), with length 91282. E.g. the following works for me in SPM12b:

 N = nifti('cope1.dtseries.nii')

 N.dat.dim % [1 1 1 1 91282]

 plot(squeeze(N.dat(1,1,1,1,:)))

I've checked that SPM12b is happy with one of the NIfTI-2 test images from here: http://nifti.nimh.nih.gov/pub/dist/data/nifti2/ and it does seem to be, so if you were not expecting these files to be 1D, then you might need to investigate further in the connectome workbench (I can't help you with that I'm afraid).

Hi Gerard

Thank you very much, you really help me and solve my problem. The 1D time series data enough  to me. Thank you again.

Osama