I am working on a large data set of T1W images and expecting to do Voxel Based Morphometry. It seems that most of the images require manual re-orientation compared with TPM prior/template and its time consuming. (one by one) I am seeking any automatic imaging tool/software or matalab programe which can be used to do it as batch (whole images together with respect to template).

Hi,

I wrote a script to reorient images automatically to MNI template (icbm152.nii) for SPM12.
If you run this script, you can select as many T1 files as you want, and the script automatically reorients all files.

If you are interested, please check my blog post below.
http://www.nemotos.net/?p=1892

Hope this helps,

Kiyotaka

Dear Kiyotaka,
Thank you very much. I will go through it.

Madu

Dear Mr.Kiotaka,

Your programme is OK for icbm152.nii. How does it change if I use with TPM template of SPM12 instead icbm152.nii?

Thank you

Madu

Hi Madu,

Please change the line

matlabbatch{i}.spm.spatial.coreg.estimate.ref = {fullfile(spm('dir'),'toolbox','DARTEL','icbm152.nii,1')};

to

matlabbatch{i}.spm.spatial.coreg.estimate.ref = {fullfile(spm('dir'),'tpm','TPM.nii,1')};

Hope this helps,

Kiyotaka



Originally posted by wasana madushanka arachchi:

Dear Sir,

I got this error when i was processing another data set? what could be the reason?

Madu