open-discussion > How to re-orient T1W image with template?
Showing 1-6 of 6 posts
Jun 30, 2017 01:06 PM | wasana madushanka arachchi - General Sir John Kotelawala Defence University
How to re-orient T1W image with template?
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).
Jun 30, 2017 01:06 PM | Kiyotaka Nemoto
RE: How to re-orient T1W image with 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
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
Jun 30, 2017 03:06 PM | wasana madushanka arachchi - General Sir John Kotelawala Defence University
RE: How to re-orient T1W image with template?
Dear Kiyotaka,
Thank you very much. I will go through it.
Madu
Thank you very much. I will go through it.
Madu
Jul 5, 2017 07:07 AM | wasana madushanka arachchi - General Sir John Kotelawala Defence University
RE: How to re-orient T1W image with template?
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
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
Jul 5, 2017 07:07 AM | Kiyotaka Nemoto
RE: How to re-orient T1W image with template?
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:
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 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
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
Oct 17, 2017 02:10 AM | wasana madushanka arachchi - General Sir John Kotelawala Defence University
RE: How to re-orient T1W image with template?
Dear Sir,
I got this error when i was processing another data set? what could be the reason?
Madu
I got this error when i was processing another data set? what could be the reason?
Madu