search

vistalab / vistasoft

VISTASOFT is the main software repository of the VISTA lab at Stanford University.
http://vistalab.stanford.edu
148 stars 142 forks source link

error message if original 4D DTI file is modified after quality control #168

Open shrimpj opened 8 years ago

shrimpj commented 8 years ago

Dear Experts,

I have a question regarding dtiRawBuildBvecs:

dtiRawBuildBvecs (26, xform, gradsFile, 1000, dtiFile) function works fine on my original 4D DTI file with 26 volumes, but error message says 'Inner matrix dimensions must agree' when I deleted few volumes due to quality controls and used matched grads files.

The original grads file is a 26_6 matrix and new grads files are N_6 matrices depending on how many volumes are deleted. Moreover, modified 4D DTI image has N volumes which matches grads file. xform is a 3x3 matrix. I don't understand why matrix dimensions don't agree?

I wonder if my only choice would be modifying bvecs and bvals files generated from the original 4D images using dtiRawBuildBvecs (26, xform, gradsFile, 1000, dtiFile) function? If that is the case, I would like to know whether column in bvecs and bvals files represents the sequence of original 4D image? Any suggestions would be a greatly appreciated!

Best wishes, Joyce

MichalBS commented 8 years ago

Instead of excluding the bad volumes from the raw data manually, you can flag the bad volume as input to the tensor fitting code, and ask it to ignore those vols. I believe this is how we deal with excluded volumes, without actually erasing them from the raw data and bvecs files. michal

On Thu, Mar 31, 2016 at 3:09 PM, shrimpj notifications@github.com wrote:

Dear Experts,

I have a question regarding dtiRawBuildBvecs:

dtiRawBuildBvecs (26, xform, gradsFile, 1000, dtiFile) function works fine on my original 4D DTI file with 26 volumes, but error message says 'Inner matrix dimensions must agree' when I deleted few volumes due to quality controls and used matched grads files.

The original grads file is a 26_6 matrix and new grads files are N_6 matrices depending on how many volumes are deleted. Moreover, modified 4D DTI image has N volumes which matches grads file. xform is a 3x3 matrix. I don't understand why matrix dimensions don't agree?

I wonder if my only choice would be modifying bvecs and bvals files generated from the original 4D images using dtiRawBuildBvecs (26, xform, gradsFile, 1000, dtiFile) function? If that is the case, I would like to know whether column in bvecs and bvals files represents the sequence of original 4D image? Any suggestions would be a greatly appreciated!

Best wishes, Joyce

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/vistalab/vistasoft/issues/168