search

nipy / nibabel

Python package to access a cacophony of neuro-imaging file formats
http://nipy.org/nibabel/
Other
655 stars 258 forks source link

par/rec volume ordering #449

Open jyeatman opened 8 years ago

jyeatman commented 8 years ago

@Eric89GXL For par/rec files the volumes can be written in an arbitrary order, but the volume number is noted in the par file. From what I can tell nibabel is not reading the image_type_mr column to correctly organize the volumes. This means in a series of images where volume 1 is intended to be the magnitude data and volume 2 the real data, the order will be randomly switched during the nifti conversion.

grlee77 commented 8 years ago

Hi @jyeatman,

I recently added an option for a more general sorting that should work correctly for your case. If you build from the current master branch, parrec.load has a new option called strict_sort which you should set as True to get the expected behavior.

Similarly, if you are using the parrec2nii command line utility, pass the option --strict-sort (you may also need --overwrite to make sure any previously created .nii files will be overwritten).

Perhaps it is worth making the new sorting the default in a future release, but for now I did not enable it by default to preserve backward compatibility.

Please let me know if for some reason this option does not work for your case and we will work to fix it!

grlee77 commented 8 years ago

also, I forgot to mention if you have more than 4 dimensions in the data, you will still get a 4D .nii volume, but there is another new option to parrec2nii called --volume-info that will write out a .csv detailing what labels the volumes along the 4th dimension correspond to (e.g. image type, echo, dynamic, cardiac phase, etc...)

jyeatman commented 8 years ago

Thanks! I will test this out with a few data sets and I will let you know if there is any unexpected behavior.

On Saturday, April 30, 2016, Gregory R. Lee notifications@github.com wrote:

also, I forgot to mention if you have more than 4 dimensions in the data, you will still get a 4D .nii volume, but there is another new option to parrec2nii called --volume-info that will write out a .csv detailing what labels the volumes along the 4th dimension correspond to (e.g. image type, echo, dynamic, cardiac phase, etc...)

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/nipy/nibabel/issues/449#issuecomment-215987009

Jason D. Yeatman, PhD Assistant Professor, Institute for Learning & Brain Sciences (I-LABS) Department of Speech & Hearing Sciences University of Washington http://depts.washington.edu/bdelab/

grlee77 commented 8 years ago

@jyeatman, has the solution I described above worked out for you? If so we can close this issue. Some additional documentation to make these new features more visible was added in #451.

jyeatman commented 8 years ago

Yes, this worked great. Thanks Gregory

Jason D. Yeatman, PhD Assistant Professor, Institute for Learning & Brain Sciences (I-LABS) Department of Speech & Hearing Sciences University of Washington http://depts.washington.edu/bdelab/

On Wed, May 25, 2016 at 3:46 PM, Gregory R. Lee notifications@github.com wrote:

@jyeatman https://github.com/jyeatman, has the solution I described above worked out for you? If so we can close this issue. Some additional documentation to make these new features more visible was added in #451 https://github.com/nipy/nibabel/pull/451.

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/nipy/nibabel/issues/449#issuecomment-221730326

matthew-brett commented 8 years ago

@jyeatman - does the current master branch work for you?

jyeatman commented 8 years ago

@libbyhuber - can you test if the master branch is working?