Help with amico.Evaluation

[mmsignes]

Hello,

I am trying to use the function amico.Evaluation in the following way: ae = amico.Evaluation("Studyname", subj), where subj is a variable with the name of the subject folder, so the script could run for all the subjects in "Studyname" folder. However, the function is not working. I tried to use it in the simplest way proposed in the wiki: ae = amico.Evaluation("Studyname", "Subject01"), where the arguments are the names of the different folders (study and first subject), but is not working either. Am I using the function in a wrong way? I would appreciate any help. Thanks!

Mar.

[daducci]

Hi,
Could you you post the output of the terminal as well as a screenshot of your folder atructure? Otherwise we cannot understand what is going on.

[mmsignes]

Hi,
My folder structure is the following:
…/Project/
Noddi_script.py
Study/
S01/
S02/
…
The output of the terminal is:

I think this happens because it cannot find the subject's folder (as the same script it's running if I launch it inside of subject's folder).

Thank you.

[nightwnvol]

Hi @mmsignes,
this error occurs when you provide an incorrect file name or path to the fsl2scheme function. Please note that the function requires the paths to your bval and bvec files relative to your Noddi_script.py file.

e.g.

fsl2scheme('Study/S01/eddy_dwi.bval', 'Study/S01/eddy_dwi.bvec')

[mmsignes]

Thank you for the reply. Then, what's amico.Evaluation for? I thought once you gave to this function the arguments of "study" and "subject", you would only have to indicate the name of bvals and bvecs files (for fsl2scheme function) but that the path was not necessary anymore.

Mar.

[nightwnvol]

You're right; after setting the study_path and subject arguments in your Evaluation object, you only have to specify the input file names for the methods of the Evaluation class, e.g. the load_data method.

ae = amico.Evaluation("Study", "S01")
ae.load_data("S01_dwi.nii.gz", "eddy_dwi.scheme", "S01_mask.nii.gz")

fsl2scheme is not a method of the Evaluation class, so you have to specify the entire path of your bval and bvec files. This is because in a study, if the data were acquired with the same acquisition parameters, the subjects will share the same bval and bvec files. Therefore, one could generate a single scheme file and use it for all the subjects in the study.

I agree with you that this can be a bit confusing. Maybe we can consider a better implementation in future releases.

[mmsignes]

Thank you! Now is clear.

Mar.