CSD always runs when multishell is set to TRUE, looking for file never generated

[njhunsak]

I'm trying to use the option 'computeCSD' and my data are multishell.

afq.params.track.multishell = true;
afq = AFQ_Create('sub_dirs', sub_dirs, 'sub_group', sub_group, 'showfigs', false, 'computeCSD', 1, 'normalization', 'ants');

I'm having issues with these options. Based on the code in AFQ_Create with the options I've included, this is the command that runs:

AFQ/functions/AFQ_Create.m

Lines 334 to 340 in dd6c478

	files = AFQ_mrtrixInit(AFQ_get(afq, 'dt6path',ii), ...
	lmax,...
	mrtrixdir,...
	afq.software.mrtrixVersion, ...
	afq.params.track.multishell, ... % true/false
	afq.params.track.tool, ...
	afq.params.track.response); % 'fsl', 'freesurfer'

That code creates a list of files:

AFQ/utilities/AFQ_mrtrixInit.m

Line 116 in dd6c478

files = AFQ_mrtrix_build_files(fname_trunk, lmax, compute5tt, multishell);

Going to that script there's several files listed for CSD, but here's the file giving me issues:

AFQ/utilities/AFQ_mrtrix_build_files.m

Line 37 in dd6c478

files.csd = strcat(fname_trunk, sprintf('_csd_lmax%i.mif',lmax));

Once you have the files listed, there's another program to check which mrtrix processes have been computed:

AFQ/utilities/AFQ_mrtrixInit.m

Line 119 in a42e157

computed = mrtrix_check_processes(files);

And here's the problem I'm having, the scripts are looking for the CSD file. However, that file is only created if multishell==0

AFQ/utilities/AFQ_mrtrixInit.m

Lines 231 to 243 in a42e157

	if multishell==0
	% Compute the CSD estimates:
	if (~computed.('csd'))
	disp('The following step takes a while (a few hours)');
	AFQ_mrtrix_csdeconv(files.dwi, ...
	files.response, ...
	lmax, ...
	files.csd, ... %out
	files.b, ... %grad
	files.brainmask,... %mask
	false,... % Verbose
	mrtrixVersion)
	end

Since I'm using multishell, that CSD file is never created, so every time I run the AFQ_Create command, it always says CSD needs to be run.

It seems like somewhere when generating file names and checking those names to determine what mrtrix processes need to be run, there needs to be different criteria if multishell is set?

---

Also I had to change -tempdir to -scratch based on my version of mrTrix:

AFQ/utilities/AFQ_mrtrix_5ttgen.m

Line 33 in dd6c478

'-nocrop -tempdir ' tmpDir];

AFQ/utilities/AFQ_mrtrix_5ttgen.m

Line 39 in dd6c478

'-nocrop -tempdir ' tmpDir];