FSL MELODIC: Account for intermediate registration to highres fMRI

[Najmahan]

In CBRAIN-Melodic interface, there has to be an option to register to "expanded functional Image"

The input files will be presented in a .CSV file. Each column of the file will correspond to

Column 1: RSfMRI_1.nii.gz (compulsory, must be UNIQUE)
Column 2: BET-MRI_1.nii.gz (compulsory, same file may be repeated across rows)
Columns3: BET-Highres-FMRI_1.nii.gz (optional)

Program fail if Column1 and 2 are empty.

[glatard]

@Najmahan could you precise the option where this "expanded functional image" should be added in the design file?

[Najmahan]

Following the same order as the FSL melodic GUI, as the rest. This means, under the registration section, the first option.

[glatard]

My question is about the name of the option in the design file. For registration, I am only aware of fmri(regstandard) (which is for the template), and set fmri(reghighres) (for the structural).

[glatard]

OK, so if fmri(reginitial_highres_yn) is set in the interface (preset from the design file), then the task will insert the file specified in the 3rd column of the CSV file in the design file. Do you know which option of the design file should be used to specific the reginitial_highres file? I don't have any example for that.

Also, what happens if fmri(reginitial_highres_yn) is set and the CSV file has 3 columns in some rows, and only 2 columns in other rows? Should this trigger an error?

[Najmahan]

Not sure I get your question, is this what you mean?

_# Initial structural space registration initialisation transformset fmri(init_initial_highres) "/dir/filenamehires/forexample"

I think triggering error is the easiest solution.

If user selects the option of initial registration, then the third column must be present. If we want to be very user-friendly, we can trigger error, but then let user go to the task parameter and deselect the subjects for which the third column is empty.

This latter implementation will be consistent with error trigger on mismatching dimensions.

On Fri, Jan 29, 2016 at 11:55 AM, Tristan Glatard notifications@github.com wrote:

OK, so if fmri(reginitial_highres_yn) is set in the interface (preset from the design file), then the task will insert the file specified in the 3rd column of the CSV file in the design file. Do you know which option of the design file should be used to specific the reginitial_highres file? I don't have any example for that.

Also, what happens if fmri(reginitial_highres_yn) is set and the CSV file has 3 columns in some rows, and only 2 columns in other rows? Should this trigger an error?

— Reply to this email directly or view it on GitHub https://github.com/aces/cbrain-plugins-neuro/issues/21#issuecomment-176858689 .

[glatard]

I have the impression that fmri(init_initial_highres) is to specify an initial transformation, and that there must be another option to specify the file to register to. In any case, it would be useful if you could provide a working design file implementing this feature.

Ok for the error.

[Najmahan]

voila (it's also on the usual provider)

On Fri, Jan 29, 2016 at 12:10 PM, Tristan Glatard notifications@github.com wrote:

I have the impression that fmri(init_initial_highres) is to specify an initial transformation, and that there must be another option to specify the file to register to. In any case, it would be useful if you could provide a working design file implementing this feature.

Ok for the error.

— Reply to this email directly or view it on GitHub https://github.com/aces/cbrain-plugins-neuro/issues/21#issuecomment-176867059 .

[glatard]

email attachment are removed from emails sent to github, and I cannot see it on CBRAIN. Can you send it by email directly, or send me the link to this file on CBRAIN?

[glatard]

OK, so fmri(reginitial_highres_yn) must be set to 1 and, for each file, initial_highres_files(i) should be set to the proper file path (column 3 of CSV file). It's clear now.