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aces / cbrain-plugins-fsl

(Deprecated) FSL models and tasks for CBRAIN
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FSL melodic: automatic parameter estimations (in task). #5

Closed glatard closed 9 years ago

glatard commented 9 years ago

Imported from Redmine ticket #7771.

It is not a good idea to do it on the portal side, as (1) it will make the portal installation dependent on FSL tools, (2) running command-line tools from the portal code can slow down the portal interface. So these adjustments have to be made on the clusters, which means that users will not be able to check/modify these values.

Najma said: we should just provide it as an option for the user to set up on the interface, with a warning that the values provided through the interface will override the values that may have been provided by the user in the fsf file.

glatard commented 9 years ago

what about fmri(totalVoxels)?

glatard commented 9 years ago

tr is pixdim4 as obtained with fslhd, right?

Yes.

glatard commented 9 years ago

If files have different TRs or npts, and if auto-correct is set, then each analysis will be done with a different TR or npts value. OK?

Naj: Sounds reasonable; TR doesn't make a difference in fMRI, but npts does. The user should have the option to 1) auto-fill 2) set # of frames. If chooses 2, then has to give a range, for instance frame 1-200, 5-250; etc. The "recommended default" should be npts extracted from the data, plus the choice of dropping x frames from the beginning of the scan.

glatard commented 9 years ago

I need more information on that in terms of which parameters of the design file will be modified. Currently, the to options are 1) auto-fill npts and TRs (selected by default), 2) set a value (not a range). I'm not sure if FSL supports a range for fmri(npts). Do you mean that we should remove some frames in the data before launching melodic?

Najmahan commented 9 years ago

Option 1 is fine. Option 2, setting a value is fine. Yes, usually (as even designed into melodic/feat interface) people drop off a few frames from the beginning of the scans (as they are not at steady state levels yet.)

On Mon, Jul 6, 2015 at 8:24 AM, Tristan Glatard notifications@github.com wrote:

I need more information on that in terms of which parameters of the design file will be modified. Currently, the to options are 1) auto-fill npts and TRs (selected by default), 2) set a value (not a range). I'm not sure if FSL supports a range for fmri(npts). Do you mean that we should remove some frames in the data before launching melodic?

— Reply to this email directly or view it on GitHub https://github.com/aces/cbrain-plugins-fsl/issues/5#issuecomment-118839320 .

glatard commented 9 years ago

OK, but this is already there through the ndelete option in the pre-processing section, right?