spm8Batch sliceTime

[mangstad]

Currently TR and slice acquisition order are hardcoded by spm8Batch's sliceTime function. We should add options to allow them to be specified (while still defaulting to the TR = 2, slice order = ascending that is currently used). Currently it's impossible to process some outside collaborator data with the sliceTime function because we can't change these options.

[rcwelsh]

Actually I think it is an option. But I can check. I know I put in for mcflirt ability to pass options via flag with realignfMRI.

Either way an easy fix.

R

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typos due to iPhone 4S

On Jul 25, 2012, at 13:52, "Mike Angstadt" reply@reply.github.com wrote:

Currently TR and slice acquisition order are hardcoded by spm8Batch's sliceTime function. We should add options to allow them to be specified (while still defaulting to the TR = 2, slice order = ascending that is currently used). Currently it's impossible to process some outside collaborator data with the sliceTime function because we can't change these options.

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#94

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[mangstad]

I didn't dig too deeply into the code, but we were looking through it while trying to preprocess some outside data and did not see an option -- and it's definitely not documented in the usage message. But yeah, just adding the ability to pass commands along to slicetimer would solve the issue.

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[rcwelsh]

Okay, I'll look at it next week? I'm away on yet another mini vacation :-)

R

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typos due to iPhone 4S

On Jul 25, 2012, at 16:50, "Mike Angstadt" reply@reply.github.com wrote:

I didn't dig too deeply into the code, but we were looking through it while trying to preprocess some outside data and did not see an option -- and it's definitely not documented in the usage message. But yeah, just adding the ability to pass commands along to slicetimer would solve the issue.

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#94 (comment)

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[shijiaguo]

@rcwelsh, I saw the TR option is added, but I didn't see anything about the slice acquisition order. Is it added? If so, what is the flag? Thanks!

[shijiaguo]

@rcwelsh is it just using something like [ -m "--odd" ]?

[rcwelsh]

Not in front of computer but the "-m" should allow options to be passed to slicetimer, so if --odd is correct than yeah.

I can check in a couple hours.

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typos due to iPhone 4S

On Aug 30, 2012, at 10:36, "Shijia Guo" <notifications@github.commailto:notifications@github.com> wrote:

@rcwelshhttps://github.com/rcwelsh is it just using something like [ -m "--odd" ]?

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Reply to this email directly or view it on GitHubhttps://github.com//issues/94#issuecomment-8161360.

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[shijiaguo]

@rcwelsh , I tested one file using spm8batch's '-m "--odd"' and one without using this option, they are identical. Seems like it's not working. Prob this option is added but is not functioning.

[rcwelsh]

Point me to the generated script file and I can look to see of it got generated correctly.

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typos due to iPhone 4S

On Aug 30, 2012, at 10:57, "Shijia Guo" <notifications@github.commailto:notifications@github.com> wrote:

@rcwelshhttps://github.com/rcwelsh , I tested one file using spm8batch's '-m "--odd"' and one without using this option, they are identical. Seems like it's not working. Prob this option is added but is not functioning.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/94#issuecomment-8162053.

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[shijiaguo]

Also, the one processed with spm8batch (without specifying sequence order, assuming it's ascending sequence) is not the same as fsl's slicetimer (without specifying sequence order) either.

[shijiaguo]

The scripts are in /net/data4/Motion/Subjects/Oulu/matlabScripts/spm8Batch/sliceTime/2012_08
The files are in /net/data4/Motion/Subjects/Oulu/sub01077/func/run_01
On PANLab cluster

[shijiaguo]

Seems like fsl's tglobal is not set to .5 as it said in the help file. I tested with specifying --tglobal 0.5 and without it, they give different results