Spm versioning

[dankessler]

This pull request addresses #46 by adding explicit versioning.

SPM versions supported

As discussed in that issue, here is the folder structure employed

SPM/
   SPM5/ #Contents of last stable released of SPM5

   SPM8/
      spm8_with_R3042/ #has been updated with all content from spm8Legacy/toolbox copied to this toolbox
      spm8_with_R4667/ #has been updated with all content from spm8Legacy/toolbox copied to this toolbox
      spm8Legacy/ #contains the version of spm8 from the cluster /net/dysthymia/spm8

   mc_patches/ #blocks of custom code that can be addpath-ed last to include custom bits
      Currently there are no custom patches. I anticipate that these will be added soon, per a request from @heffjos 

I would recommend not looking at the diff unless you have a really beefy browser. Instead, for code review, I'd recommend just checking out the Commits page. Just trust me on the commits where I copy everything from /net/misc/SPMS/spm... since those commits contribute tons of files to the diff.

Adding Appropriate Paths

By moving mcRoot/spm8 to mcRoot/SPM/SPM8/spm8Legacy, I realized that I could potentially break some old scripts. spm8Batch requires a localization script to be edited anyway, so I wasn't too worried about that. However, all of the _mc_template scripts no longer added the appropriate path. To fix this, I did the following.

src="addpath(fullfile(mcRoot,'spm8'))"
dst="addpath(fullfile(mcRoot,'SPM','SPM8','spm8Legacy'))"
sed -i "s:$src:$dst:g" `grep -rPl "addpath.*spm8\'" .`

That would find all instances of the old addpath behavior and replacement them with the new. You can see these changes in commit a4c40fd. Hopefully there were none that I missed.

This should do it. @rcwelsh let me know what you think.

[heffjos]

Looks good. I will have to check to see what version we are using.

[dankessler]

Cool. I know @rcwelsh is still planning to do some work to ensure that
toolboxes are in good shape.

On Thu, Jun 21, 2012 at 10:05 AM, heffjos <
reply@reply.github.com

wrote:

Looks good. I will have to check to see what version we are using.

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#67 (comment)

Daniel A. Kessler
Research Area Computer Specialist
Psychiatry - Rachel Upjohn Building
University of Michigan, Ann Arbor
kesslerd@umich.edu
+1 734.418.8134

[rcwelsh]

Yup, on my for this afternoon.

R

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typos due to iPhone 4S

On Jun 21, 2012, at 10:10, "Daniel A Kessler" reply@reply.github.com wrote:

Cool. I know @rcwelsh is still planning to do some work to ensure that
toolboxes are in good shape.

On Thu, Jun 21, 2012 at 10:05 AM, heffjos <
reply@reply.github.com

wrote:

Looks good. I will have to check to see what version we are using.

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#67 (comment)

Daniel A. Kessler
Research Area Computer Specialist
Psychiatry - Rachel Upjohn Building
University of Michigan, Ann Arbor
kesslerd@umich.edu
+1 734.418.8134

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[rcwelsh]

Okay, sorry for the delay, this is what is missing and I need to reconcile getting working copies into each

   Legacy                     R4290                       R4667
   ----------------           ----------------            -------------------
    ExtractVals                                            ExtractVals
    Shoot (probably won't add)
    SimpleROIBuilder
                              vbm8   
                              wfu_pickatlas                wfu_pickatlas

Also they all seem to not have "aal"

[dankessler]

@rcwelsh let me know if you add some commits on top of what you've fetched from me, and if so, into which branch you put them. I'll snag them and add to this pull request.

[rcwelsh]

working on it now.

On 6/27/12 2:31 PM, "Daniel A Kessler"
<reply+i-5171155-adba03f4f5ed929ca80c5d2144cb2cf280c6943a-1485912@reply.git
hub.com> wrote:

@rcwelsh let me know if you add some commits on top of what you've fetched
from me, and if so, into which branch you put them. I'll snag them and add
to this pull request.

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#67 (comment)
645

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[dankessler]

Hey @rcwelsh, any progress?

[rcwelsh]

ug, yes, but not i can't remember the push command

i've got it local as "SPM_versioning"

I'm heading downtown to look at monuments (we are in DC this week), but I'll push once I'm back after lunch.

:-D

[mangstad]

git push rcwelsh SPM_versioning

should do it (assuming you have your github remote set up as rcwelsh).

[rcwelsh]

I'll push tomorrow night, I'm without Internet on my laptop till then.

R

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typos due to iPhone 4S

On Jul 6, 2012, at 15:58, "Mike Angstadt" reply@reply.github.com wrote:

git push rcwelsh SPM_versioning

should do it (assuming you have your github remote set up as rcwelsh).

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[rcwelsh]

so i pushed up from my local to my verse with "git push robert_verse SPM_versioning", but now when I'm on github and go to my verse and get to the SPM_versioning france and hit "pull request" i'm getting a github error. :-(

I'll be on the road for the next 10 hours.

-R

[mangstad]

Hmm, not sure what might be going wrong. I just tried to submit a dummy pull request just to make sure it wasn't a Github problem, and it worked. Not sure if @dankessler has an idea (he's on vacation I believe through Wednesday) or maybe email Github support?

[rcwelsh]

just want to make sure i'm going it correctly. the email i sent outside of git, that procedure is correct? could it be some weirdo thing that dan also has a pull request named the same?

just sent help request to github

[mangstad]

Your steps looked fine.

So it's failing right when you hit the pull request button? Because the way it should work is that pressing pull request should direct you to a page that you can enter the title and description of the pull request before actually submitting it. If it didn't even get to that point it sounds like a github issue, although I suppose it's possible it's somehow failing due to the existing pull requests, but if you didn't even get to title it yet it shouldn't be a name conflict.

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[rcwelsh]

yeah, I get it right after hitting the "pull request". hopefully this is
not an issue of the pull request being too big? we'll just have to wait to
see what github says.

-r

On 7/9/12 10:13 AM, "Mike Angstadt"
<reply+i-5171155-adba03f4f5ed929ca80c5d2144cb2cf280c6943a-1485912@reply.git
hub.com> wrote:

Your steps looked fine.

So it's failing right when you hit the pull request button? Because the
way it should work is that pressing pull request should direct you to a
page that you can enter the title and description of the pull request
before actually submitting it. If it didn't even get to that point it
sounds like a github issue, although I suppose it's possible it's somehow
failing due to the existing pull requests, but if you didn't even get to
title it yet it shouldn't be a name conflict.

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Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues

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#67 (comment)
502

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Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[dankessler]

Additional commits by @rcwelsh are now in pull request #76, so I'm closing this issue so discussion can continue there.