fe.life about life

[francopestilli]

Thanks I need to take care of this soon. Is this breaking your workflow now?
Franco

On Nov 17, 2014, at 10:20 PM, Hiromasa Takemura <[email protected] mailto:[email protected]> wrote:

I found that the structure fe.life is removed from the newest version of feSet.m
fe.life will not be used for anymore?

I found that there are several codes which are still using fe.life, which will make bugs.

feGet.m
feConnectomeReduceFibers.m
feConnectomeReduceVoxels.m
feGetConnectomeInfo.m
feConnectomeBuildModel.m

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[htakemur]

Yeah, I have a problem in running feConnectomeInit because of the lack of fe.life at several points (e.g. feConnectomeBuildModel)

[arokem]

This pull request, if merged, should take care of it:
#35

On Tuesday, November 18, 2014, Hiromasa Takemura [email protected]
wrote:

Yeah, I have a problem in running feConnectomeInit because of the lack of
fe.life at several points (e.g. feConnectomeBuildModel)

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#38 (comment).

[francopestilli]

OK I accepted the pull request. Let me know if now works. I have not means of testing at the moment.

On Nov 18, 2014, at 10:47 PM, Ariel Rokem <[email protected] mailto:[email protected]> wrote:

This pull request, if merged, should take care of it:
#35 #35

On Tuesday, November 18, 2014, Hiromasa Takemura <[email protected] mailto:[email protected]>
wrote:

Yeah, I have a problem in running feConnectomeInit because of the lack of
fe.life at several points (e.g. feConnectomeBuildModel)

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Reply to this email directly or view it on GitHub
<#38 (comment) #38 (comment)>.

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Reply to this email directly or view it on GitHub #38 (comment).

[arokem]

You seem to have merged my other pull request (end-to-end testing), which
is also useful. Should address the issue of testing this.

Could you also merge this one:
#35 ?

That should take care of the fe.life issues.

On Wed, Nov 19, 2014 at 12:25 AM, Franco Pestilli [email protected]
wrote:

OK I accepted the pull request. Let me know if now works. I have not means
of testing at the moment.

On Nov 18, 2014, at 10:47 PM, Ariel Rokem <[email protected]
mailto:[email protected]> wrote:

This pull request, if merged, should take care of it:
#35 <
https://github.com/francopestilli/life/pull/35>

On Tuesday, November 18, 2014, Hiromasa Takemura <
[email protected] mailto:[email protected]>
wrote:

Yeah, I have a problem in running feConnectomeInit because of the lack
of
fe.life at several points (e.g. feConnectomeBuildModel)

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Reply to this email directly or view it on GitHub
<
#38 (comment) <
https://github.com/francopestilli/life/issues/38#issuecomment-63548265>>.

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Reply to this email directly or view it on GitHub <
https://github.com/francopestilli/life/issues/38#issuecomment-63551294>.

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#38 (comment).

[francopestilli]

Done. Let’s see how this goes. In general this is part of a broader change to eliminating he need to strong all the fields of the fe structure in memory at each time. The idea is to be able to load parts of the fe structure (its fields) anytime necessary. More to come.

Franco Pestilli, PhD
Assistant Professor
Psychological and Brain Sciences, Indiana University
www.francopestilli.com http://www.francopestilli.com/ | [email protected] mailto:[email protected]

On Nov 19, 2014, at 3:47 PM, Ariel Rokem <[email protected] mailto:[email protected]> wrote:

You seem to have merged my other pull request (end-to-end testing), which
is also useful. Should address the issue of testing this.

Could you also merge this one:
#35 #35 ?

That should take care of the fe.life issues.

On Wed, Nov 19, 2014 at 12:25 AM, Franco Pestilli <[email protected] mailto:[email protected]>
wrote:

OK I accepted the pull request. Let me know if now works. I have not means
of testing at the moment.

On Nov 18, 2014, at 10:47 PM, Ariel Rokem <[email protected] mailto:[email protected]
<mailto:[email protected] mailto:[email protected]>> wrote:

This pull request, if merged, should take care of it:
#35 #35 <
#35 https://github.com/francopestilli/life/pull/35>

On Tuesday, November 18, 2014, Hiromasa Takemura <
[email protected] mailto:[email protected] <mailto:[email protected] mailto:[email protected]>>
wrote:

Yeah, I have a problem in running feConnectomeInit because of the lack
of
fe.life at several points (e.g. feConnectomeBuildModel)

—
Reply to this email directly or view it on GitHub
<
#38 (comment) #38 (comment) <
#38 (comment) https://github.com/francopestilli/life/issues/38#issuecomment-63548265>>.

—
Reply to this email directly or view it on GitHub <
#38 (comment) https://github.com/francopestilli/life/issues/38#issuecomment-63551294>.

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Reply to this email directly or view it on GitHub
<#38 (comment) #38 (comment)>.

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Reply to this email directly or view it on GitHub #38 (comment).

[htakemur]

Another issue is how to deal with fe structure created by older version of the script.
Presumably, newest version of LiFE will not work for older version of the script because of different format of structure.

We need to write a wrapper function, or make a code to update the version of fe.mat file into newest version?

[francopestilli]

Is this issue resolved?

[arokem]

I think that none of these are show-stoppers, but there are still a few places in the code that have references to fe.life:

./fe/feConnectomeBuildModel.m:
178 : fe.life.dSig(dense_rows) = feGet(fe,'diffusion signal in voxel',usedVoxels(vv));
./fe/feConnectomeReduceFibers.m:
23 : fe.life.Mfiber = sparse(size(fe.life.Mfiber,1),size(fe.life.Mfiber,2));
26 : fe.life.Mfiber = fe.life.Mfiber(:,fibersToKeep);
31 : if isfield(fe.life,'fit') && ~isempty(fe.life.fit)
32 : fe.life.fit.weights = fe.life.fit.weights(fibersToKeep);
33 : fe.life.fit.results.nParams = sum(fibersToKeep);
35 : if isfield(fe.life,'voxfit') && ~isempty(fe.life.voxfit)
36 : fe.life.voxfit = [];
40 : if isfield(fe.life,'fibers') && ~isempty(fe.life.fibers.tensors)
41 : fe.life.fibers.tensors = [];
42 : fe.life.fibers.total = [];
43 : fe.life.fibers.unique = [];
./fe/feConnectomeReduceVoxels.m:
20 : fe.life.Mfiber = fe.life.Mfiber(vxRows,:);
21 : fe.life.dSig = fe.life.dSig(vxRows);
28 : fe.life.diffusion_signal_img = fe.life.diffusion_signal_img(voxelsToKeep,:);
31 : if ~isempty(fe.life.diffusion_S0_img)
32 : fe.life.diffusion_S0_img = fe.life.diffusion_S0_img(voxelsToKeep);
36 : fe.life.vovel2FNpair = [];
./fe/feConnectomeSelectFibers.m:
6 : % The connectome select process builds the parameters inside of fe.life for
7 : % a selected set of fibers. The parameters inside of fe.life that are
11 : % The fe.life.fibers entries
49 : % Take care of the field fe.life.fibers
51 : if ~isempty(fe.life.fibers.tensors)
./scripts/dipy_validation.m:
22 : weights = fe.life.fit.weights;

[arokem]

Whoops - you can ignore that last one. I only have that locally for my own validation.