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neurodata / ndgrutedb

Pipeline and tools for estimating human connectomes from Diffusion, Structural, and Functional MRI
http://neurodata.io
Apache License 2.0
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m2g generation for multiple small atlases #116

Closed gkiar closed 8 years ago

gkiar commented 9 years ago

Atlases we care about, for future reference: Desikan, cc200, Talairach, spatial downsample to 20,000 and 100,000 nodes using Disa's code.

wrgr commented 9 years ago

Send Will absolute paths to atlases, and relevant calls. Then assign back to Will.

gkiar commented 9 years ago

Relevant call: look at the m2g workflow and call exactly what is being called but sub in the new atlases.

/share0/m2g/src/fsl/data/atlases/Talairach/Talairach-labels-1mm.nii.gz /share0/m2g/src/m2g/data/Atlas/MNI152_T1_1mm_desikan_adjusted.nii The cc200 atlas @ebridge2 can put somewhere, the others haven't been generated yet but this is enough information for you to make this and then we will simply add more atlases.

gkiar commented 9 years ago

most recent version of the workflow: https://github.com/openconnectome/m2g/blob/gkiar-dev/library/workflows/m2g_sources_bc1.pipe

ebridge2 commented 9 years ago

@willgray /share0/m2g/MRN/roiforwill/CC200.nii.gz sorry for the weird location, I don't have write access anywhere else though

wrgr commented 9 years ago

Ok - I figured out how to do this, @gkiar, but there are some interesting design decisions and choices. Easy of use vs. being explicit and simple vs. requiring certain properties of input file names and what not. Can we talk first thing on Tuesday and knock this out?

gkiar commented 9 years ago

Yup, gcal inv please for when you're in. On Aug 16, 2015 6:40 PM, "William Gray" notifications@github.com wrote:

Ok - I figured out how to do this, @gkiar https://github.com/gkiar, but there are some interesting design decisions and choices. Easy of use vs. being explicit and simple vs. requiring certain properties of input file names and what not. Can we talk first thing on Tuesday and knock this out?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/m2g/issues/116#issuecomment-131636308.

jovo commented 9 years ago

fyi - i think me & jordan will be sitting in my office all day tuesday. maybe you guys wanna sit there too?

On Sun, Aug 16, 2015 at 4:42 PM, Greg Kiar notifications@github.com wrote:

Yup, gcal inv please for when you're in. On Aug 16, 2015 6:40 PM, "William Gray" notifications@github.com wrote:

Ok - I figured out how to do this, @gkiar https://github.com/gkiar, but there are some interesting design decisions and choices. Easy of use vs. being explicit and simple vs. requiring certain properties of input file names and what not. Can we talk first thing on Tuesday and knock this out?

— Reply to this email directly or view it on GitHub <https://github.com/openconnectome/m2g/issues/116#issuecomment-131636308 .

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/m2g/issues/116#issuecomment-131636386.

the glass is all full: half water, half air. openconnecto.me, jovo.me, office hours https://www.google.com/calendar/embed?src=e2ktu4lrgul8anp8hclrcminp8%40group.calendar.google.com&ctz=America/New_York

jovo commented 9 years ago

@willgray this is currently THE bottleneck in doing science on mri data.

wrgr commented 8 years ago

@gkiar - make a note of these atlases and close.

jovo commented 8 years ago

where is said list?

gkiar commented 8 years ago

This list has evolved to contain many different/additional atlases as well, and exists within the atlas tab of our MR data spreadsheet. (not linking here since we said for the time being that would be kept private, but it can be found in our internal google drive MR/data/ folder.)

Greg Kiar gkiar07@gmail.com

On Tue, Nov 24, 2015 at 1:10 PM, joshua vogelstein <notifications@github.com

wrote:

where is said list?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/m2g/issues/116#issuecomment-159359456.