FEATURE Request: implement vertstats file format for vertex statistics

[gdevenyi]

To support header labels and such,

Full details here https://github.com/BIC-MNI/oobicpl/tree/master/docs

[rdvincent]

Will look into it. What tool actually produces these files today?

[gdevenyi]

The vertstats_* tools in oobicpl. Probably surfstat (the matlab stats tool for CIVET stuff)

Soon to be RMINC https://github.com/Mouse-Imaging-Centre/RMINC/issues/69

mni.vertex.statistics (it's the default output format)

[rdvincent]

@gdevenyi Any chance you have some examples lying around?

[gdevenyi]

https://dl.dropboxusercontent.com/u/307000/Results_lme_left_surfaces_sfn_1.vertstats.gz

[gdevenyi]

For a CIVET/1.1.12 left brain

[gdevenyi]

(needs gunzipping)

[rdvincent]

@gdevenyi Thanks. Somewhat surprisingly, the code will read this vertstats file "as is", although we ignore the header. I'll work towards formally reading the headers and integrating them into the UI.

[rdvincent]

@gdevenyi It's not anything amazing, but I added the ability to display the column nanes from vertstats files (they show up in the 3D view window status line).

[gdevenyi]

It works! Mostly... Parsing is a bit messed up on this header, it's separating bits that should be grouped:

"F-statistic" "R-squared" "beta-(Intercept)" "beta-M.FF" "beta-poly(Age, 2)1" "beta-poly(Age, 2)2" "tvalue-(Intercept)" "tvalue-M.FF" "tvalue-poly(Age, 2)1" "tvalue-poly(Age, 2)2"

A few rounds of CTRL-V cycling through it:

Loaded 40962 vertex data items, in range [0.061373 ... 114.093628]
Switched to column 1 ("R-squared"), minimum 0.000485569, maximum 0.474546
Switched to column 2 ("beta-(Intercept)"), minimum 0.821048, maximum 3.85684
Switched to column 3 ("beta-M.FF"), minimum -0.18381, maximum 0.0510196
Switched to column 4 ("beta-poly(Age,), minimum -2.61163, maximum 2.432
Switched to column 5 (2)1"), minimum -1.04803, maximum 1.12645
Switched to column 6 ("beta-poly(Age,), minimum 74.4977, maximum 468.789
Switched to column 7 (2)2"), minimum -12.5768, maximum 2.75247
Switched to column 8 ("tvalue-(Intercept)"), minimum -17.5716, maximum 12.8181
Switched to column 9 ("tvalue-M.FF"), minimum -5.56344, maximum 5.43726
Switched to column 0 ("F-statistic"), minimum 0.0613733, maximum 114.094
Switched to column 1 ("R-squared"), minimum 0.000485569, maximum 0.474546
Switched to column 2 ("beta-(Intercept)"), minimum 0.821048, maximum 3.85684
Switched to column 3 ("beta-M.FF"), minimum -0.18381, maximum 0.0510196
Switched to column 4 ("beta-poly(Age,), minimum -2.61163, maximum 2.432
Switched to column 5 (2)1"), minimum -1.04803, maximum 1.12645
Switched to column 6 ("beta-poly(Age,), minimum 74.4977, maximum 468.789
Switched to column 7 (2)2"), minimum -12.5768, maximum 2.75247
Switched to column 8 ("tvalue-(Intercept)"), minimum -17.5716, maximum 12.8181
Switched to column 9 ("tvalue-M.FF"), minimum -5.56344, maximum 5.43726
Switched to column 0 ("F-statistic"), minimum 0.0613733, maximum 114.094
Switched to column 1 ("R-squared"), minimum 0.000485569, maximum 0.474546
Switched to column 2 ("beta-(Intercept)"), minimum 0.821048, maximum 3.85684
Switched to column 3 ("beta-M.FF"), minimum -0.18381, maximum 0.0510196
Switched to column 4 ("beta-poly(Age,), minimum -2.61163, maximum 2.432
Switched to column 5 (2)1"), minimum -1.04803, maximum 1.12645
Switched to column 6 ("beta-poly(Age,), minimum 74.4977, maximum 468.789
Switched to column 7 (2)2"), minimum -12.5768, maximum 2.75247
Switched to column 8 ("tvalue-(Intercept)"), minimum -17.5716, maximum 12.8181
Switched to column 9 ("tvalue-M.FF"), minimum -5.56344, maximum 5.43726

Looks like perhaps whatever separator it finds counts as a column, i.e. it's mixing separators.

[rdvincent]

Can you send me the file? Probably has quotes around the elements in the header. Will fix asap.

[gdevenyi]

Indeed it does (see above)

Here's the file https://dl.dropboxusercontent.com/u/307000/CT-quad-left.txt.gz

[rdvincent]

@gdevenyi OK, checked in some code to handle that. It works with my existing examples.

[gdevenyi]

Works! Hurrah.

You have slain brain-view2. Thanks so much, one less tool to support :)