if they are different sizes, then something is wrong. Try deleting the folder and re-running qdec.

Hello FreeSurfer Experts,

I am trying to calculate Cohen's d effect sizes for a contrast I created in QDEC. I have found multiple sources suggesting this code: 

cd glmdir/contrast

fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh

But when I use it (replacing the glmdir and contrast with my own), I get the following error: 

freesurfer-Darwin-lion-stable-pub-v5.3.0

Darwin Galactica.local 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun  4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64

mri_convert Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh

mri_convert Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh 

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh...

----------------------

mris_calc -o Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh div Bi_Eprof_Lthick/rtsd.mgh

mghRead(Bi_Eprof_Lthick/rtsd.mgh, -1): could not open file

mris_calc:

Sorry, but I seem to have encountered an error.

While checking on input filetype sizes,

I found a size mismatch, i.e. len(input1)!=len(input2)

I tried to look into the gamma.mgh and rstd.mgh files and they do appear to be different sizes. Even when I use mri_surfcluster to restrict the gamma and rstd files to a single cluster, the resulting files have different sizes, which leads me to a similar error. Can anyone help with this or is there another way I can attempt to calculate effect sizes?

Thank you,

Kelly Vaughn

-- 

Kelly Vaughn, M.A.

PhD Candidate

Developmental, Cognitive, and Behavioral Neurosciences

Laboratory for the Neural Bases of Bilingualism | University of Houston

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