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
if they are different sizes, then something is wrong. Try deleting the folder and re-running qdec.
On 4/17/18 9:04 AM, Kelly Vaughn wrote:
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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Kelly Vaughn