Thanks, Caspar

On Wednesday, October 9, 2013, Douglas N Greve wrote:

If it is just an effect size you can compute gamma.mgh/rstd.mgh
doug

On 10/09/2013 01:39 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
this is coming from a seed-based resting state analysis. I would like to show effect size instead of p-values.
I thought you calculate them from the slopes or the t-values?
Caspar

2013/10/9 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

Oh, yes, sorry. The reason that mri_glmfit_pcc is failing is
because this is a one-sample group mean (design matrix a column of
all 1s). What are you trying to compute the correlation between?
Or do you just want to convert the p-values to a correlation
coefficient?

On 10/09/2013 01:26 PM, Caspar M. Schwiedrzik wrote:

Hi Doug, did you already have a chance to look into this?
Thanks, Caspar

2013/10/4 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>
<mailto:cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>>>

Done. Thank you very much for looking into this.
Caspar

2013/10/4 Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>

Can you tar up you glmfit dir and drop it to me on our
file drop?

On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,

thank you very much for sending the Matlab
function. When
I run this, it creates a pcc.mgh file for my osgm
contrast. However, the values seem strange. They range
from -630 to 36 for my particular dataset.
I was expecting something between -1 and 1.
Caspar

2013/10/4 Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>

I think you are conflating the 1st level and
the 2nd
level. You
could get pcc out of the 2nd level regardless
of what
you are
using for the input from the first level. I've
attached a matlab
script that will compute the pcc for
mri_glmfit output

doug

On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik
wrote:

Hi Doug,
I guess it boils down to the question how
to get a
group PCC
map after a RFX GLM?
Using -m PCC seems to only give me a map per
subject. Are you
calculating PCC from the t- values? Thanks,
Caspar

On Thursday, October 3, 2013, Caspar M.
Schwiedrzik wrote:

Hi Doug,

On Thursday, October 3, 2013, Douglas
N Greve
wrote:

It sounds like two issues:
1. p-values not consistent with your
program. What did
you use
to compute? Did you do a two-sided
(which
is what
fsfast uses)?

I used ttest in Matlab, two sided.

2. Using pcc maps. Why not use -m pcc?

Isn't that giving me a map per
subject? How do
I get the
group map
that is consistent with the results of
mri_glmfit run on
ces.nii?

Thanks, Caspar

doug

On 10/03/2013 01:10 PM, Caspar M.
Schwiedrzik wrote:

Hi Doug,
I loaded the pcc.nii file that
I got from
isxconcat-sess
into Matlab and then ran a t-test
against 0 over
the 4th
dimension. I converted the
resulting
p-values to
-log10
and then compared them to the
output of
mri_glmfit, namely
sig.vol.
This was the mri_glmfit command:
mri_glmfit \
--surf averagesubject hemisphere \
--y pcc.nii \
--no-cortex \
--osgm \
--glmdir analysisname
I was expecting the p-values
to be the
same, which
apparently is not the case,
unless I am
doing/understanding something
wrong.

By now, I am actually more
inclined to
use the
regression
coefficients instead. However, I'd
still like to
get pcc
maps from them, if there is a
way to
do so in FSFAST.
Thanks, Caspar

2013/10/3 Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:gr <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>

On 10/03/2013 10:39 AM,
Caspar M.
Schwiedrzik
wrote:

Hi Doug,

when I run a
two-tailed t-test
against 0
in Matlab
on the Rs
in pcc.nii that I get
out of
isxconcat-sess with
-m pcc, and
DOF from ffxdof.dat, I get
different -log10(p)
values than the
ones that come out of
mri_glmfit.

I don't understand what
you mean.
Can you
elaborate?

I am not sure why this is
happening.
In principle, I just
want pcc
maps as
final output
to show
them on the surface
(instead
of p-values).
So I'd
be happy to
follow your advice
regarding
the biasing
effects
of noise and
autocorrelation and use the
regression
coefficients. However,
mri_glmfit (v5.1) does not
seem to output
pcc maps
of the
contrasts (contrary to
selxavg3-sess on
the single
subject
level). How would I
get those?

Thanks, Caspar

2013/10/1 Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
<mailto:greve@nmr.mgh.harvard.edu
<m <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>

<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
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<tel:617-726-7422 <tel:617-726-7422>>>

Bugs:
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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Outgoing:
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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