Hi Doug,
so you
1. edited the cross sectionals and surfaces look fine (make sure you
edit the brain.finalsurfs.manedit.mgz file, which you create as a copy
of the brain.finalsurfs.mgz)
2. checked/edited the base and surfaces look fine too
3. ran the longitudinal from scratch (w/o any edits)
a
Hi Khadka,
Although it is an old mail (sorry), because this topic came up in
another thread, I reply here also.
You need to edit the brain.finalsurfs.manedit.mgz file. Create this file
by copying :
cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
then edit the manedit file.
Best, Martin
The FSGD looks right (you have a 2x4 design, so 8 classes, plus 2
covariates).
[1 1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0] tests for a difference between
NoFocus and RhFocus (No-RH)
[0 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0] tests for a difference between
RhFocus and LhFocus (RH-RH)
probably you can
Dear Marie,I want to run a group analysis on a set of subjects, correcting for
gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus
inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like
thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_Fem
Hmmm, I'm not sure an effect size makes sense. I guess I would use the
one from the chosen p-value
doug
On 5/2/14 12:52 PM, Caspar M. Schwiedrzik wrote:
Hi!
I am doing some conjunction analyses (Nichols et al.) on my fMRI data,
and I was wondering whether anyone can make a recommendation ho
It is the number of samples in the time series. Eg, if you scan for
10min with a TR=2, then you would have 600/2=300 time points
doug
On 5/2/14 3:07 PM, Conchy PF wrote:
Dear Douglas,
I would like to use optseq2 to set up my experiment sequence. However
it is not clear for me what "number
If you are compiling with clang openmp might not work.
Peace,
Matt.
On 5/2/14, 2:13 PM, "Bruce Fischl" wrote:
>Hi Lukas
>
>sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going
>on?
>Does OpenMP have to be enabled somehow?
>
>Bruce
>
>
>On Fri, 2 May 2014,
>lukas.sch...@ukb.u
Hi Lukas
sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on?
Does OpenMP have to be enabled somehow?
Bruce
On Fri, 2 May 2014,
lukas.sch...@ukb.uni-bonn.de wrote:
Hi Bruce!
I just run: recon-all -s ernie2 -autorecon2 -openmp 4
mri_ca_register uses 100.9% CPU at
Hi Bruce!I just run: recon-all -s ernie2 -autorecon2 -openmp 4
mri_ca_register uses 100.9% CPU at most ...
Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option?
Best wishes,Lukas>Hi Bruce!
Dear Douglas,
I would like to use optseq2 to set up my experiment sequence. However it is
not clear for me what “number of time points” means. I guessed that it was
the number a waveform is sampled, but I saw in some mailing lists that it
is the time the event is repeated during the run.
In case
FYI
-- Forwarded message --
Date: Fri, 2 May 2014 11:28:11 -0400
From: Polina Golland
To: Bruce Fischl
Subject: MICCAI PC workshop -- May 16
Hi Bruce,
Can you please forward this around?
Thanks,
Polina.
MICCAI PC Workshop
May 16, 2014, 1-6pm, CSAIL Kiva and Star Conferen
Yes you can do something like this:
XM = [X, pvr(:,i)];
Best
-Jorge
El Jueves 1 de Mayo de 2014 23:39, Marnie Shaw
escribió:
Hi Jorge,
>
>Thanks for your reply. Actually I don’t want to have different numbers of
>columns in the design matrix for different vertices. Instead I want to add
Hi!
I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and
I was wondering whether anyone can make a recommendation how to display
effect sizes for this kind of analyses?
Would you show the effect size estimate corresponding to the p-value that
is chosen, an average, or anything
Hi Bruce,
Great, that will simplify things considerably. Thank you for the info.
Jon
On Fri, Apr 25, 2014 at 9:35 PM, Bruce Fischl wrote:
> Hi Jon
>
> yes, that works fine. The mprage gives better CNR/unit time in the cortex,
> but if you are really only interested in MEG that is probably a s
Dear Freesurfer experts,
I have a question regarding longitudinal edits. Specifically the
brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in
Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525).
The problem that I am having is that the edits saved
Hi Bruce!
Thanks for the fast response. I used the current stable version 5.3.0.1
(freesurfer-Darwin-lion-stable-pub-v5.3.0.1).
So I will try as you have suggested ...
Best wishes,
Lukas
> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700
>
> Hi Luke
>
> what version of FS are you running? We see s
Hello FS experts,
I have had a continuing curiosity regarding when/what to edit in FS cortical
reconstructions. The wiki does a good job at showing how to deal with large
scale problems, (i.e. invalid tal transformation, white matter not being
recognized, large portions of the skull included in
Hi Luke
what version of FS are you running? We see significant speedups. Try
running top in a unix terminal and seeing if the cpu usage of
mri_ca_register (during autorecon2, the longest single step) is more than
100%
cheers
Bruce
On Fri, 2 May 2014,
lukas.sch...@ukb.uni-bonn.de wrote:
Hi folks!
I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do
not see any accelartion when processing a single data set with or without
the flag -openmp flag set.
recon-all -s ernie_1 -all
leads to ~6,4h processing time.
Unfortunately
recon
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