Thanks Doug, here is the preproc log using the debug option:
nmr. set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err
Hi Melissa
we need to know more about your environment. What kind of machine are
you running on? Are you running it directly on the terminal, or using
some type of remote access or virtual machine?
cheers,
Bruce
On Wed, 12 Sep 2012, Melissa
Lancaster wrote:
Hi,
It seemed I had successful
Hi Missy,
yes, that sounds like at least part of your problem. What trouble did you
have sourcing our env file? Can you send us the screen output?
Bruce
On Wed, 12
Sep 2012, Melissa Lancaster wrote:
Hi again-
I should have added that I am using Mountain Lion. I have downloaded Quartz
and
> Dr. Fischl,
>
> Thanks so much. Unfortunately, I had closed the window. But here is what
> happened:
>
> I set the environment: setenv FREESURFER_HOME /Applications/freesufer
>
> However, after typing the next command: source
> $FREESURFER_HOME/SetUpFreeSurfer.csh I got the following error:
>
> F
Thanks Doug and Bruce
Does anyone have an opinion regarding the necessity of scanning the ADNI
phantom?
Best wishes
Heath
On Wed, Sep 12, 2012 at 1:03 PM, Douglas N Greve
wrote:
> If you include scanner as an interaction nuisance variable and balance
> your design so that there are an equal num
Hi New Fei, I did some digging and found the docs for the output (pasted
below). Translations (displacement) are in mm, rotations are in degrees
doug
1. n : time point
2. roll : rotation about the I-S axis (degrees CCW)
3. pitch : rotation about the R-L axis (degrees CCW)
4. ya
Are you sure that oa_txeffect_verum.fsgd has more than two subjects? This run
seems different than the one you sent yesterday which only found one subject.
doug
On 09/13/2012 08:48 AM, spa...@nmr.mgh.harvard.edu wrote:
> Thanks Doug, here is the preproc log using the debug option:
>
> nmr. set
Is that the one used to measure distances? If you have it, it's probably
not a bad idea. If all your scanners have the same metric, then that's
good, though it is not clear what you do post hoc with the information
if they don't.
doug
On 09/13/2012 10:57 AM, Heath Pardoe wrote:
> Thanks Doug an
Hi. Thanks for the response below. Does the fact that choroid plexus varies
so much in intensity mean that Freesurfer does not always accurately measure CP
volume? Do you think we should do some manual tracing to confirm Freesurfer
results?
Thanks,
Tracy
From: Bruce Fischl
Date: Wed, Sep
Hi Tracy
I guess so. We haven't quantified it at all.
cheers
Bruce
On Thu, 13 Sep 2012, Tracy A.
Butler wrote:
> Hi. Thanks for the response below. Does the fact that choroid plexus varies
> so much in intensity mean that Freesurfer does not always accurately measure
> CP volume? Do you thi
Hi Doug,
Can you point out the name of file that I should be looking at?
I assumed they were either the mcextreg and mcprextreg output files, but
these only have 6 columns.
Thanks,
New Fei
> Hi New Fei, I did some digging and found the docs for the output (pasted
> below). Translations (displac
Either fmcpr.mcdat or fmc.mcdat
On 09/13/2012 02:07 PM, New Fei Ho wrote:
> Hi Doug,
>
> Can you point out the name of file that I should be looking at?
>
> I assumed they were either the mcextreg and mcprextreg output files, but
> these only have 6 columns.
>
> Thanks,
> New Fei
>
>> Hi New Fei,
Yes, it still has 22 subjects. The only difference between yesterday and
today was that I individually ran mris_preproc on subjects 005, 006, 007,
and 010 to test whether any of those files were corrupt or missing. All 4
successfully ran mri_surf2surf, however this morning when I ran
mris_preproc a
Hi Freesurfers,
I've recently moved onto Ubuntu 12.04. The Freesurfer installation has
required me to download various libraries and create many symbolic links to
have it working. Further more I've had to set the doublebufferflag=1
(whatever that is) in order for tkmedit and freeview to work (they
Something very strange is going on. What platform are you using? What
version of FreeSurfer? Can you send me the fsgd file as an attachment
instead of pasting it into email?
doug
On 09/13/2012 03:58 PM, spa...@nmr.mgh.harvard.edu wrote:
> Yes, it still has 22 subjects. The only difference betwee
Dear FS folkers,
I am working on a functional probabilistic atlas. I find that some
functional regions (particular along a big sulcus) show quite high
probability value over a large sample, whereas the probability for some
regions are quite lower. I think this disparity could be accounted for by
t
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