tkmedit works fine on the machine, when working directly on it (not ssh'ing
to it)
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
zkauf...@nmr.mgh.harvard.edu
Sent: Thursday, May 21, 2015 11:53 AM
To: Freesurfer support list
Cc: freesu
Hi Freesurfer folks
I am SSH'ing from one MAC to another. both mac's are running Mac Os 10.6.8
I am ssh'ing with -Y option
when I try to run tkmedit I get the error;
Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] :
kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 2763
Thu May 21
Dear freesurfer experts.
is it possible for tkmedit to display volumes in neuroscience format (R is R)
rather than radiologic format (R is L)?"
Thanks
Jon
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From: Jon Alan Wieser
Sent: Monday, January 5, 2015 11:13 AM
To: jorge luis; Freesurfer support list
Subject: Re: [Freesurfer] longitudinal statistics LGI
HI Jorge,
how do you determine the number of rows(L) in the contrast matrix?
so if we want to test the
From: Jon Alan Wieser
Sent: Tuesday, December 30, 2014 8:11 PM
To: jorge luis
Cc: Kristin Elizabeth Maple
Subject: Re: [Freesurfer] longitudinal statistics LGI
Hi Jorge,
Following your instructions, so far we have done the following:
1-Read your label
umber of columns as the number
of fixed effects (population parameters) in your model.
Best
-Jorge
____
De: Jon Alan Wieser
Para: jorge luis
CC: "freesurfer (freesurfer@nmr.mgh.harvard.edu)"
Enviado: Domingo 28 de diciembre de 2014 10:23
Asunto: Re: [Freesu
demonstrates the unique effect of cannabis
5. What Contrast matrix do we use for the LME_mass_F program
Thanks
Jon
From: jorge luis
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl Medina; alic
HI Jorge
What should we use for our Contrast Matrix (CM) ?
Jon
From: jorge luis
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl Medina; alicia.thomas@gmail.com
Subject: Re: [Freesurfer
Hi Jorge,
One more newbie question.
what's a good way to visualize the lhstats1.lreml values across the vertices?
Thanks
Jon
From: jorge luis
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl M
ew to longitudinal LME analyses.
Thanks again
Jon
From: jorge luis
Sent: Wednesday, December 17, 2014 9:25 AM
To: Freesurfer support list; Jon Alan Wieser
Cc: Krista Lisdahl Medina; alicia.thomas@gmail.com
Subject: Re: [Freesurfer] longitudinal statistics LG
effects
as explained above.
-Jorge
De: Jon Alan Wieser
Para: "freesurfer (freesurfer@nmr.mgh.harvard.edu)"
Enviado: Martes 2 de diciembre de 2014 12:29
Asunto: [Freesurfer] longitudinal statistics LGI
HI freesurfer experts
I have a question
HI freesurfer experts
I have a question about the statistical analysis of longitudinal data. we have
run our data through the longtudinal data processing stream.
We are looking at the longitudinal effect on the LGI data
We are looking at doing a Mixed effects analysis.our main Model Fac
mri_glmfit-sim --help
On 11/21/2014 01:51 PM, Jon Alan Wieser wrote:
>
>
> hi
>
> please explain the differece between --sim-sign abs, neg, and pos
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
hi
please explain the differece between --sim-sign abs, neg, and pos
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The information in this e-mail is intended only for the pers
esurfer-boun...@nmr.mgh.harvard.edu
on behalf of Z K
Sent: Friday, November 14, 2014 2:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] qdec and recon-all crashes
Yes, the directories and files will all exist under the Dropbox folder
and will thus be backed up by Dropbox. But I s
ashes
Yes, the directories and files will all exist under the Dropbox folder
and will thus be backed up by Dropbox. But I suggest you test this for
yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
> thanks Zeke,
>
> I have created the symbolic link.
>
>
&
con-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/
$> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\
Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001
$> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec
cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and
()'s in it, it is causing the two programs to crash
ech
t
need to add a label to that.
doug
On 09/11/2014 10:59 AM, Jon Alan Wieser wrote:
> thanks, but we are using qdec to do the inital analysis , not mri_glmfit
> Jon
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Dou
://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
doug
On 09/11/2014 10:49 AM, Jon Alan Wieser wrote:
>
> HI freesurfer experts
>
>
> We were wondering if it is possible to restrict the Monte Carlo
> analysis run by mri_glmfit-sim to a specific region fo the surface ,
> instead of
HI freesurfer experts
We were wondering if it is possible to restrict the Monte Carlo analysis run by
mri_glmfit-sim to a specific region fo the surface , instead of the whole
surface, by using a mask or label to specify the ROI?
I didn't see a --mask or --label option in mri_glmfit-sim
Thank
Hi Tara
try:
recon-all -s -randomness -all
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Tara Miskovich
Sent: Friday, August 22, 2014 12:07 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI Topological Defect
Hi all,
I am gett
HI doug,
thanks for getting back to me. I was able to solve the problem on my own.
thanks again
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Thursday, July 31, 2014 4:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subjec
04:52 PM, Jon Alan Wieser wrote:
> I ran the analysis in qdec, not mri_glmfit . I did a few analyses in qdec
>
> Jon
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N Greve
>
> Sent: Tuesday, July 29,
age. By this I mean to compute the mean
age over all subjects regardless of group, then subtract the mean from
all ages.
doug
On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:
>
> I'm getting the following erorr when running Qdec "Analyze"
>
> Model Factors:
&g
] MRI_glmfit-sim error
I'm not sure how that could have happened. Did you run mri_glmfit
multiple times by any chance?
On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
>
>
> I'm running a monte carlo sim and am getting an error:
>
>
> command line:
>
>
I'm running a monte carlo sim and am getting an error:
command line:
mri_glmfit-sim \
--glmdir MTA_persistanceCP \
--sim mc-z 1000 1.3 mc-z.negative \
--sim-sign abs --cwpvalthresh 0.999 \
--overwrite
output:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd
I'm getting the following erorr when running Qdec "Analyze"
Model Factors:
Discrete (fixed factors)
ADHD_Persist
MJ_group
Nuisance factor:
Age
ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4
Possible problem with experimental design:
HI freesurfer experts,
I am running a qdec analysis, my first factor has 3 levels, my other 2 factors
have 2 levels, I select my first and second factors and hit "Analyze"
I get the error ? :
Error in Analyze: command failed
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 level
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