gt; the wiki.
>
> Hope it works, let me know,
>
> Marie
>
>
> On Oct 28, 2013, at 3:38 AM, Linn Mittlestein
> wrote:
>
> Dear Marie,
>
> Thank you, I use bash and changed my .bashrc and this worked, I
> previously had used wrong syntax. Thank you very much
be
> sure that your path has been modified, then the getmatlab command from
> FreeSurfer should give you the correct location.
>
> Best,
>
> Marie
>
>
> On Oct 23, 2013, at 12:23 AM, Linn Mittlestein
> wrote:
>
> Hi, thank you. I am using Linux. I not sure where
b path is not set correctly; it is calling an older
> version of matlab however I need it to point to matlab2013b. I have tried
> numerous things like changing the startup.m file, the .bashrc file and
> exporting the matlab path, however It keeps calling another version of
> Matlab. Can
exporting the matlab path, however It keeps calling another version of
Matlab. Can someone please tell me how exactly the path is set and where?
Best Wishes and thank you,
Linn
-- Forwarded message --
From: Linn Mittlestein
Date: Mon, Oct 21, 2013 at 9:33 AM
Subject: Fwd: LGI path
From: Linn Mittlestein Date: Fri, Oct 18, 2013 at
1:30 PM
Subject: LGI path problem
To: freesurfer@nmr.mgh.harvard.edu
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I
Hi,
I am trying to compute lgi measures, and I think my problem lies in the
fact that the matlab path is not set correctly; it is calling an older
version of matlab however I need it to point to matlab2013b. I have tried
numerous things like changing the startup.m file, the .bashrc file and
export
9s
> Run it with --help to see all the options.
> doug
>
>
> On 08/06/2013 08:24 AM, Linn Mittlestein wrote:
> > Hi all,
> >
> > I bit confused about how to create labels from annotation2label
> > command to create DLPFC. I want make DLPFC label by merging
&
Hi,
I just mean that it is not an option in the drop down menu at all? And I
thought it would be?
On Fri, Jul 26, 2013 at 6:19 PM, Douglas Greve wrote:
>
> Hi Linn, what do you mean that you cannot select it? Is it grayed out?
> doug
>
>
>
> On 7/26/13 4:20 AM, L
Hi all,
I bit confused about how to create labels from annotation2label command to
create DLPFC. I want make DLPFC label by merging G_frontal_middle.label,
S_frontal_inferior.label and S_frontal_middle.label (available in the 2009
atlas). But I only can get annotation2label to work with the other
Dear freesurfer experts,
I am currently do group analysis in qdec, and I canot select jacobian white
from the drop down menu, I thought this would be an option? Do I do have
additional steps to get these values?
Kind Regards,
Linn
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Hello,
I wondering if possible using fsgd files to do group analysis with two
factors (one with 3 levels, one with 2 levels), with one covariate. On fsgd
example list I cannot find this example?
Kind Regards,
Linn
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Freesurfer
Dear Freesurfer group.
I am having some concerns about Freesurfer and the different steps. I have
used version 5.0 for the cross-sectional timepoints, and I am now using
version 5.3 for the longitudinal processing. I am doing therefore the
several different steps involved in longitudinal processin
gt;
> cheers
> Bruce
>
> On Mon, 25 Mar 2013, Linn Mittlestein wrote:
>
> Dear Freesurfer experts,
>>
>> I have a question about trying to extract statistics from merged labels
>> using mris_anatomical_stats. I have used
>> the mri_annotation2label, and then
Dear Freesurfer experts,
I have a question about trying to extract statistics from merged labels
using mris_anatomical_stats. I have used the mri_annotation2label, and then
the mri_merge label, however now when trying to do mris_anatomical stats, I
get the error ; could not read input volume, eg F
Dear list,
I was wondering whether you have any suggestions on how to optimize
accuracy of the Freesurfer output (both cortical and subcortical) in images
aquired on lower scanning resolutions than 3 T (for examle 1 T)?
Kind Regards, Linn
___
Freesurfer
Dear Freesurfer experts,
I have a question about qdec...as it is supposed to be doing whole brain
cortical analyses, how come one first has to generate statistical tables,
and chose thicknesses of different regions from these tables? Is this just
an option, rather than being necessary for qdec?
Dear Bruce,
Thank you for your reply
Regards, Linn
On Tue, Feb 12, 2013 at 4:14 PM, Bruce Fischl wrote:
> Hi Linn
> that sounds normal to me
>
> cheers
> Bruce
>
> On Tue, 12 Feb 2013, Linn Mittlestein wrote:
>
> Dear freesurfer experts,
>>
>> i
Dear freesurfer experts,
i have a question regarding making my own average. I received this message
Tue Feb 12 10:54:34 GMT 2013
make_average_volume done
However, the stats file in the average subject is empty, and the tmp
folder, but the other folders are not empty. Is this "normal"? Does the
a
Dear freesurfer experts,
I have a question. I am trying to complete the longitudinal tutorial, and
in freeview tutorial it states:
"In order to analyze your longitudinal data, you have different options.
You could, e.g., open the stats text files in each
tpN.long.templateID/stats/ dir, containin
Dear freesurfer experts,
I have a question regarding white matter hyperintensities (ie values above
110)..if these are included in the brainmask accurately, ie as white matter
when it is indeed white matter, does hyperintensities still cause problems,
and if so why?
Regards Linn
_
rt of the recon-all process and ends up in one
> of the stats files. Is that good enough?
> Bruce
>
> On Tue, 5 Feb 2013, Linn Mittlestein wrote:
>
> Hi,
>>
>> Is there a command that can be used just to extract just the intracranial
>> volume of all participa
Hi,
Is there a command that can be used just to extract just the intracranial
volume of all participants?
Many kind regards
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The inf
thank you. Sorry but is there documentation on the wiki/anywhere on how to
create an own average?
On Fri, Feb 1, 2013 at 6:40 PM, Douglas N Greve
wrote:
> yes, unless you make your own average
> doug
> On 02/01/2013 09:42 AM, Linn Mittlestein wrote:
> > Dear Freesurfer Experts,
Dear Freesurfer Experts,
Are the fsaverage files necessary for qdec analysis?
Regards
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The information in this e-mail is intended on
Dear Freesurfer experts,
I just tried creating the -base for longitudinal processing on two time
points using
recon-all -base -tp -tp ... -all
After doing this, I received no error messages and a third folder
named after the template name I had given
it it was present in the subjects direct
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