External Email - Use Caution
Hi Sara,
It is a bit difficult to tell what exactly is the cause of the problem, but as
a potential solution, you might try to exclude the vertices from further
analysis by excluding them from the analysis mask (e.g., ‚lhcortex' variable).
To furthe
External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to analyze thickness changes in a longitudinal design using a
mass-univariate approach, as described on the Linear Mixed Effects tutorial at
https://secure-web.cisco.com/1HwLf5wG3aIAhV84T5KTL4VUiVpoa1DISeYUy
Sarah
>>
>>
>>
>> ----
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>> on behalf of Bruce Fischl
>>
>> *Sent:* Wednesday, October 19, 2016 2:58 PM
>> *To:* Freesurfer s
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce
Fischl
Sent: Wednesday, October 19, 2016 2:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Matlab scripts for reading and writing
files
Hi Sarah
I believe that both load_mgh and MRIread don't load any tag
gt; on behalf of Bruce Fischl
>
> *Sent:* Wednesday, October 19, 2016 2:58 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Freesurfer Matlab scripts for reading and
> writing files
> Hi Sarah
>
> I believe that both load_mgh and MRIread don't load any
du
on behalf of Bruce Fischl
Sent: Wednesday, October 19, 2016 2:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer Matlab scripts for reading and writing
files
Hi Sarah
I believe that both load_mgh and MRIread don't load any tags, so if you
use them to load, then MRIwrit
Hi Sarah
I believe that both load_mgh and MRIread don't load any tags, so if you
use them to load, then MRIwrite or save_mgh to write back to disk all the
tags should be gone.
cheers
Bruce
On Wed, 19 Oct 2016, Keefe, Sarah wrote:
Hi,
I am part of the Freesurfer anonymization project men
Hi,
I am part of the Freesurfer anonymization project mentioned in an earlier
thread- sorry to start a new thread but I was unable to reply to the previous
one. We are trying to find out how to remove all provenance information from
.mgh files.
I am having trouble reading .mgh files into Mat
permission denied"??? What
> should I do next?
>
>
> Many thanks,
>
>
>
>
> DH
>
>
>
>
> > From: sebastian.moell...@rwth-aachen.de
> > Date: Sun, 26 Jan 2014 16:33:40 +0100
> > To: gr...@nmr.mgh.harvard.edu
> > CC: freesurfer@nmr.mgh.harvard.
ould I
do next?
Many thanks,
DH
> From: sebastian.moell...@rwth-aachen.de
> Date: Sun, 26 Jan 2014 16:33:40 +0100
> To: gr...@nmr.mgh.harvard.edu
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
>
> Hi Dusan,
>
>
>
>
> > Date: Fri, 24 Jan 2014 17:07:08 -0500
> > From: zkauf...@nmr.mgh.harvard.edu
> > To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> >
> > Hello Dusan,
> >
> > Are you
uot;command not found" is the answer.
>>
>> I guess your hypothesis is true and the matlab binary is not in my path. Why
>> not? What should I do next?
>>
>> Thanks a lot!
>>
>> DH
>>
>>
>> > Subject: Re: [Freesurfer] Freesurfer
nd" is the
answer.
I guess your hypothesis is true and the matlab binary is not in my
path. Why not? What should I do next?
Thanks a lot!
DH
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> From: sebastian.moell...@rwth-aachen.de
> Date: Sun, 26 Jan 2014 10:33:3
:-( "command not found" is the answer.
I guess your hypothesis is true and the matlab binary is not in my path. Why
not? What should I do next?
Thanks a lot!
DH
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> From: sebastian.moell...@rwth-aachen.de
> Date: Sun, 26 J
Hi Dusan,
(I saw your PN earlier but had no idea and hence did not reply).
But this has more information, so I try again ;)
On Jan 25, 2014, at 02:00 , Dusan Hirjak wrote:
> Dear Freesurferexperts,
>
> I still have the Problem because I can not run the the mris-command to
> estimate the gyri
Dear Freesurferexperts,
I still have the Problem because I can not run the the mris-command to estimate
the gyrification-index, because Freesurfer is not recognizing Matlab: "ERROR:
Matlab is required to run mris_compute_lgi"Im not sure why this is happening?
Does someone have an idea???
Im star
Hi Zeke,
I have one more question: It seems that I did not copied the the "recommended
lines" from thehomepage to matlab startup-file correct. when I type "recon-all
-lgi -s G01" Im getting the following message:
ERROR: Matlab is required to run mris_compute_lgi!
When Im trying to run Qdec, the
Fri, 24 Jan 2014 17:07:08 -0500
> From: zkauf...@nmr.mgh.harvard.edu
> To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
>
> Hello Dusan,
>
> Are you sure you typed the entire command? Because your sys
H
>
>
>
>
>
>
>
>
>
> > Date: Fri, 24 Jan 2014 11:35:17 -0500
> > From: zkauf...@nmr.mgh.harvard.edu
> > To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> >
> > Hello
es (ARM64
objects only)
What should I do next to be able to use Freesurfer and Matlab on Maverick???
Many thanks!!!
DH
> Date: Fri, 24 Jan 2014 11:35:17 -0500
> From: zkauf...@nmr.mgh.harvard.edu
> To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [F
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed
the latest version of XQuartz (http://xquartz.macosforge.org/landing/)?
If not, please do that first.
If you installed XQuartz, than can you please type the following on the
command line and provide me with t
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access
to Freesurfer. I already added the "recommended lines" from the homepage to
matlab startup-file, but it is still not working. Im trying to estimate the
local gyrification index. However when I type "reco
Sorry -- appended the wrong version of 'mris_display.
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
function [hf, hp, av_filtered] = mris_display(astr_mris,
Bruce Fischl wrote:
(2) Import that surface onto Matlab and visualize it there.
There is such a visualizer in the 'dev' tree of FreeSurfer -- called
'mris_display'. I've appended the relevant m files -- just save to a dir
on your MatLAB path.
-=R
--
Rudolph Pienaar, M.Eng, D.Eng / email:
Thanks all.
The reason to use start FreeSurfer within Matlab would be to, for
example, build a kind of integrated GUI able to accomplish DICOM ->
Surface Visualization. But, for my case, its not that necessary; running
FreeSurfer externally is acceptable.
Thanks again for your help,
Raghav
O
Hi Raghav,
yes, people have done visualization of surfaces in matlab, maybe Thomas
(ccd) can comment. As for 2, I'm not sure I understand what you mean. Why
would you need to run freesurfer from within matlab? I guess you could use
eval to run recon-all if you had to, but I wouldn't think you w
Hi all,
I am working on a project that aims to:
(1) Use an MRI image, skullstrip and convert the brain volume to a surface
(2) Import that surface onto Matlab and visualize it there.
(3) On top of that surface in Matlab, add pictures of electrodes as well
as 3D "heat maps" of neural activity.
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