[Freesurfer] FS Developer v6 Hippocampal Segmentation

[Noah Markowitz]

Hello,

We’re going to be rerunning FS Recon-all using the newest version of FS v6 
developer’s edition. Before any data is pre-processed, we wanted to receive 
input from other users on their own experience using it, specifically the 
Hippocampal subfield segmentation protocol. Are people receiving any unusual 
errors? Is there a lower resolution or less accurate segmentation of other 
cortical or subcortical structures? Any input would be great.

Cheers,

Noah Markowitz
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[Freesurfer] Help with V6

[Noah Markowitz]

Hi,

I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the 
error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and 
source just as described for previous versions.

Also, I have Matlab 2014b downloaded on the computer (obviously comes with 
runtime) but am unsure if the runtime folder needs to be placed in the FS 
folder or is fine where it is. 

Any FS experts help with these two problems and concerns? Much appreciated if 
you do.

Cheers,

Noah Markowitz
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Re: [Freesurfer] Help with V6

[Noah Markowitz]

Hey Eugenio,

I was able to resolve it with the help of another expert. One of the problems 
definitely was that 2014b doesn’t run on the hippocampal-subfields module. 
Maybe try adding that as a note to the website as numerous people have access 
to the 2014b version and 2015a was just released. Thanks again for all the help.

Cheers,
Noah

> On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias  wrote:
> 
> Hi Noah,
> this error is pretty weird. Can you please send us the exact command you 
> executed?
> Regarding the runtime: your 2014b runtime won't work. You need to follow the 
> instructions here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
> Cheers,
> Eugenio
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> - Original Message -
> From: "Noah Markowitz" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, July 3, 2015 4:20:02 AM
> Subject: [Freesurfer] Help with V6
> 
> Hi,
> 
> I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the 
> error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and 
> source just as described for previous versions.
> 
> Also, I have Matlab 2014b downloaded on the computer (obviously comes with 
> runtime) but am unsure if the runtime folder needs to be placed in the FS 
> folder or is fine where it is. 
> 
> Any FS experts help with these two problems and concerns? Much appreciated if 
> you do.
> 
> Cheers,
> 
> Noah Markowitz
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Re: [Freesurfer] (no subject)

[Noah Markowitz]

On the surface it seems like you moved the FS directory from one pathway to 
another. If you place FS back into your applications folder, it may work. Also, 
if you have Matlab 2014b or 2015a installed, it won’t work. You need 
2012b-2014a for the process to run. 

Hope this helps in any way.

Noah

> On Jul 7, 2015, at 1:01 PM, jinyi  wrote:
> 
> Hello Freesurfers
> 
> I meet a problem in calculate Lgi 
> 
> I run fs in vituralBOX, matlab is installed. At the begining everything seems 
> fine .but error come in "make_outer_surface". The details are in below.
> 
> 
> 
> 
> =
> xubuntu-VirtualBox:~> recon-all -s test001 -localGI
> 
> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
> 
> INFO: FreeSurfer build stamps do not match
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rwxrwxrwx 1 fsuser fsuser 495621 Nov 17  2014 
> /usr/local/freesurfer/subjects/test001/scripts/recon-all.log
> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
> UTC 2012 i686 i686 i386 GNU/Linux
> INFO: current FREESURFER_HOME does not match that of previous processing.
> Current: /usr/local/freesurfer
> Previous: /Applications/freesurfer
> /usr/local/freesurfer/subjects/test001/surf
> #
> #@# Local Gyrification Index lh Mon Jul  6 22:51:12 EDT 2015
> 
>  mris_compute_lgi --i lh.pial 
> 
> =
> rm -Rf 
> /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mkdir -p 
> /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mris_fill -c -r 1 lh.pial 
> /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> =
> reading surface from lh.pial...
> writing filled volume to 
> /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
> conforming output volume
> setting resolution for intermediate calculations to 1.
> =
> make_outer_surface('/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
>  exit
> =
> ERROR:: Too many arguments.
> 
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[Freesurfer] tkregister2_cmdl

[Noah Markowitz]

Hi,

I’m running FS6 and everything seems to be running fine except that a txt file 
filled with this error message is created:

rm: No match.
tkregister2_cmdl: Command not found.
tkregister2_cmdl: Command not found.
tkregister2_cmdl: Command not found.
tkregister2_cmdl: Command not found.
tkregister2_cmdl: Command not found.
tkregister2_cmdl: Command not found

I don’t know the precise function of this command but from what I’ve gathered 
it has something to do with coregistration. Can anyone let me know the function 
of this precise command and if I should be rerun this program or not? 

Much appreciated,

Noah___
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[Freesurfer] Extend pial surface

[Noah Markowitz]

Hi all, I’m trying to extend the pial surface to include missing GM. Part of 
the problem is that the wm.mgz seems to include the WM, but does not extend the 
border of the pial surface. I’ve attached links to pictures of the one of the 
scans. Any help would be greatly appreciated.

Noah

Without wm.mgz overlay: 
http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png 

With mg.mgz overlay: 
http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png 



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[Freesurfer] Pial Problem #2

[Noah Markowitz]

Hi, I just sent a question a few minutes ago but forgot to include an important 
bit in it. Some pial I’m trying to include doesn’t have WM to add that will 
push the pial surface back. I attached a link to an example. This happens in 
the parietal lobe, temporal pole, as well as frontal pole. Any suggestions?

Noah

http://www.mediafire.com/file/it2ukdeg15pphyk/missing_GM2.png 

http://www.mediafire.com/view/8x3avz4l9lxpoeg/missing_GM1.png___
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[Freesurfer] Error on rawavg

[Noah Markowitz]

Hi all,

As I’m doing manual edits, one of my subjects stops running due to the 
following error:

ERROR: could not read subj1/mri/rawavg.mgz as type 3

Any ideas how to correct this? Please let me know.

Noah

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[Freesurfer] surfaceRAS to vertex coordinates

[Noah Markowitz]

External Email - Use Caution

Hi all,

I’m trying to get the coordinates for specifice vertices of an inflated 
surface. I noticed there’s a difference between surfaceRAS and vertex 
coordinates (though I don’t understand it much). 

After getting the index of the specific vertex of interest I load the inflated 
surface through matlab with `vert = read_surf(‘lh.inflated’);` but notice that 
the coordinates it outputs is in surfaceRAS. 

ex: For fsaverage vertex 34686
SurfaceRAS = -17.53, -15.27, 48.87
Vertex = -46.54,-28.5,56.26

Is there a way I can get the vertex coordinates from those surfaceRAS 
coordinates? Please let me know when you get the chance.

Have a good day,

Noah


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