Re: [Freesurfer] ASeg Stats and Cortical Ribbon Mask in autorecon2?

2013-03-16 Thread Hiroki Kurashige 
I'm sorry.
I forgot to tell you the version of my freesurfer.
The version is v5.2.0.

Thanks,
Hiroki.

(2013/03/17 13:51), Hiroki Kurashige wrote:
> Dear freesurferers,
>
> I have two questions about the recon-all with -autorecon2 option.
>
> First one is about ASeg Stats (mri_segstats).
> In the following status log, I found that ASeg Stats step was executed
> as a final step of -autorecon2:
>
> status file for recon-all
> Sat Mar 16 21:50:42 JST 2013
> #@# EM Registration Sat Mar 16 21:50:42 JST 2013
> #@# CA Normalize Sat Mar 16 22:13:19 JST 2013
> #@# CA Reg Sat Mar 16 22:15:14 JST 2013
> #@# CA Reg Inv Sun Mar 17 01:57:37 JST 2013
> #@# Remove Neck Sun Mar 17 01:58:47 JST 2013
> #@# SkullLTA Sun Mar 17 02:00:06 JST 2013
> #@# SubCort Seg Sun Mar 17 02:23:38 JST 2013
> #@# Merge ASeg Sun Mar 17 02:50:50 JST 2013
> #@# Intensity Normalization2 Sun Mar 17 02:50:50 JST 2013
> #@# Mask BFS Sun Mar 17 02:54:56 JST 2013
> #@# WM Segmentation Sun Mar 17 02:54:58 JST 2013
> #@# Fill Sun Mar 17 02:57:59 JST 2013
> #@# Tessellate lh Sun Mar 17 02:58:54 JST 2013
> #@# Smooth1 lh Sun Mar 17 02:59:01 JST 2013
> #@# Inflation1 lh Sun Mar 17 02:59:04 JST 2013
> #@# QSphere lh Sun Mar 17 02:59:28 JST 2013
> #@# Fix Topology lh Sun Mar 17 03:02:37 JST 2013
> #@# Make White Surf lh Sun Mar 17 03:23:10 JST 2013
> #@# Smooth2 lh Sun Mar 17 03:33:13 JST 2013
> #@# Inflation2 lh Sun Mar 17 03:33:17 JST 2013
> #@# Curvature Stats lh Sun Mar 17 03:35:12 JST 2013
> #@# Tessellate rh Sun Mar 17 03:35:17 JST 2013
> #@# Smooth1 rh Sun Mar 17 03:35:23 JST 2013
> #@# Inflation1 rh Sun Mar 17 03:35:26 JST 2013
> #@# QSphere rh Sun Mar 17 03:35:50 JST 2013
> #@# Fix Topology rh Sun Mar 17 03:39:04 JST 2013
> #@# Make White Surf rh Sun Mar 17 03:56:40 JST 2013
> #@# Smooth2 rh Sun Mar 17 04:06:43 JST 2013
> #@# Inflation2 rh Sun Mar 17 04:06:46 JST 2013
> #@# Curvature Stats rh Sun Mar 17 04:08:41 JST 2013
> #@# ASeg Stats Sun Mar 17 04:08:46 JST 2013
> recon-all -s bert finished without error at Sun Mar 17 04:11:54 JST 2013
>
> According to the help document for recon-all, ASeg Stats should run in
> the -autorecon3 step, not in -autorecon2.
> Is this some kind of bug?
> http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1?action=print
>
> Second questions is about Cortical Ribbon Mask.
> At the Manual-Intervention Workflow Directives in recon-all help,
> Cortical Ribbon Mask is classified into the part of -autorecon3.
> However, the Step Description Summaries says that the -autorecon2 stage
> ends at the Cortical Ribbon Mask.
> Which one is right?
> http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
>
>
> Thanks,
> Hiroki
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
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[Freesurfer] ASeg Stats and Cortical Ribbon Mask in autorecon2?

2013-03-16 Thread Hiroki Kurashige 
Dear freesurferers,

I have two questions about the recon-all with -autorecon2 option.

First one is about ASeg Stats (mri_segstats).
In the following status log, I found that ASeg Stats step was executed
as a final step of -autorecon2:

status file for recon-all
Sat Mar 16 21:50:42 JST 2013
#@# EM Registration Sat Mar 16 21:50:42 JST 2013
#@# CA Normalize Sat Mar 16 22:13:19 JST 2013
#@# CA Reg Sat Mar 16 22:15:14 JST 2013
#@# CA Reg Inv Sun Mar 17 01:57:37 JST 2013
#@# Remove Neck Sun Mar 17 01:58:47 JST 2013
#@# SkullLTA Sun Mar 17 02:00:06 JST 2013
#@# SubCort Seg Sun Mar 17 02:23:38 JST 2013
#@# Merge ASeg Sun Mar 17 02:50:50 JST 2013
#@# Intensity Normalization2 Sun Mar 17 02:50:50 JST 2013
#@# Mask BFS Sun Mar 17 02:54:56 JST 2013
#@# WM Segmentation Sun Mar 17 02:54:58 JST 2013
#@# Fill Sun Mar 17 02:57:59 JST 2013
#@# Tessellate lh Sun Mar 17 02:58:54 JST 2013
#@# Smooth1 lh Sun Mar 17 02:59:01 JST 2013
#@# Inflation1 lh Sun Mar 17 02:59:04 JST 2013
#@# QSphere lh Sun Mar 17 02:59:28 JST 2013
#@# Fix Topology lh Sun Mar 17 03:02:37 JST 2013
#@# Make White Surf lh Sun Mar 17 03:23:10 JST 2013
#@# Smooth2 lh Sun Mar 17 03:33:13 JST 2013
#@# Inflation2 lh Sun Mar 17 03:33:17 JST 2013
#@# Curvature Stats lh Sun Mar 17 03:35:12 JST 2013
#@# Tessellate rh Sun Mar 17 03:35:17 JST 2013
#@# Smooth1 rh Sun Mar 17 03:35:23 JST 2013
#@# Inflation1 rh Sun Mar 17 03:35:26 JST 2013
#@# QSphere rh Sun Mar 17 03:35:50 JST 2013
#@# Fix Topology rh Sun Mar 17 03:39:04 JST 2013
#@# Make White Surf rh Sun Mar 17 03:56:40 JST 2013
#@# Smooth2 rh Sun Mar 17 04:06:43 JST 2013
#@# Inflation2 rh Sun Mar 17 04:06:46 JST 2013
#@# Curvature Stats rh Sun Mar 17 04:08:41 JST 2013
#@# ASeg Stats Sun Mar 17 04:08:46 JST 2013
recon-all -s bert finished without error at Sun Mar 17 04:11:54 JST 2013

According to the help document for recon-all, ASeg Stats should run in
the -autorecon3 step, not in -autorecon2.
Is this some kind of bug?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1?action=print

Second questions is about Cortical Ribbon Mask.
At the Manual-Intervention Workflow Directives in recon-all help,
Cortical Ribbon Mask is classified into the part of -autorecon3.
However, the Step Description Summaries says that the -autorecon2 stage
ends at the Cortical Ribbon Mask.
Which one is right?
http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all


Thanks,
Hiroki
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[Freesurfer] question about hippocampus subfield segmentation flag

2013-03-16 Thread Mehul Sampat 
Hi Folks,
I had a question about the hippocampus subfield segmentations as described
here :
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation

I am planning to use this processing outline:

1. recon-all -s  -autorecon1 -autorecon2
2. add control points
3. recon -all -s  -autorecon2-cp
4. recon -all -s  -autorecon3 -hippo-subfields

Is this permissible or do I need to need to introduce the -hippo-subfields
flag earlier.
Thanks
Mehul
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Re: [Freesurfer] Coordinates of center of gravity of a cluster in Freesurfer

2013-03-16 Thread Maleki, Nasim 
Thanks so much Doug.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Saturday, March 16, 2013 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Coordinates of center of gravity of a cluster in 
Freesurfer

With mri_surfcluster you can add --centroid to the command line to get centroid 
of the cluster instead of max stat. You can do the same thing with 
mri_glmfit-sim

doug


On 3/14/13 3:06 PM, Maleki, Nasim wrote:
Hi all,

I would like to calculate the coordinates of center of gravity of a cluster in 
Freesurfer. Is there a way to do this in Freesurfer?

Thanks,
Nasim



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Re: [Freesurfer] Coordinates of center of gravity of a cluster in Freesurfer

2013-03-16 Thread Douglas Greve 
With mri_surfcluster you can add --centroid to the command line to get 
centroid of the cluster instead of max stat. You can do the same thing 
with mri_glmfit-sim


doug


On 3/14/13 3:06 PM, Maleki, Nasim wrote:

Hi all,

I would like to calculate the coordinates of center of gravity of a 
cluster in Freesurfer. Is there a way to do this in Freesurfer?


Thanks,
Nasim


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Re: [Freesurfer] Use a dfs file for measurements

2013-03-16 Thread Bruce Fischl 

Hi Valtina

if you can get your brainsuite surfaces into matlab then you should be 
able to write them out with write_surf.m


cheers
Bruce
On Sat, 16 Mar 2013, Valtina 
Pouegue wrote:



Hi Freesurfers, 
I,ve done a segmentation with Brainsuite and as result I have dfs file  for
Pial surfaxe L/R hemisphere. I would like to do some measurement with
mris_anatomical_stats of Freesurfers.   But this fonction of FreeSurfer only
accept surface of extension like ( .pial).  How can I do this conversion ? 
Thanks . 
VP 

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[Freesurfer] Use a dfs file for measurements

2013-03-16 Thread Valtina Pouegue 
Hi Freesurfers, 
I,ve done a segmentation with Brainsuite and as result I have dfs file  for 
Pial surfaxe L/R hemisphere. I would like to do some measurement with 
mris_anatomical_stats of Freesurfers.   But this fonction of FreeSurfer only 
accept surface of extension like ( .pial).  How can I do this conversion ? 
Thanks . VP ___
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