Hello-
The 'RB_all_2008-03-26.gca' and 'RB_all_withskull_2008-03-26.gca' files are
packaged with the 5.1 release.
Is there any reason the 2011 versions ('RB_all_2011-10-25.gca' &
'RB_all_withskull_2011-10-25.gca ')are not included in the 5.1 release or users
should not update to these newer v
Hi-
This is an useful addition. I have a couple of questions about the outputs:
1. " has 36 outliers": I assume this refers to the volumetrics
as compared to FS Average, where an outlier is a volume +/- 2 SDs?
2. "7927 vertices did not have an annotation!:" I understand what this
Hello-
I just downloaded the updated freeview.bin (8/23/2012) file (from:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/).
I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42
CDT 2012 x86_64 x86_64 x86_64 GNU/Linux).
When I tried to exe
ansky [mailto:ni...@nmr.mgh.harvard.edu]
|Sent: Tuesday, October 09, 2012 1:52 PM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Error with updated freeview.bin
|
|Wil,
|
|I've just uploaded the latest-greatest dev build of freeview.bin for
|centos6 he
Hi-
I've come across a peculiar behavior with recon_checker, and am hoping someone
can shed some light on this.
I have used it 100's of times in the past, but not for about 2 months. I
recently processed a large set of cases I wanted to QC. When I ran it, some,
but not all, of the snaps were c
-contained.
This is a real mystery
-Wil
-Original Message-
From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, January 08, 2013 6:29 PM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA Tools Snaps Scrambled
Hi Irwin,
It sounds
aving problems with any of the other
apps running on my system. Obviously I'm not asking you to help diagnose the
health of my system, but though you might have some thoughts/suggestions.
Regards,
Wil
-Original Message-----
From: Irwin, William
Sent: Wednesday, January 09, 2013 5:37 AM
n this?
Thanks,
Wil
-Original Message-
From: Irwin, William
Sent: Wednesday, January 09, 2013 6:22 AM
To: Louis Nicholas Vinke
Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William
Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification
Hi Louis-
I was speaking cryptically an
Hi Bruce-
The teams at UCSF and the SFVAMC would be more than willing to provide letters
of support.
Regards,
Wil
───
William Irwin | Imaging Core Supervisor
University of California | Mission Bay
Sandler Neurosciences Building
Memory and Aging Center | MC: 1207
675 Nel
Hello-
Our group occasionally encounters patients with various syndromes such that
'excessive' head movement is an issue. One solution on which we rely is
acquiring an "accelerated" MPRAGE sequences (Siemens GRAPPA) which takes about
½ the time. For those not familiar with this method, the res
Hi Bruce-
Is this fix going to be put on the site as a patch/fix download (e.g.,
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/)
or distributed on a per-user need?
Thanks,
Wil
William Irwin | Brain Imaging Coordinator
UCSF |
Bruce,
Until it is determined if there is enough interest, how do I obtain it for
centos4_x86_64?
Thanks much,
Wil
|-Original Message-
|From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Friday, August 05, 2011 12:10 PM
|To: Irwin, William
|Cc: Christopher Luna; freesurfer
Hi-
I'm at a bit of a loss as to how to address and/or fix these errors.
The native input images are very good quality; the conversion to T1.mgz is
fine; the brainmask.mgz is good, a bit of dura remained at the
parietal/occipital region (very common); otherwise, the skull stripping is very
cle
Hi-
Note, this bug still exists in 5.1. Below is my exchange with Martin and Nick a
several months ago.
-Wil
---
|-Original Message-
|From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
|Sent: Wednesday, May 25, 2011 3:52 PM
|To: Irwin, William; Martin Reuter
|Subject: RE: 5.1.0
Hello-
In the FreeSurferColorLUT.txt,v 1.70.2.1 2011/05/02 file, there are labels for
sub-regions of interest. For example amygdala and brainstem.
How does one go about extracting the volumes for these regions?
Thank you in advance,
Wil
#No. Label Name:
fis...@nmr.mgh.harvard.edu]
|Sent: Wednesday, August 24, 2011 12:28 PM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Procedure to get amygdalar sub-regions and
|brainstem Brainstem consituents volumes
|
|Hi Wil
|
|sorry, we don't have anything for that yet, althoug
Hi
For purposes of de-identification, is there an easy way to "rename" all the
contents of data for a processed subject?
For example, If I want to do share data or do reliability training on an
existing subject (e.g., "ABC1234"), I want to rename everything associated with
this case to "Case1"
That is not going to change the information in associated files, for example
stats files.
-Wil
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: Thursday, September 01, 2011 8:09 AM
To: Irwin, William
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Thursday, September 01, 2011 8:58 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Renaming a processed subject
|
|I think the .mgh/.mgz files and surfaces contain some cmdline info in them, so
|it may not be so trivial. R
Hi-
I'm a bit stumped by a cased. The input volume looks very good. The first error
was the Talairach transform would not complete, so I used the '-notal-check'
flag. As I have been focused on other things, I just let the job run, but after
2 weeks, it is stuck (I assume) as indicated. It is ru
on to .mgz seem likely to explain why the
Talairach transform failed.
Suggested on what would cause this glitch?
Thanks,
Wil
|-Original Message-
|From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
|Sent: Monday, October 17, 2011 6:27 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.h
Hi Nick-
I was explicitly told by you there was not stable centos5 release of 5.1. And
unless it is located elsewhere, it is not located in:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/
Can you please clarify this?
Thanks,
Wil
|-Original Message-
|From: Nick Schmansky [
Hi -
The link to download the QATools script
(http://surfer.nmr.mgh.harvard.edu/fswiki/QATools) for non-MGH users is broken,
and I couldn't find it by looking through the ftp download directories.
Regards,
Wil
___
Freesurfer mailing list
Freesurfer@n
Hi Doug-
I wanted to follow up on this procedure and ask for a bit of clarification. As
an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz'
lobar volume with both WM and GM for both RH and LH.
1:
mri_annotation2label --s --hemi rh --lobesStrict lobe
mri_annotation2la
might be a less manual way of doing this.
Thanks,
Wil
|-Original Message-
|From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
|Sent: Thursday, April 05, 2012 8:30 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] lobar WM volumes
|
|You don't
Hi-
This is probably a question for Koen, but perhaps others could help me out.
I want to read into Matlab the 'posterior_*.mgz' files generated by the
subfield segmentation. I'm not exactly sure the format/content of these files,
but in addition to any information (e.g., some coordinate refere
Hi-
It would appear the stable release for centos6 is ready for primetime
'stable5.1-bin.tgz'; Is this correct? There is an updated version of
'mri_info' based on file size
(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/).
mri_info in 'stable5.1-bin.tgz': 978
Hi Koen,
Yes, Thanks. A stupid syntax/typo on my part.
-Wil
|-Original Message-
|From: Koen Van Leemput [mailto:k...@nmr.mgh.harvard.edu]
|Sent: Monday, April 09, 2012 12:35 AM
|To: Irwin, William
|Cc: freesurfer@nmr.mgh.harvard.edu
|Subject: Re: [Freesurfer] Reading/loading posterior_
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