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Today's Topics:
1. No FTP Access (Rockers, Elijah D.)
2. Re: No FTP Access (Rockers, Elijah D.)
3. Re: gzip: stdin: unexpected end of file (Z K)
4. Re: Re-running after Base Image Edits (Steros)
5. Re: FS 6.0 Freeview (peng)
6. Re: FS 6.0 Freeview (Kevin Aquino)
7. Virtualbox for FS v6.0 ? (Randolph Andrews)
8. recon-all error (6.0) (Trisanna Sprung-Much)
9. deformation fields (Worker, Amanda)
10. How to output particular area from stats subdir (Jing Gu)
---------- Forwarded message ----------
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Wed, 22 Feb 2017 17:22:06 +0000
Subject: [Freesurfer] No FTP Access
Is there by any chance another way to download Freesurfer? My
institution does not allow FTP connections (HIPPA...) Same goes for the
tutorial data, but obviously Freesurfer is the priority here... thanks.
- Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
---------- Forwarded message ----------
From: "Rockers, Elijah D." <edrockers@houstonmethodist.org>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Wed, 22 Feb 2017 17:24:23 +0000
Subject: Re: [Freesurfer] No FTP Access
Nevermind. I discovered if I just change ftp to https in the download
link, it works fine.
- Eli
On Wed, 2017-02-22 at 12:22 -0500, Elijah Rockers wrote:
> Is there by any chance another way to download Freesurfer? My
> institution does not allow FTP connections (HIPPA...) Same goes for the
> tutorial data, but obviously Freesurfer is the priority here... thanks.
>
> - Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
---------- Forwarded message ----------
From: Z K <zkaufman@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Bcc:
Date: Wed, 22 Feb 2017 12:54:38 -0500
Subject: Re: [Freesurfer] gzip: stdin: unexpected end of file
Its probably a corrupted download. What do you get when type 'sha1sum
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz'?
$> sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
1723ef916c4e74ee8fff72438e9c6c91c79bd4cb
You should get the 1723ef... number from above.
On 02/21/2017 07:27 PM, Kambiz Tavabi wrote:
>
> After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt
> 16.04 (64b) machine with
>
> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
>
> Returns an error:
> gzip: stdin: unexpected end of file
> tar: Child returned status 1
> tar: Error is not recoverable: exiting now
>
> Is there a way around this?
>
>
> ------------------------------------------------------------
> Kambiz Tavabi PhD
> Institute for Learning & Brain Sciences
> 1715 Columbia Road N
> Portage Bay Building
> Box 357988
> University of Washington
> Seattle, WA 98195-7988
> Tel: 206-685-6173
> ------------------------------------------------------------
>
> /Confidentiality Notice: Because email is not secure, please be aware
> that we cannot guarantee the confidentiality of information sent by
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---------- Forwarded message ----------
From: Steros <steros@nmr.mgh.harvard.edu>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Wed, 22 Feb 2017 12:08:40 -0800
Subject: Re: [Freesurfer] Re-running after Base Image EditsHello Corrina,I believe the answer to your question is Pho.Best,StephanieThanks in advance for any help!Hi there,We are attempting edits on base images and a couple of questions came up when re-running through the pipeline:
1. After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”).
2. When re-running a base, after edits, starting at autorecon2, is it necessary to include all the timepoints in the command like (ie. “-tp subj1 –tp subj2”)? It’d make things simpler if that wasn’t necessary and our reading of the longitudinal processing protocol seems to suggest all the “tp” related stuff happens in autorecon1 when the norm image and transformations are generated. After that, the doc suggests that it simply processes that averaged image per-usual.Corrina Fonseca
Staff Research Associate IISenior Imaging Technician
Center for Imaging of Neurodegenerative DiseasesSan Francisco VA Medical Center
4150 Clement Street (114M)
San Francisco, CA 94121
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---------- Forwarded message ----------
From: peng <prion.w@gmail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Thu, 23 Feb 2017 12:58:31 +0100
Subject: Re: [Freesurfer] FS 6.0 FreeviewDear Ruopeng,I have the same problem even before the current version 6 release, and it was "solved" by invoke freeview from the command line (term). I guess, to start from the icon, it might use different setup files.bestPengOn Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:Or would it be possible to send us the full crash report?On Feb 17, 2017, at 10:17 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:Hi Dan. Is there an error output to the screen or terminal window? We
will probably need that to help diagnose the issue.
On 02/17/2017 05:31 AM, Daniel Carey wrote:Dear All,_______________________________________________
I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
to load volumes in Freeview. When selecting 'File > Load volume', the
dialog box appears, but when I select any T1.mgz and click Ok, Freeview
immediately crashes.
Has anyone encountered this same issue?
Best wishes,
Dan
---
Dr. Daniel Carey
Post-Doctoral Research Fellow - Statistician
The Irish LongituDinal Study on Ageing (TILDA)
Trinity College Dublin
Dublin 2, Ireland.
Email: careyda@tcd.ie <mailto:careyda@tcd.ie>
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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---------- Forwarded message ----------
From: Kevin Aquino <aquino.km@gmail.com>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Thu, 23 Feb 2017 23:45:10 +1100
Subject: Re: [Freesurfer] FS 6.0 FreeviewI've had the same problem,the only solution I have is to only open Freeview from terminalCheers,KevoDear Ruopeng,I have the same problem even before the current version 6 release, and it was "solved" by invoke freeview from the command line (term). I guess, to start from the icon, it might use different setup files.bestPengOn Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:Or would it be possible to send us the full crash report?On Feb 17, 2017, at 10:17 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:Hi Dan. Is there an error output to the screen or terminal window? We
will probably need that to help diagnose the issue.
On 02/17/2017 05:31 AM, Daniel Carey wrote:Dear All,_______________________________________________
I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
to load volumes in Freeview. When selecting 'File > Load volume', the
dialog box appears, but when I select any T1.mgz and click Ok, Freeview
immediately crashes.
Has anyone encountered this same issue?
Best wishes,
Dan
---
Dr. Daniel Carey
Post-Doctoral Research Fellow - Statistician
The Irish LongituDinal Study on Ageing (TILDA)
Trinity College Dublin
Dublin 2, Ireland.
Email: careyda@tcd.ie <mailto:careyda@tcd.ie>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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dispose of the e-mail.
---------- Forwarded message ----------
From: Randolph Andrews <randrews@admdx.com>
To: <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Thu, 23 Feb 2017 08:33:25 -0600
Subject: [Freesurfer] Virtualbox for FS v6.0 ?In past releases of FreeSurfer, there had been a version of the software suite contained in a VirtualBox (alongside the MacOS and Linux versions). Currently, I only see Mac & Linux. Is there a plan to release a VirtualBox edition of 6.0 ?
---------- Forwarded message ----------
From: Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Thu, 23 Feb 2017 11:48:26 -0500
Subject: [Freesurfer] recon-all error (6.0)TrisannaBestAny ideas?Hi AllI am trying to run a subject in 6.0 (it ran perfectly well in 5.3) and it stops when trying to transform to the "conformed" space. I get the following error after about a minute. I have not seen this error before.
mri_convert ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.2860/nu1.mnc orig_nu.mgz --like orig.mgz --conform
ncopen: filename "./tmp.mri_nu_correct.mni.2860/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.2860/nu1.mnc
mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.2860/nu1.mnc
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.2860/nu1.mnc...
Linux kaplan 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s icbm-131 exited with ERRORS at Thu Feb 23 11:40:53 EST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting--Ph.D. CandidateMcGill UniversityIntegrated Program in NeurosciencePsychology
---------- Forwarded message ----------
From: "Worker, Amanda" <amanda.worker@kcl.ac.uk>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc:
Bcc:
Date: Thu, 23 Feb 2017 16:55:09 +0000
Subject: [Freesurfer] deformation fields
Hi All,
I am trying to use the subcortical segmentation of regions from the longitudinal template to propogate to each time point using deformation fields.
Does anyone know how if this is possible and if so, how can I do it?
Thanks in advance,
Amanda
---------- Forwarded message ----------
From: Jing Gu <gujing2009@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Bcc:
Date: Thu, 23 Feb 2017 11:55:59 -0500
Subject: [Freesurfer] How to output particular area from stats subdirDear FreeSurfer Developers,_______________________________________________By using the following code, we can get volume data of different areas from stats file.asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txtHow can I get information of one or two areas, such as hippocampal? thanksBest,Gina
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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