Re: [Freesurfer] gzip: stdin: unexpected end of file

I just did a test download on my home network and I got the correct sha

1723ef916c4e74ee8fff72438e9c6c91c79bd4cb freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

Perhaps your network times out after a certain time period, or has a cap on the file size?

sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz returns da39a3ee5e6b4b0d3255bfef95601890afd80709

A corrupted download three times! Do I just try downloading again?

On Thu, Feb 23, 2017 at 9:02 AM freesurfer-request@nmr.mgh.harvard.edu wrote:

...

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When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." 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 <(206)%20685-6173>

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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 Edits Hello Corrina,

I believe the answer to your question is Pho.

Best, Stephanie

On Feb 21, 2017, at 5:22 PM, Corrina Fonseca cosfonse@gmail.com wrote:

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.

Thanks in advance for any help!

*Corrina Fonseca* Staff Research Associate II

Senior Imaging Technician *Center for Imaging of Neurodegenerative Diseases*

*San Francisco VA Medical Center*

*4150 Clement Street (114M)*

*San Francisco, CA 94121*

*http://www.radiology.ucsf.edu/cind http://www.radiology.ucsf.edu/cind*

*(415) 221-4810 x23088 <(415)%20221-4810>*

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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 Freeview Dear 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.

best Peng

On 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 careyda@tcd.ie>

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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 Freeview

I've had the same problem, the only solution I have is to only open Freeview from terminal

Cheers, Kevo

On 23 Feb 2017, at 10:58 pm, peng prion.w@gmail.com wrote:

Dear 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.

best Peng

On 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 careyda@tcd.ie>

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---------- 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) Hi All

I 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

Any ideas?

Best

Trisanna

Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

---------- 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 subdir Dear 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.txt

How can I get information of one or two areas, such as hippocampal? thanks

Best, Gina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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