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-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > 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." <edrock...@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." <edrock...@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 <zkauf...@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> > > ------------------------------------------------------------ > > > > /Confidentiality Notice: Because email is not secure, please be aware > > that we cannot guarantee the confidentiality of information sent by > > email. If you are not the intended recipient of this email, please > > notify the sender by reply email, and then destroy all copies of the > > message and any attachments./ > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ---------- Forwarded message ---------- > From: Steros <ste...@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 <cosfo...@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>* > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ---------- Forwarded message ---------- > From: peng <prio...@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 <rpw...@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 <zkauf...@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: care...@tcd.ie <mailto:care...@tcd.ie <care...@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 > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > > > ---------- Forwarded message ---------- > From: Kevin Aquino <aquino...@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 <prio...@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 <rpw...@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 <zkauf...@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: care...@tcd.ie <mailto:care...@tcd.ie <care...@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 > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > 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 > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > > ---------- Forwarded message ---------- > From: Randolph Andrews <randr...@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-m...@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.wor...@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 <gujing2...@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 > > > 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 > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
_______________________________________________ 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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
