I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu?
Thoughts?
Pros vs Cons?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads)
On 10/13/2016 01:25 PM, Brad Matushewski wrote:
Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 12:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement.
The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version.
On 10/13/2016 12:39 PM, Brad Matushewski wrote:
I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 11:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Brad Matushewski bjmatush@uwo.ca Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine.
See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying).
-Zeke
On 10/13/2016 10:58 AM, Brad Matushewski wrote:
Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir t u alImage
...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements.
What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 13, 2016 9:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device miicv_put: MINC package entry point nu_evaluate: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768)
as for what would have been next, that of course depends on what you want to study
cheers Bruce
On Thu, 13 Oct 2016, Brad Matushewski wrote:
I just tried to run my first recon-all.
What now?
Logo
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447
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
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
Which version of Ubuntu are you trying to install? I ask because I too had issues when installing ubuntu14 on a new laptop with laptop with UEFI.
Try using Ubuntu16 instead if you haven't already. And more luck with that, and here is a link to more information as setting up these dual boots has gotten more difficult on newer laptops: https://help.ubuntu.com/community/UEFI
On Dec 2, 2016, at 8:26 AM, Brad Matushewski bjmatush@uwo.ca wrote:
I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu?
Thoughts?
Pros vs Cons?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads)
On 10/13/2016 01:25 PM, Brad Matushewski wrote: Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 12:53 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement.
The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version.
On 10/13/2016 12:39 PM, Brad Matushewski wrote: I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 11:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Brad Matushewski bjmatush@uwo.ca Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine.
See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying).
-Zeke
On 10/13/2016 10:58 AM, Brad Matushewski wrote: Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir t u alImage
...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements.
What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 13, 2016 9:43 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device miicv_put: MINC package entry point nu_evaluate: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768)
as for what would have been next, that of course depends on what you want to study
cheers Bruce
On Thu, 13 Oct 2016, Brad Matushewski wrote:
I just tried to run my first recon-all.
What now?
Logo
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ubuntu 14.04.5 LTS
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: December 2, 2016 8:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Ubuntu or Centos?
Which version of Ubuntu are you trying to install? I ask because I too had issues when installing ubuntu14 on a new laptop with laptop with UEFI.
Try using Ubuntu16 instead if you haven't already. And more luck with that, and here is a link to more information as setting up these dual boots has gotten more difficult on newer laptops: https://help.ubuntu.com/community/UEFI
On Dec 2, 2016, at 8:26 AM, Brad Matushewski <bjmatush@uwo.camailto:bjmatush@uwo.ca> wrote: I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu?
Thoughts?
Pros vs Cons?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads)
On 10/13/2016 01:25 PM, Brad Matushewski wrote:
Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 12:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all exited with ERRORS
I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement.
The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version.
On 10/13/2016 12:39 PM, Brad Matushewski wrote: I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 11:03 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; Brad Matushewski <bjmatush@uwo.camailto:bjmatush@uwo.ca> Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine.
See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying).
-Zeke
On 10/13/2016 10:58 AM, Brad Matushewski wrote: Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir t u alImage
...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements.
What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 13, 2016 9:43 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device miicv_put: MINC package entry point nu_evaluate: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768)
as for what would have been next, that of course depends on what you want to study
cheers Bruce
On Thu, 13 Oct 2016, Brad Matushewski wrote:
I just tried to run my first recon-all.
What now?
Logo
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK - I went with Ubuntu. I had trouble getting the license.txt file in place due usr/local requiring authentication. I bypassed the password part by leading using "sudo gedit" which obviously prompted me for a password but let me edit / paste license text into file.
When I tried this:
$> cd $FREESURFER_HOME/subjects $> mri_convert sample-001.mgz sample-001.nii.gz
I got:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz
When I tried:
$> cd $FREESURFER_HOME/subjects $> freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red
I got:
freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory
Not sure what I did wrong.
Suggestions?
________________________________ From: Brad Matushewski Sent: Friday, December 2, 2016 8:48:11 AM To: Freesurfer support list Subject: RE: [Freesurfer] Ubuntu or Centos?
Ubuntu 14.04.5 LTS
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: December 2, 2016 8:42 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Ubuntu or Centos?
Which version of Ubuntu are you trying to install? I ask because I too had issues when installing ubuntu14 on a new laptop with laptop with UEFI.
Try using Ubuntu16 instead if you haven't already. And more luck with that, and here is a link to more information as setting up these dual boots has gotten more difficult on newer laptops:
https://help.ubuntu.com/community/UEFI
UEFI - Community Help Wikihttps://help.ubuntu.com/community/UEFI help.ubuntu.com Introduction. The Extensible Firmware Interface (EFI) or its version 2.x variant, Unified EFI (UEFI) is a firmware type that is widespread on recent ...
On Dec 2, 2016, at 8:26 AM, Brad Matushewski <bjmatush@uwo.camailto:bjmatush@uwo.ca> wrote:
I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu?
Thoughts?
Pros vs Cons?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all exited with ERRORS
Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads)
On 10/13/2016 01:25 PM, Brad Matushewski wrote:
Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment?
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 12:53 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement.
The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version.
On 10/13/2016 12:39 PM, Brad Matushewski wrote:
I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact.
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 11:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; Brad
Matushewski <bjmatush@uwo.camailto:bjmatush@uwo.ca>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine.
See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying).
-Zeke
On 10/13/2016 10:58 AM, Brad Matushewski wrote:
Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir
t
u
alImage
...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements.
What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD.
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce
Fischl
Sent: Thursday, October 13, 2016 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination
status=768)
as for what would have been next, that of course depends on what you
want to study
cheers
Bruce
On
Thu,
13 Oct
2016, Brad Matushewski wrote:
I just tried to run my first recon-all.
What now?
Logo
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health School of Kinesiology Western
University Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x 89066
Fax: (519) 850-2447
_______________________________________________
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Looks like a permissions issue. Either open the permissions on the $FREESURFER_HOME/subjects directory. Or, try copying over the sample-001.mgz file to somewhere where root permissions are not required, then run the same command.
-Zeke
On 12/02/2016 01:08 PM, Brad Matushewski wrote:
OK - I went with Ubuntu. I had trouble getting the license.txt file in place due usr/local requiring authentication. I bypassed the password part by leading using "sudo gedit" which obviously prompted me for a password but let me edit / paste license text into file.
When I tried this:
$> cd $FREESURFER_HOME/subjects $> mri_convert sample-001.mgz sample-001.nii.gz
I got:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... niiWrite(): error opening file sample-001.nii.gz ERROR: failure writing sample-001.nii.gz
When I tried:
$> cd $FREESURFER_HOME/subjects $> freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red
I got:
freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory
Not sure what I did wrong.
Suggestions?
*From:* Brad Matushewski *Sent:* Friday, December 2, 2016 8:48:11 AM *To:* Freesurfer support list *Subject:* RE: [Freesurfer] Ubuntu or Centos?
Ubuntu 14.04.5 LTS
*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Z K *Sent:* December 2, 2016 8:42 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Ubuntu or Centos?
Which version of Ubuntu are you trying to install? I ask because I too had issues when installing ubuntu14 on a new laptop with laptop with UEFI.
Try using Ubuntu16 instead if you haven't already. And more luck with that, and here is a link to more information as setting up these dual boots has gotten more difficult on newer laptops:
https://help.ubuntu.com/community/UEFI
UEFI - Community Help Wiki https://help.ubuntu.com/community/UEFI help.ubuntu.com Introduction. The Extensible Firmware Interface (EFI) or its version 2.x variant, Unified EFI (UEFI) is a firmware type that is widespread on recent ...
On Dec 2, 2016, at 8:26 AM, Brad Matushewski <bjmatush@uwo.ca mailto:bjmatush@uwo.ca> wrote:
I have had some issues with Ubuntu (installation stops before completing). I am currently trying to get a dual boot set up with Windows 10. Someone mentioned I should try Centos instead of Ubuntu? Thoughts? Pros vs Cons? -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: October 13, 2016 1:34 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all exited with ERRORS Yes, that would be a good option. Its a little work but here is a guide that I dug up which helps explain the process. For the version of linux to use... I would recommend Ubuntu 14.04.5 LTS (https://www.ubuntu.com/download/alternative-downloads) On 10/13/2016 01:25 PM, Brad Matushewski wrote: Would a feasible approach be to set up a dual-boot on my PC so that I can boot directly into either a Windows or Linux environment? -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 12:53 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all exited with ERRORS I was afraid this was the case. Normally in this situation I would say set up a shared folder between the host and the virtual machines. But unfortunately there is a known bug in the the MNI tools shipped with freesurfer which makes this an incompatible arrangement. The disk space was assigned to allow perhaps a few subjects worth of data onto the virtual image, otherwise the download size would have been prohibitively large. If you want to process numerous subjects the VirtualBox version is insuffiecient, you will have to use the Mac or Linux version. On 10/13/2016 12:39 PM, Brad Matushewski wrote: I would appear that the allotted hard drive space is fixed as a function of the Freesurfer installation. There does not appear to be an option to expand allotted space either at time of installation or after the fact. -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Thursday, October 13, 2016 11:03 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>; Brad Matushewski <bjmatush@uwo.ca <mailto:bjmatush@uwo.ca>> Subject: Re: [Freesurfer] recon-all exited with ERRORS I think its referring to the hard disk space in the virtual machine. You probably ran out which is not surprising, as the amount of free space provided with the disk image is fairly small. The fact the your host machine has 305Gb of HD on the host machine is unknown to the virtual machine. See if you can expand the hard disk space of the virtual machine (not sure if this is adjustable or not). Also, try setting up a shared folder between the two (this has other potential issues, but is worth trying). -Zeke On 10/13/2016 10:58 AM, Brad Matushewski wrote: Thank you, Bruce for the rapid reply. I am running Freesurfer on a (Windows 10 based), virtual machine. I installed / set it up according to the directions posted here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVir t u alImage ...specifically referring to the recommended memory suggestions of 4MB. Otherwise, I saw no other options for specifying memory requirements. What is the nature of this memory error and how do I go about fixing it? I know that I have 305 Gb of HD. -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 13, 2016 9:43 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all exited with ERRORS Hi Brad it looks like the recon failed as you ran out of disk space: cvarput: ncid 5: No space left on device miicv_put: MINC package entry point nu_evaluate: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) as for what would have been next, that of course depends on what you want to study cheers Bruce On Thu, 13 Oct 2016, Brad Matushewski wrote: I just tried to run my first recon-all. What now? Logo Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Brad Matushewski -
Z K