Hi Bruce, Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... Is this correct? Thanks Catherine
Hi Catherine
I don't have much experience with virtual boxes, but I suspect that is the windows name for the path, not the unix one in the virtual box. Someone who knows more about this than I do can confirm/correct.
cheers Bruce
On Sat, 23 Apr 2011, Rongxiang Tang wrote:
Hi Bruce, Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... Is this correct? Thanks Catherine
Hi Catherine
You need to mount the external harddisk inside the virtualbox and give its path as $SUBJECTS_DIR.
The path starting with E:\data.. is how Windows 7 sees the harddisk.
Unfortunately, there is no easy way to do this.
* The hardwork is to make the Guest OS ( ubuntu in this case ) see the external harddisk. Here is a start -- http://superuser.com/questions/87221/how-can-i-mount-an-external-hard-drive-...
* once the Guest OS sees it, you need to know where it's mounted ( if it's done automatically )
or use the mount command to mount it to a location like /media/external
* Then your $SUBJECTS_DIR will be
setenv $SUBJECTS_DIR /media/external/data/Ventricle-freesurfer/......
etc.
also recommend you to read the "Shared Folders" section in the VirtualBox user manual http://download.virtualbox.org/virtualbox/UserManual.pdf
-Krish
On Sat, Apr 23, 2011 at 11:12:53AM -0400 Bruce Fischl wrote:
Hi Catherine
I don't have much experience with virtual boxes, but I suspect that is the windows name for the path, not the unix one in the virtual box. Someone who knows more about this than I do can confirm/correct.
cheers Bruce
On Sat, 23 Apr 2011, Rongxiang Tang wrote:
Hi Bruce, Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... Is this correct? Thanks Catherine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Krish,
Thanks for the help. It's calculating now... One more questions...I noticed that when I entered in these commands:
FreeSurfer:~> setenv $SUBJECTS_DIR /media/external/data/Ventricle-freesurfer FreeSurfer:~> recon-all -i /media/external/data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028508.dcm \ -all -s ben
the -subjectid and results seems to save in the default directory.../home/virtualuser/apps/freesurfer/subjects...yet i would like to save them in the "/media/external/data"
Is there any way to change that? will this command work: recon-all -i /media/external/data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028508.dcm \ -all -s ben / -sd /media/external/data/
--- On Sat, 4/23/11, Krish Subramaniam krish@nmr.mgh.harvard.edu wrote:
From: Krish Subramaniam krish@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Change the default SUBJECTS_DIR... To: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Cc: "Rongxiang Tang" rongxiangtang@yahoo.com, freesurfer@nmr.mgh.harvard.edu Date: Saturday, April 23, 2011, 4:28 PM
Hi Catherine
You need to mount the external harddisk inside the virtualbox and give its path as $SUBJECTS_DIR.
The path starting with E:\data.. is how Windows 7 sees the harddisk.
Unfortunately, there is no easy way to do this.
* The hardwork is to make the Guest OS ( ubuntu in this case ) see the external harddisk. Here is a start -- http://superuser.com/questions/87221/how-can-i-mount-an-external-hard-drive-...
* once the Guest OS sees it, you need to know where it's mounted ( if it's done automatically )
or use the mount command to mount it to a location like /media/external
* Then your $SUBJECTS_DIR will be
setenv $SUBJECTS_DIR /media/external/data/Ventricle-freesurfer/......
etc.
also recommend you to read the "Shared Folders" section in the VirtualBox user manual http://download.virtualbox.org/virtualbox/UserManual.pdf
-Krish
On Sat, Apr 23, 2011 at 11:12:53AM -0400 Bruce Fischl wrote:
Hi Catherine
I don't have much experience with virtual boxes, but I suspect that is the windows name for the path, not the unix one in the virtual box. Someone who knows more about this than I do can confirm/correct.
cheers Bruce
On Sat, 23 Apr 2011, Rongxiang Tang wrote:
Hi Bruce, Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... Is this correct? Thanks Catherine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Catherine,
When setting the variable, drop the "$" sign. So, type simply: setenv SUBJECTS_DIR /media/external/data/Ventricle-freesurfer
Anderson
On 04/23/2011 04:04 PM, Rongxiang Tang wrote:
Hi Krish,
Thanks for the help. It's calculating now... One more questions...I noticed that when I entered in these commands:
FreeSurfer:~> setenv $SUBJECTS_DIR /media/external/data/Ventricle-freesurfer FreeSurfer:~> recon-all -i /media/external/data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028508.dcm \ -all -s ben
the -subjectid and results seems to save in the default directory.../home/virtualuser/apps/freesurfer/subjects...yet i would like to save them in the "/media/external/data"
Is there any way to change that? will this command work: recon-all -i /media/external/data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028508.dcm \ -all -s ben / -sd /media/external/data/
--- On *Sat, 4/23/11, Krish Subramaniam /krish@nmr.mgh.harvard.edu/* wrote:
From: Krish Subramaniam <krish@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Change the default SUBJECTS_DIR... To: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> Cc: "Rongxiang Tang" <rongxiangtang@yahoo.com>, freesurfer@nmr.mgh.harvard.edu Date: Saturday, April 23, 2011, 4:28 PM Hi Catherine You need to mount the external harddisk inside the virtualbox and give its path as $SUBJECTS_DIR. The path starting with E:\data\.. is how Windows 7 sees the harddisk. Unfortunately, there is no easy way to do this. * The hardwork is to make the Guest OS ( ubuntu in this case ) see the external harddisk. Here is a start -- http://superuser.com/questions/87221/how-can-i-mount-an-external-hard-drive-in-a-virtualbox-machine * once the Guest OS sees it, you need to know where it's mounted ( if it's done automatically ) or use the mount command to mount it to a location like /media/external * Then your $SUBJECTS_DIR will be setenv $SUBJECTS_DIR /media/external/data/Ventricle-freesurfer/...... etc. also recommend you to read the "Shared Folders" section in the VirtualBox user manual http://download.virtualbox.org/virtualbox/UserManual.pdf -Krish On Sat, Apr 23, 2011 at 11:12:53AM -0400 Bruce Fischl wrote: > Hi Catherine > > I don't have much experience with virtual boxes, but I suspect that > is the windows name for the path, not the unix one in the virtual > box. Someone who knows more about this than I do can > confirm/correct. > > cheers > Bruce > > On Sat, 23 Apr 2011, Rongxiang Tang wrote: > > >Hi Bruce, > > > >Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... > >Is this correct? > > > >Thanks > >Catherine > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu </mc/compose?to=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.
freesurfer@nmr.mgh.harvard.edu
-
Anderson Winkler -
Bruce Fischl -
Krish Subramaniam -
Rongxiang Tang