Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum
You will need to register your volume with the anatomical with bbregister. bbregister will take a "template" which should be the time point you used for motion correction. Then run mri_vol2surf to create a new data set sampled on the surface doug
On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote:
Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you fore responding. I ran recon-all and it worked fine. however when i run bbregister i get an error "ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have installed fsl 5.0 and FSLDIR set right i am running this in ubuntu 12.04 using freesurfer 5.3. am I doing some thing wrong thank you Aaron Tanenbaum
On Wed, Jul 10, 2013 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
You will need to register your volume with the anatomical with bbregister. bbregister will take a "template" which should be the time point you used for motion correction. Then run mri_vol2surf to create a new data set sampled on the surface doug
On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote:
Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Does that file exist? doug
On 7/10/13 8:25 PM, Aaron Tanenbaum wrote:
Thank you fore responding. I ran recon-all and it worked fine. however when i run bbregister i get an error "ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have installed fsl 5.0 and FSLDIR set right i am running this in ubuntu 12.04 using freesurfer 5.3. am I doing some thing wrong thank you Aaron Tanenbaum
On Wed, Jul 10, 2013 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You will need to register your volume with the anatomical with bbregister. bbregister will take a "template" which should be the time point you used for motion correction. Then run mri_vol2surf to create a new data set sampled on the surface doug On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote: > Hola Freesurfers, > I am new to Freesurfer and still learning the basics. I have been > given a project and have not found a way to do it. Part of this task > involves taking a 4dfp volume time series and convert it to a time > series of a surface. This 4dfp I have is a statistical analysis mapped > on to a specific atlas volume. Does anyone know of a way to do this. > Any help will be highly appreciated. > Gracias > Aaron Tanenbaum > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
The .sch file is used for running command line version of flirt/siena for 2d registration with the -schedule option and is located in $FSLDIR/etc/flirtsch
If it is not there then ftp from the fsl site and copy them there.
Hope this helps. Shantanu
On Wed, July 10, 2013 10:03 pm, Douglas Greve wrote:
Does that file exist? doug
On 7/10/13 8:25 PM, Aaron Tanenbaum wrote:
Thank you fore responding. I ran recon-all and it worked fine. however when i run bbregister i get an error "ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have installed fsl 5.0 and FSLDIR set right i am running this in ubuntu 12.04 using freesurfer 5.3. am I doing some thing wrong thank you Aaron Tanenbaum
On Wed, Jul 10, 2013 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You will need to register your volume with the anatomical with bbregister. bbregister will take a "template" which should be thetime point you used for motion correction. Then run mri_vol2surf to create a new data set sampled on the surface doug
On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote: > Hola Freesurfers, > I am new to Freesurfer and still learning the basics. I have been > given a project and have not found a way to do it. Part of thistask > involves taking a 4dfp volume time series and convert it to a time > series of a surface. This 4dfp I have is a statistical analysis mapped > on to a specific atlas volume. Does anyone know of a way to do this. > Any help will be highly appreciated. > Gracias > Aaron Tanenbaum > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
P.S. .sch files are for 3d registration also- The one that you are looking for is the one that achieves 3d registration.
On Wed, July 10, 2013 10:29 pm, Shantanu Ghosh wrote:
The .sch file is used for running command line version of flirt/siena for 2d registration with the -schedule option and is located in $FSLDIR/etc/flirtsch
If it is not there then ftp from the fsl site and copy them there.
Hope this helps. Shantanu
On Wed, July 10, 2013 10:03 pm, Douglas Greve wrote:
Does that file exist? doug
On 7/10/13 8:25 PM, Aaron Tanenbaum wrote:
Thank you fore responding. I ran recon-all and it worked fine. however when i run bbregister i get an error "ERROR: cannot find /usr/lib/fsl/etc/flirtsch/xyztrans.sch". I have installed fsl 5.0 and FSLDIR set right i am running this in ubuntu 12.04 using freesurfer 5.3. am I doing some thing wrong thank you Aaron Tanenbaum
On Wed, Jul 10, 2013 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You will need to register your volume with the anatomical with bbregister. bbregister will take a "template" which should be thetime point you used for motion correction. Then run mri_vol2surf to create a new data set sampled on the surface doug
On 07/10/2013 12:32 PM, Aaron Tanenbaum wrote: > Hola Freesurfers, > I am new to Freesurfer and still learning the basics. I have been > given a project and have not found a way to do it. Part of thistask > involves taking a 4dfp volume time series and convert it to a time > series of a surface. This 4dfp I have is a statistical analysis mapped > on to a specific atlas volume. Does anyone know of a way to do this. > Any help will be highly appreciated. > Gracias > Aaron Tanenbaum > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Aaron
the first thing you'll need to do is find an anatomical volume that is in the atlas coordinates (or maybe is the atlas) and run recon-all on it. Then you can run bbregister to register the time series to the recon and mri_vol2surf to sample it onto the surface.
cheers Bruce
On Wed, 10 Jul 2013, Aaron Tanenbaum wrote:
Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum
freesurfer@nmr.mgh.harvard.edu
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Aaron Tanenbaum -
Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Shantanu Ghosh