I ran Freesurfer on OASIS longitudinal data with the longitudinal pipeline. I want to work with the full brain image (with gray level intensities) which is intensity normalized and skull stripped and all the timepoints of a subject are rigidly registered to the 1st time point. There were many brain mgz files created during the processing. What is the best final image which I should be working with?
Thanks, Prasanna
Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not sure what you mean by all the images registered to the 1st time point. If you are doing a longitudinal analysis, then following the longitudinal stream will result in a set of norm.mgz's that will be in alignment (but not to the 1st time point, which you would not want because it causes bias). doug
On 12/13/2012 12:28 PM, Prasanna M wrote:
I ran Freesurfer on OASIS longitudinal data with the longitudinal pipeline. I want to work with the full brain image (with gray level intensities) which is intensity normalized and skull stripped and all the timepoints of a subject are rigidly registered to the 1st time point. There were many brain mgz files created during the processing. What is the best final image which I should be working with?
Thanks, Prasanna
--
Let there be peace on earth... And let it begin with me.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I had one more question: What transform do I apply to get all the norm.mgz of all timepoints of a subject to get the normalized image in MNI atlas space. Is this the one inside mri/transforms/talairach.xfm? More precisely, for all subjects, will something like this work? mri_convert norm.mgz normInMNI.img --apply_transform transforms/talairach.xfm -oc 0 0 0 -oni 256 -onj 256 -onk 256 -vs 1.0 1.0 1.0 --out_data_type float"
Thanks, Prasanna
On Thu, Dec 13, 2012 at 10:30 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not sure what you mean by all the images registered to the 1st time point. If you are doing a longitudinal analysis, then following the longitudinal stream will result in a set of norm.mgz's that will be in alignment (but not to the 1st time point, which you would not want because it causes bias). doug
On 12/13/2012 12:28 PM, Prasanna M wrote:
I ran Freesurfer on OASIS longitudinal data with the longitudinal pipeline. I want to work with the full brain image (with gray level intensities) which is intensity normalized and skull stripped and all the timepoints of a subject are rigidly registered to the 1st time point. There were many brain mgz files created during the processing. What is the best final image which I should be working with?
Thanks, Prasanna
--
Let there be peace on earth... And let it begin with me.
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: 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.
Just use mri_convert norm.mgz normInMNI.img --apply_transform transforms/talairach.xfm -oc 0 0 0 no need for the other arguments doug
On 12/15/2012 12:38 PM, Prasanna M wrote:
I had one more question: What transform do I apply to get all the norm.mgz of all timepoints of a subject to get the normalized image in MNI atlas space. Is this the one inside mri/transforms/talairach.xfm? More precisely, for all subjects, will something like this work? mri_convert norm.mgz normInMNI.img --apply_transform transforms/talairach.xfm -oc 0 0 0 -oni 256 -onj 256 -onk 256 -vs 1.0 1.0 1.0 --out_data_type float"
Thanks, Prasanna
On Thu, Dec 13, 2012 at 10:30 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Prasanna, the norm.mgz sounds like the best fit. Though I'm not sure what you mean by all the images registered to the 1st time point. If you are doing a longitudinal analysis, then following the longitudinal stream will result in a set of norm.mgz's that will be in alignment (but not to the 1st time point, which you would not want because it causes bias). doug On 12/13/2012 12:28 PM, Prasanna M wrote: > I ran Freesurfer on OASIS longitudinal data with the longitudinal > pipeline. I want to work with the full brain image (with gray level > intensities) which is intensity normalized and skull stripped and all > the timepoints of a subject are rigidly registered to the 1st time > point. There were many brain mgz files created during the processing. > What is the best final image which I should be working with? > > Thanks, > Prasanna > > -- > -- > Let there be peace on earth... > And let it begin with me. > > > > > > > _______________________________________________ > 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: 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.--
Let there be peace on earth... And let it begin with me.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Prasanna M