Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
Hi Jason
why not map them all to fsaverage and display them on a common surface?
cheers Bruce
On Fri, 4 Feb 2011, Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I guess the problem I have at hand is how to map them to fsaverage. Do I have to convert the arrays somehow to nifti format first? I tried looking this up on the web but couldn't find a solution ...
Many thanks,
Jason.
On 04/02/2011 13:48, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Jason
why not map them all to fsaverage and display them on a common surface?
cheers Bruce
On Fri, 4 Feb 2011, Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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.
you should be able to use mri_surf2surf to map them all to fsaverage On Fri, 4 Feb 2011, Jason Connolly wrote:
Hi Bruce,
I guess the problem I have at hand is how to map them to fsaverage. Do I have to convert the arrays somehow to nifti format first? I tried looking this up on the web but couldn't find a solution ...
Many thanks,
Jason.
On 04/02/2011 13:48, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Jason
why not map them all to fsaverage and display them on a common surface?
cheers Bruce
On Fri, 4 Feb 2011, Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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,
I'm trying to normalize ADC maps into a template image of my choice using SPM8. In this purpose, I converted my DICOM files into nifti files using "mri_convert" and now I would like to modify the origin of the volumes. Is that possible?
Thanks,
Vincent
You can try setting the location of the center with the -ic (same as --in_center) option.
doug
Vincent Roch wrote:
Hi,
I'm trying to normalize ADC maps into a template image of my choice using SPM8. In this purpose, I converted my DICOM files into nifti files using "mri_convert" and now I would like to modify the origin of the volumes. Is that possible?
Thanks,
Vincent _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, you can use it to sample volume data onto the surface using mri_vol2surf
On Sat, 5 Feb 2011, Jason Connolly wrote:
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ...
Any ideas would be great ...
tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh unrecognized subject is bert hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/bert/mri surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz ltMNIreadEx: could not open file /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm Permission denied surfer: Talairach xform file not found (ignored) surfer: vertices=131547, faces=263090 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
On 05/02/2011 00:32, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
no, you can use it to sample volume data onto the surface using mri_vol2surf
On Sat, 5 Feb 2011, Jason Connolly wrote:
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ...
Any ideas would be great ...
tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh unrecognized subject is bert hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/bert/mri surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz ltMNIreadEx: could not open file /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm Permission denied surfer: Talairach xform file not found (ignored) surfer: vertices=131547, faces=263090 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
On 05/02/2011 00:32, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
no, you can use it to sample volume data onto the surface using mri_vol2surf
On Sat, 5 Feb 2011, Jason Connolly wrote:
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
> Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). > > Although the initial segmentations were done in freesurfer, my question is: > > Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface? > > If so, is the pipeline documented? > > Many thanks, > > Jason. > > _______________________________________________ > 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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Final question:
My values are normalized: from 0 to 1 ... How do I change the overlay colours so that this is scaled correctly?
I am assuming I have to make a file of some sort ...
Thanks, I think I am almost there ... -jason.
On 05/02/2011 01:03, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ...
Any ideas would be great ...
tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh unrecognized subject is bert hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/bert/mri surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz ltMNIreadEx: could not open file /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm Permission denied surfer: Talairach xform file not found (ignored) surfer: vertices=131547, faces=263090 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
On 05/02/2011 00:32, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
no, you can use it to sample volume data onto the surface using mri_vol2surf
On Sat, 5 Feb 2011, Jason Connolly wrote:
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
> Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). > > Although the initial segmentations were done in freesurfer, my question is: > > Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface? > > If so, is the pipeline documented? > > Many thanks, > > Jason. > > _______________________________________________ > 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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I think that the problem may lie with MRIread.
I have 1 x 82 Array of phase volumes.
I also then have a separate 3 x 82 array of coordinates (that correspond to each of the normalized 0 to 1 phase values above.
My question is: if I input the phases in vol, what field do I place the coordinates for the phase values in?
Many thanks,
Jason.
On 05/02/2011 01:03, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
try one '-' in '-overlay', not two On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
I used mri_vol2surf, but there appears to be no overlay colours ... Here is the output ...
Any ideas would be great ...
tksurfer bert rh inflated --overlay /Applications/fesurfer/subjects/bert/surf/test_LH.mgh WARNING: flag --overlay unrecognized WARNING: flag /Applications/freesurfer/subjects/bert/surf/test_LH.mgh unrecognized subject is bert hemi is rh surface is inflated surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer/subjects/bert/mri surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz ltMNIreadEx: could not open file /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm Permission denied surfer: Talairach xform file not found (ignored) surfer: vertices=131547, faces=263090 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
On 05/02/2011 00:32, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
no, you can use it to sample volume data onto the surface using mri_vol2surf
On Sat, 5 Feb 2011, Jason Connolly wrote:
Can I display register.dat in tksurfer?
Thanks, -j.
On 05/02/2011 00:21, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
that writes the file named register.dat that has the affine registration matrix (and some other things)
On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Bruce,
Here it is:
bbregister --s bert --mov /Applications/freesurfer/subjects/bert/mri/f_RH.mgz --reg register.dat --bold --init-header
-jason.
On 05/02/2011 00:18, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
can you send us your command line? On Sat, 5 Feb 2011, Jason Connolly wrote:
Hi Doug,
I am now at the bbregister stage ... I ran this but it is not clear to me where the output is? I don't see an output flag ...
Can you tell me where to look for my output?
Almost there!
Many thanks, Jason.
On 04/02/2011 23:49, "Jason Connolly" jason.connolly@newcastle.ac.uk wrote:
Thank you. -jason.
On 04/02/2011 23:48, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You can load in the functional with MRIread since you are going to be replacing all the pixel data anyway with your single time point. Just use the single argument. The second is if you dont want to read in the pixel data.
Jason Connolly wrote:
Thanks.
So, to clarify, I am trying to just make an overlay. So do I use MRIread with a functional .img as input?
Is the second argument in MRIread my scanCoords for my phase-value pixels?
Almost there ...
On 04/02/2011 23:35, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It's the vol field. doug
Jason Connolly wrote:
Hi Doug,
You state:
"then replace the pixel data with your analyzed data"
I cannot seem to find the field for the pixel data. Can you tell me where to position these values?
Thanks! -jason.
On 04/02/2011 18:15, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
> Dear freesurfer experts: > > I have been using matlab to analyze a retinotopic dataset. > > However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface). > > Although the initial segmentations were done in freesurfer, my question is: > > Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface? > > If so, is the pipeline documented? > > Many thanks, > > Jason. > > _______________________________________________ > 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
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.
-- 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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Jason Connolly -
Vincent Roch