Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me).
Thanks, Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
< sagittal .png
< Screenshot_horizontal .png>_______________________________________________ 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 Thomas,
That worked - thanks so much!
Best, Corey
On Fri, Jul 2, 2010 at 10:06 AM, ythomas ythomas@csail.mit.edu wrote:
Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me).
Thanks, Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
<sagittal.png><Screenshot_horizontal.png>_______________________________________________ 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 Freesurfers,
I have now successfully registered the functional volume and transformed the volume to a surface via mri_vol2surf. I then loaded the nifti surface into matlab with MRIread (nii = MRIread('example.nii'). nii.vol is a 1x149x797 matrix. Additionally, there are variables of vox2ras and vox2ras1 transformation matrices in the nii struct. Do you know how I get nii.vol into RAS coordinates and eventually plotted? Thanks!
Best, Corey
On Fri, Jul 2, 2010 at 10:06 AM, ythomas ythomas@csail.mit.edu wrote:
Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me).
Thanks, Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
<sagittal.png><Screenshot_horizontal.png>_______________________________________________ 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.
Those fields are not valid for surface data.
doug
Corey Keller wrote:
Hi Freesurfers,
I have now successfully registered the functional volume and transformed the volume to a surface via mri_vol2surf. I then loaded the nifti surface into matlab with MRIread (nii = MRIread('example.nii'). nii.vol is a 1x149x797 matrix. Additionally, there are variables of vox2ras and vox2ras1 transformation matrices in the nii struct. Do you know how I get nii.vol into RAS coordinates and eventually plotted? Thanks!
Best, Corey
On Fri, Jul 2, 2010 at 10:06 AM, ythomas ythomas@csail.mit.edu wrote:
Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me).
Thanks, Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
<sagittal.png><Screenshot_horizontal.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I figured out how to plot it on my pial surface. Here's my code if anyone is wondering. Thanks again for your help.
In freesurfer
bbregister --s CL --mov ./CL/lfo_example.nii.gz --init-fsl --reg register.dat --bold tkregister2 --mov ./CL/lfo_example.nii.gz --reg register.dat --surf mri_vol2surf --src --reg register.dat --out *.nii.gz --hemi lh
In matlab
mgh = MRIread('*.mgh'); surf_data = mgh.vol; iter = round((surf_data+2)*16)'; % indexing colormap map = cmap(round((surf_data+2)*16),:); tripatch(cortex.lh,h,map); shading interp; lighting gouraud; material dull; switch 'l' case 'r' l=light('Position',[1 0 0]); view(90,0) case 'ri' l=light('Position',[1 0 0]); view(90,-90) case 'l' l=light('Position',[-1 0 0]); view(270,0) case 'li' l=light('Position',[-1 0 0]); view(270,-45) end axis off, hold on
On Fri, Jul 2, 2010 at 11:19 AM, Corey Keller corey.j.keller@gmail.com wrote:
Hi Freesurfers,
I have now successfully registered the functional volume and transformed the volume to a surface via mri_vol2surf. I then loaded the nifti surface into matlab with MRIread (nii = MRIread('example.nii'). nii.vol is a 1x149x797 matrix. Additionally, there are variables of vox2ras and vox2ras1 transformation matrices in the nii struct. Do you know how I get nii.vol into RAS coordinates and eventually plotted? Thanks!
Best, Corey
On Fri, Jul 2, 2010 at 10:06 AM, ythomas ythomas@csail.mit.edu wrote:
Is this a preprocessed (whole brain regression, bandpass filter, etc) rest-state volume? If so, I would suggest using the volume before the preprocessing (which works well for me).
Thanks, Thomas
On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
Hi Bruce,
Thanks for the info. I am trying to register a resting state functional nifti file. I ran bbregister but it was not well aligned (pictures are attached). Our thought is that the contrast was not strong enough for freesurfer to detect enough common points with the anatomical volume. If we feed another example functional file with better contrast, could we then use that register file to apply to our data? Any thoughts on how we can do this betterwithout manually aligning? Thanks again.
Best, Corey
On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Corey,
yes, or you can try bbregister to do it automatically.
cheers Bruce On Fri, 2 Jul 2010, Corey Keller wrote:
Hi Freesurfers,
I know this is probably an easy question, but I am having some trouble with it. I am trying to plot functional data (in nifti format) onto a pial or inflated surface in matlab. I am uring mri_vol2surf but am missing the register file. Do I find this from registering the functional data to the anatomical surface via tkregister? Thanks.
-Corey _______________________________________________ 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.
<sagittal.png><Screenshot_horizontal.png>_______________________________________________ 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
-
Corey Keller -
Douglas N Greve -
ythomas