So you want to map the labels in fsaverage into MNI152 volumes pace,
right? After mris_divide_parcellation, you should have a parcellation in
fsaverage space. Use mri_surf2surf (or mris_apply_reg) to map that into
the MNI152 that you ran recon-all on. Look in the recon-all.log file for
the command that created the aparc+aseg.mgz file (mri_aparc2aseg).
Change that command line to use your new annotation, and specify a
different output. If you want to view it in freeview, then you will also
need to create a new color table like $FREESURFER/FreeSurferColorLUT.txt
but it will need your new labels in it. You can get the indicies by
loading the volume into freeview and clicking on the labels.
On 11/3/2021 4:41 AM, Alvarado,Luis R wrote:
External Email - Use Caution
External Email - Use Caution
Hi all,
I am having a bit of a hard time figuring out the best option to
convert surface labels to mni volume masks.
For my ROI FS analysis, I divided the fsaverage S1 and M1 labels into
5 sub-labels using *mris_divide_parcellation*. I then used
*mri_label2label* to map those labels to each of my subjects to study
differences in thickness among 2 groups.
I am now trying to map those same labels from fsaverage to mni space
in order to use them as ROI for resting-state connectivity analysis in
the conn toolbox pipeline. From reading The Mail Archive I have come
across multiple pieces of advice on how one might go about doing this.
These range from a) using *mri_label2vol* and *mri_vol2vol*; b)
creating a new annotation file for fsaverage from the labels and using
*mri_aparc2aseg* and then *mri_vol2vol*; to c) running mni152 through
*recon-all*.
As you can probably tell by now, I am a bit confused about the most
efficient and accurate way to accomplish this.
any advice would be greatly appreciated.
Luis R. Alvarado
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1-Siaw-_eWHTOyyt0LP4I4VtfJboT2ix07EfcLtP5uepkuVkGkHN1VEisxSf4elTCC1a6mQhHvciRp4CMZciKESxdrkhrsLG4xZozfo5sr-rx3iPj4XgLARRPT-6l388miHeNOzUPEOpG84rLCUTRUNF1RPw4Wx1KY7LLEPMz_KfSfGy7y6GpMcUZ-veHewtte41x1TInm1DupjHJTq29Z1G20J0tAa9EHMN11oB17FU78lUYy-u4x_4BZMpPtmqX80mZdkD9KN0avMQVnHHlwA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
