Dear FS experts, I run recon all on several patients, manual edited all the outputs and rerun recon all. I'm interested in subcortical segmentation and I extracted all the data with the aseg stats command. Is it now possible to select a structure (let's say the accumbens) and save it as a .nii (or wathever format) ROI in ordero to export it and open it with other softwares (e.g. mricron, fsl etc)? thank you in advance Fabrizio Piras --------------------------- Fabrizio Piras Ph.D. --------------------------- Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213
Hi Fabrizio, You can use mri_extract_label for this. You need to specify the index number of the structure which you can find here: $FREESURFER_HOME/FreeSurferColorLUT.txt
On Tue, 15 Feb 2011, fabrizio piras wrote:
Dear FS experts, I run recon all on several patients, manual edited all the outputs and rerun recon all. I'm interested in subcortical segmentation and I extracted all the data with the aseg stats command. Is it now possible to select a structure (let's say the accumbens) and save it as a .nii (or wathever format) ROI in ordero to export it and open it with other softwares (e.g. mricron, fsl etc)? thank you in advance Fabrizio Piras
Fabrizio Piras Ph.D.
Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure. mri_binarize or mri_extract_label will do this for you (see the FreeSurferColorLUT.txt file for the correct indices to use)
cheers Bruce On Tue, 15 Feb 2011, fabrizio piras wrote:
Dear FS experts, I run recon all on several patients, manual edited all the outputs and rerun recon all. I'm interested in subcortical segmentation and I extracted all the data with the aseg stats command. Is it now possible to select a structure (let's say the accumbens) and save it as a .nii (or wathever format) ROI in ordero to export it and open it with other softwares (e.g. mricron, fsl etc)? thank you in advance Fabrizio Piras
Fabrizio Piras Ph.D.
Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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fabrizio piras