Re: [Freesurfer] Using Freesurfer Commands for Neonate

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mg

Re: [Freesurfer] How to Divide the Brain Surface Parcells to more regions

External Email - Use Caution Dear Doug, Special appreciation for your help. Actually, I have created the annotation and the color table files and finally I have divided the parcels. Also, I checked the primary and the division parcels on the .pial surface that they were corr

Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

and the new output name. On 8/1/2019 4:58 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the anno

Re: [Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

External Email - Use Caution Dear Doug, Thanks for your reply. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz

Re: [Freesurfer] Using Freesurfer Commands for Neonate

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz

[Freesurfer] Using Freesurfer Commands for Neonate

External Email - Use Caution Dear Experts, I have a neonate MRI Image which its parcellation file, surface files and the ribbon are not created by freesurfer. I have created an annotation file for it using "write_annotation". Now, for further processing I need to use freesurf

[Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a

[Freesurfer] How to Divide the Brain Surface Parcells to more regions

External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical

[Freesurfer] How to Create Cortex Parcellation Using "mri_aparc2aseg"?

External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a

[Freesurfer] Using Freesurfer Commands for Neonate

External Email - Use Caution Dear Experts, I have a neonate MRI Image which its parcellation file, surface files and the ribbon are not created by freesurfer. I have created an annotation file for it using "write_annotation". Now, for further processing I need to use freesur

[Freesurfer] How to Divide the Surface Parcellations of the Brain

External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation file? I mean what information, it needs? Regards Mahshid _

Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 11

e so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Skull Strip (Bruce Fischl) 2. How to Divide the Surface Parcellations of the Brain (Mahshid Fouladivanda) 3. Re: How to Divide the Surface Parcellations of the Brain (Bruc

[Freesurfer] How to Divide the Surface Parcellations of the Brain

External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical

Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex

and cerebellum and brainstem?? and then show them by using tksurfer or tkmedit??? Regards, Mahshid From: Bruce Fischl To: Mahshid Fouladivanda Cc: freesurfer@nmr.mgh.harvard.edu, "dgr...@mgh.harvard.edu" Date: Sun, 12 May 2019 10:47:23 -0400 (EDT) Subject: Re: [Freesurfer] A Ques

Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex

External Email - Use Caution Dear Prof. Fichl and Prof. Douglas Thanks for your replay. By the way, My parcels have not been extracted from Freesurfer by using "recon-all". While, the command "mri_vol2surf" needs registration file as input. Still, is it possible to use the men

[Freesurfer] How Can I Keep up Brain-stem and Cerebellum while Creating .pial and .inflated Surfaces by using "Recon all" Command?

External Email - Use Caution Dear Freesurfer Experts, I need a brain cortex surface including Brain-stem and Cerebellum. Using "recon-all" command, Brain-stem and Cerebellum has been removed from the output pial files. How can I set the command in order to keep up Brain-stem

[Freesurfer] How to Display Specific Cortical Parcels (not the output of the recon-all) on Brain Surface

External Email - Use Caution Dear Freesurfer Experts, I have a predetermined cortical parcels in native space. I want to display them on brain surface, As shown in the last image of page bellow: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have loa

[Freesurfer] Problem with freesurfer installation on mint 19 (ubuntu based OS)

External Email - Use Caution Hi Dear experts, I downloaded and installed freesurfer on CentOS without any problem and also worked with it. Recently I've switched on mint 19 (an Debian based operating system) and I tried to setup freesurfer but, it does not worked. I would appre