Hey Bruce, I have two more questions. 1) I was suggested to use mri_binarize with brain.mgz to get the total brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume.
2)I learnt that using T2 weighted image along with T1 weighted image from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer. May the FreeSurfer experts guide me through this.
Thanks, Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging.
cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple
recon
all command :=Recon-all -s (subject file name) -all or do I need to have some additional l flags so that recon all command will use the three T1 images to get one output file? Thanks, Rashmi
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