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 [fis...@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 > > 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
