what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping
For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura. cheers Bruce On Fri, 13 Sep 2013, Rashmi Singh wrote: > Thank you Bruce ! > mri_binarize was suggested to me by the freesurfer group, so now I am a > little concerned when you say that this has not been assessed for accuracy. > May you suggest how otherwise do you get the total brain volume ( which you > suggest is more accurate), as this measurement is not present in the > freesurfer output stat files. > > May you please elaborate a little more the steps of using T2-FlAIR for recon > all or suggest me where I can find the detail information ( may be on the > website). While scanning we do collect T2-FLAIR that is linked with T1 for > each subject. Is that what you mean by get a T2-FLAIR? Also, what is a > -T2Flair swicht? > Sorry, with a background of molecular biology and being a novice in image > analysis, it really takes me time and lots of effort to understand imaging > and its analysis. Your guidance is appreciated. > Thanks, > > Rashmi > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Friday, September 13, 2013 8:46 AM > To: Rashmi Singh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] recon all question > > 1. I don't think I know anyone who has done this, and we haven't assessed > it for accuracy. > > 2. The best thing to do is get a T2-FLAIR and run it with the -T2Flair > switch after recon-all is done. This does a great job avoiding dura > > cheers > Bruce > > > On Fri, 13 Sep 2013, Rashmi Singh wrote: > >> 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
