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 [fischl@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.
- 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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