On 2/7/2022 5:29 PM, Salar Dini, Elaheh wrote:

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Thank you so much. This actually worked well. Just two simple follow-up questions:


  1. Do I assume right that this solution doesn't work on aparc+aseg?
Correct, that will not work

  2. If I want to run recon-all -autorecon2 -autorecon3 on a subject that I have a proper brain mask for (named brainmask.nii), can I simply run the command:
  3. recon-all -autorecon2 -autorecon3 -i brainmask.nii -s <subjectid> ? or do I need more proper flags?
That might work. You can also run it up to where it creates the brainmask.mgz and just copy your file into over it and re-run
Thank you again.


From: Douglas N. Greve

Sent: Fri, 04 Feb 2022 05:24:23 -0800

Subject: Re: Recon-all reconstructed image coordinates


          
You can try registering them together like
mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta
Then


          mri_vol2vol --mov betmaskvol.nii.gz --targ
              orig.mgz --reg.lta --o betmask-in-fs.mgz --interp nearest The betmaskvol should be the intensity
              image (like orig.mgz) and not a binary mask or segmentation

        

      

      

        

      

      

      
From: Salar
          Dini, Elaheh <elaheh.salardini@yale.edu>

          Sent: Wednesday, February 2, 2022 4:05 PM

          To: Freesurfer support list
          <freesurfer@nmr.mgh.harvard.edu>

          Subject: Re: Recon-all reconstructed image coordinates
        
 

      

      

        

          Hi all,

        

          

        

        

          I just wanted to follow-up on this message with one extra
          piece of information added:

        

          

        

        

          The two brains are exactly identical. Considering that we have
          two identical reconstructed brains (exactly the same as each
          other), with the only difference being that one of them is a
          little bit shifted and rotated in comparison to the other one,
          if there a way to measure the amount of this rotation and
          shift? If yes, can this information be used to counteract this
          rotation and shift? In other words, can we rotate and shift
          the second brain back in the exact opposite direction, so it
          completely overlays the first brain using freesurfer?

        

          

        

        

          Thank you and all the best,

        

          Ela

        

        
From:
            Salar Dini, Elaheh

            Sent: Monday, January 31, 2022 6:46 PM

            To: Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu>

            Subject: Recon-all reconstructed image coordinates
          
 

        

        

          

            Dear Freesurfer developers,

          

             In the link below, you see two brains belonging to the same
            subject:

          

            

          

          

            MailScanner has detected a possible fraud
                  attempt from "secure-web.cisco.com" claiming to be
https://www.dropbox.com/s/c2gsp8h8jj7c93d/Screen%20Shot%202022-01-26%20at%201.40.23%20PM.png?dl=0

          

          

            
          

          

            

          

          

            

          

          

            while one of them is reconstructed with FS7.2, the other one
            is reconstructed with a pipeline that uses another code for
            extracting brain tissue (BET Mask) and then use FS6 for the
            remaining stages of the reconstruction. 

          

            

          

          

            While the final result of both constructions matches in most
            aspects, they don't occupy the same coordinates in space. Is
            there a way that we can match the coordinates of each voxel
            for two images? Or in other words make them compatible. 

          

            

          

          

          

          The Platform we use is
          CentOS7 .
          

            

            

          

            Thanks
              and all the best,

          

            Ela

          

            

              

                

          

        

      

      

      

      
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