Re: [Freesurfer] recon-all

The 001.mgz should already be in native space. sameer kumar wrote: Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz the images in the native space are not in the same orientation as 001.mgz, whic

Re: [Freesurfer] recon-all

can you try one of our viewers and see if it looks correct (e.g. freeview)? On Fri, 26 Jun 2009, sameer kumar wrote: I am using mricro to view the images. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] recon-all

I am using mricro to view the images. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all

how do you know they are not in the same orientation? What are you using to check? On Fri, 26 Jun 2009, sameer kumar wrote: Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz the images in the native spa

Re: [Freesurfer] recon-all

Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz the images in the native space are not in the same orientation as 001.mgz, which i got from the dicoms. ___ Fre

Re: [Freesurfer] recon-all

Hi Sameer, can you just use the dicom? Bruce On Fri, 26 Jun 2009, sameer kumar wrote: Hi Bruce, I used mricro to convert from PAR REC. The problem is that when I tried to convert the results back to the native space, they are flipped, and are not in the same orientation as the original.

Re: [Freesurfer] recon-all

Hi Bruce, I used mricro to convert from PAR REC. The problem is that when I tried to convert the results back to the native space, they are flipped, and are not in the same orientation as the original. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar

Re: [Freesurfer] recon-all

is there any reason you can't just start with the dicom? You can check the orientation on the converted files to see if it's wrong - that's usually what happens. How did you convert from PAR REC? cheers, Bruce On Fri, 26 Jun 2009, sameer kumar wrote: Hi guys, I have the raw PAR REC and DI

[Freesurfer] recon-all

Hi guys, I have the raw PAR REC and DICOM files from the scanner. I converted the PAR REC files to mgz and ran recon-all but it exited with errors. But when I converted the DICOM files into mgz and ran recon-all, it was running fine. Can anyone tell me why this is happening. Regards, Sameer __

Re: [Freesurfer] surfaces in slicer3

not sure, you'll have to ask the slicer folks On Fri, 26 Jun 2009, Gregory Dierksen wrote: Hi, I'm trying to convert a binary volume to a surface that can be viewed with slicer3. I've used the following commands: mri_tesselate microbleeds.mgz 1 lh.microbleeds mris_smooth lh.microbleeds

[Freesurfer] surfaces in slicer3

Hi, I'm trying to convert a binary volume to a surface that can be viewed with slicer3. I've used the following commands: mri_tesselate microbleeds.mgz 1 lh.microbleeds mris_smooth lh.microbleeds -n 5 lh.microbleeds-smooth When I attempt to ope the lh.microbleeds-smooth surface using slicer