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If you're doing a recon, then there should be an mri/orig.mgz which is
conformed (ie, the dimension and voxel size will be 256^3 and 1mm^3)
regardless of what you start with. This is what you should be doing all
of your operations on (not necessarily orig.mgz, but a conformed
volume). doug Faden, Eric (NIH/NIMH) [F] wrote: So my images come off the scanner as DICOM. Steps For Both: 1) Convert DICOM to ANALYZE 2) Align and Average the scansSteps For Broken: 3) Convert to minc to create a brain mask and do some normalization 4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys) 5) Use mri_convert to convert MNC to MGZ Steps for Working: 3) Convert Analyze to AFNI 4) Use 3drefit (AFNI) to fake 1.0mm voxels 5) Use mri_convert to convert BRIK to MGZ -Eric -----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED]] Sent: Tue 8/1/2006 2:27 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems) can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz? -Eric -----Original Message----- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting |
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