[Freesurfer] editing masks
Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill those in. Thanks Dan -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dicom to mgz
Hi, I am trying to change my dicom files to mgz format. I know recon-all can do this, however after the mgz file is created, tkmedit will not display it. As described in the freesurfer-wiki site, there are steps outlining 2 acquisition directories. What does this specifically refer to? I assumed that I only had one, and therefore entered the following: recon-all -i /mnt/win/MRI_data/MWIN4/O-08-003/DICOM/08021516/3342/9003-0001-0001-1.dcm -s O_08_003.mgz The error message said there might be something wrong with the data file (unreadable, or wrong size). Is my command wrong? Thanks. Dan -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] GTCA
Does anyone know if GTCA is part of the freesurfer commands? My protocol requires that I use a GTCA command to create a better surface image for stg. If not, can anyone direct me towards a resource to explain what it is and how to use it? Thanks. -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_mask
Hi, I have tried applying a binary mask, specifically for STG, in conjunction with the mri_mask command. We applied it to a brainmask volume, but we did not get the result we wanted. The output we recieved was simply the mask that we used. We wish to produce an output that gives the STG volume alone from the brain, and not from the binary mask. Are we using the command incorrectly? Thanks -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: mri_mask
Please note the command we used: mri_mask brainmask.mgz lh.stg.mask.mgz brainout.mgz and the result we got was: Writing masked volume to brainout.mgz...done. On Fri, May 9, 2008 at 2:39 PM, Daniel H Choi [EMAIL PROTECTED] wrote: Hi, I have tried applying a binary mask, specifically for STG, in conjunction with the mri_mask command. We applied it to a brainmask volume, but we did not get the result we wanted. The output we recieved was simply the mask that we used. We wish to produce an output that gives the STG volume alone from the brain, and not from the binary mask. Are we using the command incorrectly? Thanks -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] -- Daniel Horim Choi Northwestern University Class of 2009 [EMAIL PROTECTED] or [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
