Hi Yang, It sounds like the automatic cutting plane failed.
If you have a copy of the FreeSurfer Tutorial or Manual, then just go to the section "Failure of the Automatic Cutting Planes" for a visual guide to what you need to do to solve this problem. Otherwise, what you need to do is manually define the sagittal cutting plane by going through the following steps: 1) Load the wm volume. 2) Click on a point in the middle of the brain (coronal section) near the fornix. 3) Now switch to sagittal view. 4) You should find a slice where the corpus callosum is detached from the rest of the cortex. It may be the slice you're already on, or it may be a few slices lateral to it. If you cannot find a slice in this area with the corpus callosum detached, then you can erase a fine line of wm voxels in order to manually detach it from the cortex, then select File-->Save Volume. 5) Once you have clicked on a vertex on the white matter of the corpus callosum in sagittal section, use its Talairach coordinates (these can be displayed on the TkMedit Tools window by clicking View--> Information -->MNI Coordinates. Then, run the following command in the subject's scripts/ directory: mri_fill -C x y z ../mri/wm ../mri/filled (where x y z are the MNI coordinates of the point you clicked) After this is complete, run the following: inflate_subject-lh yoursubjectname inflate_subject-rh yoursubjectname Good luck! On Tue, 5 Aug 2003, Yang Jiang (NIH/NIMH) wrote: > Hello, > > I am a new user of FreeSurfer. I met some problems when I create an > inflated surface with FreeSurfer. Please kindly give me some > instruction. The problems I met are shown below (I tried the suggestions > of previous posts, including renormalize_subject and mri_watershed, but > failed too): > > 1. In FreeSurfer GUI, I chose "Create Surface" to create the inflated > surface. But the process is interrupted due to the error --- " Images > (filled).... /mri/filled/COR-001... not found.... wmfill first". > 2. In command line, I typed in "inflate_subject subject_name". It still > failed due to the error --- "mri_fill: could not find valid seed for the > cc, mri_fill:could not find corpus callosum" > > Any help will be appreciated! > > Best, > Yang > > -- Ev
