Mithra,
Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 256^3 while the norm.mgz and aseg.mgz files are FOV^3 (where FOV > 256).
A work-around is to use the --cropsize option of mri_convert (see its -- help for details) to convert the orig.mgz file to 256^3. I've attached a new recon-all which has flag called -cropsize256 that handles this for you.
Copy the attached file, recon-all.gz, to your $FREESURFER_HOME/bin, then:
cd $FREESURFER_HOME/bin gunzip recon-all.gz chmod a+x recon-all
Then re-run recon-all:
recon-all -s <subjid> -autorecon1 -cropsize256
You will then see, using mri_info, that orig.mgz has dimensions 256^3.
The next release of freesurfer will have this -cropsize256 flag.
Nick
On Tue, 2007-04-03 at 16:49 -0500, Mithra wrote:
Hello FS Group, I get "segmentation fault" error during autorecon2 step. I checked the talairach transformation. It seemed to be fine. The skull strip did not seem to be correct. I manually edited the brainmask.mgz and saved the data. But still I get the error. I am not sure what the problem is. Any help would be great!
I have the output form mri_info for the original surface. .
Thanks. Mithra.
Output for mri_info: mri_info $SUBJECTS_DIR/asm1_004/mri/orig.mgz Volume information for /usr/pubsw/freesurfer/subjects/asm1_004/mri/orig.mgz type: MGH dimensions: 301 x 301 x 301 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 301.000 xstart: -150.5, xend: 150.5 ystart: -150.5, yend: 150.5 zstart: -150.5, zend: 150.5 TR: 4.97 msec, TE: 1.21 msec, TI: 500.00 msec, flip angle: 11.00 deg rees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 40.3653 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.5037
talairach xfm : /usr/pubsw/freesurfer/subjects/asm1_004/mri/transforms/talairach .xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 150.5000 0.0000 0.0000 1.0000 -110.1347 0.0000 -1.0000 0.0000 123.9963 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 150.5000 -0.0000 -0.0000 -1.0000 123.9963 0.0000 1.0000 0.0000 110.1347 0.0000 0.0000 0.0000 1.0000 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer