I'm still having problems...
With control points saved, I did in :
mri_normalize -f $SUBJECTS_DIR/<subjid>/tmp/control.dat -no1d $SUBJECTS_DIR/<subjid>/mri/orig $SUBJECTS_DIR/<subjid>/mri/T1
Then I ran recon-all -stage1 -nomotioncor -subjid subjid and got: . . . Intensity Normalization Fri Jun 3 12:26:01 PDT 2005 $SUBJECTS_DIR/<subjid>/mri mri_normalize orig T1 reading from orig... normalizing image... talairach transform 0.712 0.146 -0.143 -13.113; -0.203 0.572 -0.426 -76.656; 0.026 0.448 0.590 151.306; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 Segmentation fault ERROR: mri_normalize exited with non-zero status ------------------------------------------
Then I did: recon-all -stage1 -nomotioncor -nuintensitycor -subjid subjid
which also exited with non-zero status
Then I did: recon-all -stage1 -nomotioncor -nonormalization -subjid subjid and got . . . white matter segmentation took 8.9 minutes writing output to wm... --------------------------------------------- Fill Fri Jun 3 13:25:01 PDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -xform transforms/talairach.xfm wm filled $SUBJECTS_DIR/subjid/mri INFO: Volume /tmp/mritotal_2558/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.712 -0.143 -0.146 73.651; 0.026 0.590 -0.448 -51.272; 0.203 0.426 0.572 -67.608; 0.000 0.000 0.000 1.000; mri_fill: could not find valid seed for the cc No such file or directory Looking for area (min, max) = (350, 1400) area[0] = 15 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status ------------------------------------------
Then I did recon-all -stage1 -lh-xyz -29.9 -45.8 162.2 -rh-xyz 36.2 -54.3 152.3 -cc-xyz -7.3 -68.4 188.9 -nomotioncor -nonormalization -subjid subjid
and got . . . white matter segmentation took 8.9 minutes writing output to wm... --------------------------------------------- Fill Fri Jun 3 14:09:14 PDT 2005 INFO: Uses mri/transforms/talairach.xfm mri_fill -C -7.3 -68.4 188.9 -rh 36.2 -54.3 152.3 -lh -29.9 -45.8 162.2 -xform transforms/talairach.xfm wm filled $SUBJECTS_DIR/subjid/mri using Talairach position (-7, -68, 189) as corpus callosum seed point using Talairach position (36.2, -54.3, 152.3) as rh seed using Talairach position (-29.9, -45.8, 162.2) as lh seed INFO: Volume /tmp/mritotal_8012/nu_8_dxyz.mnc cannot be found. INFO: Using transforms/talairach.xfm and its offset for Talairach volume ... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.712 -0.143 -0.146 73.651; 0.026 0.590 -0.448 -51.272; 0.203 0.426 0.572 -67.608; 0.000 0.000 0.000 1.000; Segmentation fault ERROR: mri_fill exited with non-zero status ------------------------------------------
Any suggestions? Michele