Thanks Bruce and Jenni,
I see that I left out the conform step when going from rawavg.mgz to orig.mgz. I was grad_unwarping the 00?.mgz's before averaging them, and I started recon-all with the -nomc flag.
I conformed nu.mgz and it's norm.mgz is a full volume now.
Thanks, Vasanth
On Fri, 24 Mar 2006, Bruce Fischl wrote:
Hi Vasanth,
your orig.mgz hasn't been conformed. That is, it should be 1mm isotropic in a 256^3 volume, but it's not:
mri_info /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz Volume information for /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1.0000, 1.0000, 1.3300 type: FLOAT (3) fov: 256.000 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -85.1, zend: 85.1 . . .
how did you generate it?
Bruce On Fri, 24 Mar 2006, Vasanth Pappu wrote:
Hi,
I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do:
on machine vader
source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/
which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize
cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz
output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds.
But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz
I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz
how do I check if the transforms/talairach.lta is ok?
Thanks, Vasanth _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer