Hi,
The log says that it could not find $subject/mri/transforms/talairach.xfm for this volume.
Tosa
Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (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..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (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..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
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Yasunari Tosa, Ph.D. Email: [EMAIL PROTECTED]
NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street
Charlestown, MA 02129
USA
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