So, even though it says it will substitute the identity matrix for the transform, I still need a transform or it won't work? Is the only way to create a transform with that separate MNI software? Thanks, Margaret
On Wed, 1 Dec 2004, Yasunari Tosa wrote: > 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 > >>> > >>>_______________________________________________ > >>>Freesurfer mailing list > >>>[EMAIL PROTECTED] > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > > > >_______________________________________________ > >Freesurfer mailing list > >[EMAIL PROTECTED] > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
