Hi all, Sorry to labour this point, but I'm stuck with the MNI tools and am having trouble progressing through my freesurfer analyses. I can't create the talairach.xfm and was hoping for some help. If I run mri_convert in the command line, I get the following:
mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc ----------------------------------------------------------------- INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 211 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/...
Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages:
segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm'
As far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex