Hi Phoebe, mincresample is an MNI tool, so you'll have to find it and put it in your both to get mri_motion_correct to work. Alternatively, you could do motion correction and averaging using some other package (AFNI, AIR, SPM).
Bruce On Tue, 15 Jan 2002, Phoebe Chan wrote: > Hi Bruce, > > I've downloaded and source the minc tools from: > > http://surfer.nmr.mgh.harvard.edu/download.html > > together with the freesurfer. However, it didn't help. Any suggestions? > > > > Phoebe. > > Bruce Fischl wrote: > > > Hi Phoebe, > > > > you will have to get the MNI tools from their website - we don't distribute > > them. > > > > Bruce > > > > On Mon, 14 Jan 2002, Phoebe Chan wrote: > > > > > Hi Evelina, > > > > > > I'm using the freesurfer version downloaded from the webpage, instead of the one >in > > > the NMR center. I've followed the instructions in INSTALL to source the >environment > > > and csurf can be open. I've tried to source the environment again and setenv > > > SUBJECTS_DIR, however, it didn't help the mri_motion_correct. Any suggestion? > > > > > > Phoebe. > > > > > > Evelina Busa wrote: > > > > > > > Hi Pheobe > > > > > > > > Maybe you could try sourcing the following before mri_motion_correct: > > > > > > > > source ~inverse/.cshrc > > > > > > > > I hope it helps. > > > > > > > > Ev > > > > > > > > On Sun, 13 Jan 2002, orphoebe wrote: > > > > > > > > > Hi, > > > > > > > > > > I've just setup the Oct 2001 version of freesurfer on my linux box. When I > > > > > tried to average 3 scans of the same subject using interactive mode, it > > > > > prompted: > > > > > > > > > > Convert(010722AZ) failed -- working on: > > > > > orig/002/COR-%03d > > > > > orig/001/COR-%03d > > > > > orig/003/COR-%03d > > > > > > > > > > In the log viewer, it showed: > > > > > ********************* > > > > > /home/phoebe/bin/freesurfer_alpha/bin/Linux/mri_average -conform > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/001/COR-.info > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/002/COR-.info > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/003/COR-.info > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig > > > > > interpolating volume to be isotropic 1mm^3 > > > > > reading > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/001/COR-.info... > > > > > mri_read(): couldn't determine type of file > > > > > /home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/001/COR-.info > > > > > /home/phoebe/bin/freesurfer_alpha/bin/Linux/mri_average: > > > > > >MRIread(/home/phoebe/bin/freesurfer_alpha/subjects/010722AZ/mri/orig/001/COR-. > > > > > info) failed > > > > > > > > > > Command Finished > > > > > ********************* > > > > > > > > > > After that, I exit the interactive mode and tried the mri_motion_correct, it > > > > > prompted: > > > > > > > > > > [phoebe@bunny orig]$ mri_motion_correct . 001 002 003 > > > > > /home/phoebe/bin/freesurfer_alpha/bin/Linux/mri_convert > > > > > checking for mincresample... ERROR > > > > > mri_motion_correct: couldn't find mincresample > > > > > transcript of last command is in /tmp/mmc-transcript.1193 > > > > > cleaning up... > > > > > > > > > > I've checked the /homes/nmrnew/home/inverse/minc and there is no >mincresample. > > > > > Do you know how to fix it and get the averaging done? > > > > > > > > > > Thanks. > > > > > > > > > > Phoebe. > > > > > > > > > > > > > -- > > > >
