Hi Tim, First download netcdf 3.5 and install it. I think there is an rpm for it for some distributions on www.rpmfind.net. That makes it easier because you will not have to compile it (not that there is anything wrong with compiling!). Compile the latest version of MNI tools. Usually the trickiest part is getting the MNI configure to find netcdf. You can tell it where to find netcdf stuff in the configure command (check the INSTALL or README files). Then make, make test, make install (or something close to that). You need to intall the MNI average305. You can download this from their site and installation was straightforward.
If all is well after that, you let freesurfer know where everything is. I do this by making edits to my .cshrc. Mine looks like this: setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin setenv MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib setenv FREESURFER_HOME /home/freesurfer/freesurfer_alpha setenv CSURF_DIR /home/freesurfer/freesurfer_alpha setenv MINC_DIR /homes/nmrnew/home/inverse/minc #afni for freesurfer setenv AFNI_DIR /home/freesurfer/freesurfer_alpha/afni setenv NO_FSFAST setenv SUBJECTS_DIR /home/brian/FREESURFER_data setenv FSLDIR /apps/fsl When you source the Free*Env.csh it will not override the variables set in your .cshrc. I can't remember why my installation of minc is in the above directory structure. I think I read somewhere that freesurfer likes that location, but maybe not. If you set your environment variables, you should be fine. When you are finished test it all out by: 1) by converting a COR volume to mnc format and running mritotal yourinput.mnc talairach.xfm (this needs the MNI binaries and average305 to work) 2) mri_motion_correct2 -o . -i 001 -i 002 -i 003 (motion correcting and averaging-this does a super job for automated registration) or mri_motion_correct -o . -i 001 -i 002 -i 003 (depending on your version) If it all works, then freesurfer could find your MNI tools. Good luck. brian > ----- Original Message ----- > From: "Timothy Souza" <[EMAIL PROTECTED]> > To: <[EMAIL PROTECTED]> > Sent: Thursday, October 03, 2002 6:32 AM > Subject: Installing MNI registration utilities > > > > HI all, > > > > When I first installed the latest version of Freesurfer, I did not > > initially install the MNI registration utilities from > > (www.bic.mni.mcgill.ca). I would now like to install these tools, but > have > > been unable to locate instructions on doing this. Could someone provide > me > > with brief instuctions, or point me to the appropriate documentation, to > > install the MNI tools utility post-Freesurfer installation? In the > > FreeSurferDefs.csh setup file, I currently have the env variable "setenv > > NO_MINC" as well. > > > > Thanks, > > Tm Souza > > ---------------------- > > Timothy Souza > > Brown University > > Department of Neuroscience > > [EMAIL PROTECTED] > > ph: 401-863-1258 > > fax: 401-863-1074 > > ------------------------ > > >
