Brian, Thanks for the advice, I'll give it a shot. Out of curiosity, can MNI tools use the MNI average152 template dataset instead of the MNI average 305? We had been using the MNI_152 template in another normalization scheme we had worked out using flirt in FSL.
Thanks, Tim >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 >> > ------------------------ >> > >> ---------------------- Timothy Souza Brown University Department of Neuroscience [EMAIL PROTECTED] ph: 401-863-1258 fax: 401-863-1074 ------------------------
