Tim, When using mritotal to fit a dataset, you can specify -model and use the base name average152. make sure average152 and its various datasets (average152_16_blur.mnc, average152_8_blur.mnc, average152_8_dxyz.mnc, average152_16_mask.mnc, average152_8_mask.mnc, average152_headmask.mnc) are in the mni_autoreg directory or wherever you store your model.
good luck. brian On Thu, 2002-10-03 at 13:32, Timothy Souza wrote: > 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 > ------------------------
