Hi all, Just for clarification sake, when people in the Freesurfer community refer to" MNI tools", is this actually a reference to the MNI_Autoreg utility? I have installed netcdf 3.5, but wasn't able to find a utility that is actually called MNI tools at www.bic.mni.mcgill.ca. Also, on the Freesurfer download page, there is a generalized download link labelled "MINC". Upon downloading and unpacking it, it appears to be mostly symbolic links, I'm guessing, to the location in which one would install MNI tools. Is this still current/necessary, or should I only download MNI tools from the MNI web page?
Thanks in advance, Tim Souza >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 >> ------------------------ ---------------------- Timothy Souza Brown University Department of Neuroscience [EMAIL PROTECTED] ph: 401-863-1258 fax: 401-863-1074 ------------------------
