Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

recon-all stage3
by Fornito, Alexander 14 Jun '05

14 Jun '05

Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32 and tol=1.000e-01 integrating with navgs=32 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 taking momentum steps... integrating with navgs=8 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 taking momentum steps... integrating with navgs=2 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 integrating with navgs=0 and tol=1.000e-01 pass 1 complete, delta sse/iter = 0.16/60 = 0.00 final distance error %31.34 optimization complete. unfolding took 0.81 hours --------------------------------------------- Fix Topology lh Sat Jun 11 04:24:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192/scripts mris_fix_topology 1000192 lh reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_fix_topology: could not read original surface orig No such file or directory reading T1 volume from T1... reading wm segmentation from wm... recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005

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Problems in pial surface?
by Fornito, Alexander 14 Jun '05

14 Jun '05

Hi, I've been using freesurfer with only one run (image) pers subject and have generally been obtaining good results. I've just noticed a few quirks in the estimation of the pial surface that I was seeking some clarification. 1 - the algorithm consistently misses portions of grey matter in the medial temporal lobes (amygdala/hippocampus). I've noticed that this "missed" area becomes part of the "medial wall" region when parcellate_subject is run. Does the algorithm intentionally avoid estimatiung the grey/csf surface in the medial temporal lobes? 2 - Sometimes a portion of the other hemisphere gets included in estimates of the pial surface. Any tips for dealing with this? I was thinking of manually deleting a thin line of voxels through the midline of the T1 to emphasise the medial surface in areas where the algorithm has trouble? As an aside, where can I find the average7? I thought it would be in /usr/local/freesurfer/average/, but all I have is .gcs, .tif, and .txt files. Thanks as always, Alex

1 0

Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 13 Jun '05

13 Jun '05

Nick, Thanks. Yes, I used 'cd packages' and did the installation. After setting the environment and the subjit it works without errors. One more question, can I do a similar conversion for one .orig file having both hemisphere data points and generate one inflated surface or would have to use lh and rh.orig files seperately? Thanks, Arvind Gururajan On 13 Jun 2005, Nick Schmansky wrote: > Arvind, > > You are right, the MINC installation instructions are mistaken. A 'cd > packages' is missing: > > mkdir -p packages > cd packages <<<<< missing statement > tar xvfz mni.$OS.tar.gz > > As for the ZM error, is this the name of a subject? If so, preface it > with -subjid, like this: > > recon-all -smooth1 -subjid ZM > > The -smooth1 argument is not one normally used outright, but it will > work, once certain variables are set, namely these: > > setenv DoCANormalize 0 > setenv DoCAReg 0 > setenv DoCALabel 0 > setenv EditWMwithASeg 0 > > Nick > > On Mon, 2005-06-13 at 12:58 -0500, Arvind Gururajan wrote: > > > > Nick, > > > > Thanks for the clear description. I repeated the exact installation and got > > the same errors. I noticed that the 'current' directory was wrongly placed > > in this path. /usr/pubsw/mni/current. Repeated the same steps again, but > > now installed in the right directory. Getting the following errors: > > > > [root@node1 noarch]# ./recon-all -smooth1 ZM > > ######################################## > > program versions used > > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ > > mri_convert --version > > $ > > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v > > 6.3 1999/10/19 14:45:31 neelin Exp $ > > minctracc.c > > $Header: > > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 > > 2000/03/15 08:42:41 stever Exp $ > > $Header: > > /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 > > 1999/10/19 14:45:27 neelin Exp $ > > $Header: > > /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 > > 1999/10/19 14:45:18 neelin Exp $ > > $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > mri_convert --version > > $ > > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > > # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > $ > > ####################################### > > ERROR: Flag ZM unrecognized. > > -smooth1 ZM > > > > Your feedback will be appreciated. > > > > Thanks, > > Arvind > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > > > --=-yST7vkqiza7BNyzh64R8 > > > Content-Type: text/plain > > > Content-Transfer-Encoding: 7bit > > > > > > Arvind > > > > > > I'm suspect that our instructions may be a bit confusing. The files to > > > download are not the netcdf and minc files from the MNI distribution > > > site, but rather the file mni.Linux.tar.gz from our site (where it says > > > 'Download MNI binaries for Linux and/or SunOS.', click on Linux). > > > Following the instructions, this will result in an installation of files > > > in the directory /usr/pubsw/packages/mni/current. Then, the line: > > > > > > source $FREESURFER_HOME/FreeSurferEnv.csh > > > > > > will add MINC_BIN_DIR to the path. > > > > > > Also, where the instructions say to type: > > > > > > ln -s `which perl` perl > > > > > > be sure you are using the ` key, which is the far upper left corner key > > > on the keyboard (not to be confused with the ' key). > > > > > > The important thing is to have perl in the /usr/pubsw/bin directory. If > > > its already there, then no need to create a link. > > > > > > Hope this helps. > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > > > > > Hi Nick, > > > > > > > > I am running it on Linux platform. I followed the same instruction > > > > described here. > > > > http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html > > > > and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 > > > > > > > > I am not sure, if I created the symbolic link correctly. > > > > ln -s 5.8.0 perl - > > > > ln: `perl': File exists [ Same output even the first time] > > > > > > > > Also, there are no tools in the path, I manually created current/bin > > and > > > > current/lib. Is there a way to fix this, can I moved all the tools to > > these > > > > two directories? > > > > > > > > Your help is really appreciated. > > > > > > > > Arvind Gururajan > > > > > > > > > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > > Arvind, > > > > > > > > > > Hi. On what platform are you running? Linux? > > > > > > > > > > Did you follow the special installation instructions, involving > > making > > > > > the symbolic links? Lastly, are the tools in your path? > > > > > > > > > > If you are feeling brave, an alternative to installing the binaries > > is > > > > > to compile the MNI package from source on your platform, and install > > > > > those binaries. Instructions to do this are here: > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > > > > > > > > > and the gzip file is here: > > > > > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > I downloaded the entire MNI package. Although I see all these MNI > > > > files, I > > > > > > still get the same error, file not found. Any clues why this might > > be? > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > Arvind Gururajan > > > > > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > > > just download and install the whole MNI package. Much easier than > > > > trying > > > > > > > to install various pieces.... > > > > > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > I am very new to Freesurfer. Could anybody please tell me which > > > > > > specific > > > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > > > > > > > >> > > > > > > > >> I tried the following command. > > > > > > > >> > > > > > > > >> ./recon-all -smooth1 ZM > > > > > > > >> ######################################## > > > > > > > >> program versions used > > > > > > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > > > > > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp > > $fire > > > > > > > >> mri_convert --version > > > > > > > >> $ > > > > > > > >> strings: rawtominc:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: minctracc:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: mincresample:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: mincaverage:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > > > > > > >> mri_convert --version > > > > > > > >> $ > > > > > > > >> strings: mritotal:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> strings: nu_correct:: No such file or directory > > > > > > > >> strings: Command: No such file or directory > > > > > > > >> strings: not: No such file or directory > > > > > > > >> strings: found.: No such file or directory > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> $ > > > > > > > >> ####################################### > > > > > > > >> ERROR: Flag ZM unrecognized. > > > > > > > >> -smooth1 ZM > > > > > > > >> > > > > > > > >> > > > > > > > >> The folder ZM has only one orig file in the surf directory. > > There > > > > are > > > > > > no > > > > > > > >> raw data(.COR files). Please let me know your feedback. > > > > > > > >> > > > > > > > >> Sincerely, > > > > > > > >> > > > > > > > >> Arvind Gururajan > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > --=-yST7vkqiza7BNyzh64R8 > > > Content-Type: text/html; charset=utf-8 > > > Content-Transfer-Encoding: 7bit > > > > > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN"> > > > <HTML> > > > <HEAD> > > > <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> > > > <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> > > > </head> > > > <BODY> > > > Arvind > > > > > > I'm suspect that our instructions may be a bit confusing. The files to > > > download are not the netcdf and minc files from the MNI distribution > > site, > > > but rather the file mni.Linux.tar.gz from our site (where it says > > 'Download > > > MNI binaries for <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a> > > > and/or <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a > > >. > > > ', > > > click on Linux). Following the instructions, this will result in an > > > installation of files in the directory /usr/pubsw/packages/mni/current. > > > Then, the line: > > > > > > source $FREESURFER_HOME/FreeSurferEnv.csh > > > > > > will add MINC_BIN_DIR to the path. > > > > > > Also, where the instructions say to type: > > > > > > ln -s `which perl` perl > > > > > > be sure you are using the ` key, which is the far upper left corner key > > on > > > the keyboard (not to be confused with the ' key). > > > > > > The important thing is to have perl in the /usr/pubsw/bin directory. If > > > its already there, then no need to create a link. > > > > > > Hope this helps. > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > <BLOCKQUOTE TYPE=CITE> > > > <PRE> > > > Hi Nick, > > > > > > I am running it on Linux platform. I followed the > > same > > > instruction > > > described here. > > > <A > > > > > HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html">http > > :/ > > > /surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a> > > > and downloaded these two files: NetCDF 3.5.0 and > > MINC > > > 1.0 > > > > > > I am not sure, if I created the symbolic link > > > correctly. > > > ln -s 5.8.0 perl - > > > ln: `perl': File exists [ Same output even the > > first > > > time] > > > > > > Also, there are no tools in the path, I manually > > > created current/bin and > > > current/lib. Is there a way to fix this, can I > > moved > > > all the tools to these > > > two directories? > > > > > > Your help is really appreciated. > > > > > > Arvind Gururajan > > > > > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > > Arvind, > > > > > > > > Hi. On what platform are you running? Linux? > > > > > > > > > > > Did you follow the special installation > > > instructions, involving making > > > > the symbolic links? Lastly, are the tools in > > your > > > path? > > > > > > > > If you are feeling brave, an alternative to > > > installing the binaries is > > > > to compile the MNI package from source on your > > > platform, and install > > > > those binaries. Instructions to do this are > > > here: > > > > > > > > <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp:// > > su > > > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a> > > > > > > > > and the gzip file is here: > > > > > > > > <A > > > > > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp:// > > su > > > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a> > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind > > > Gururajan wrote: > > > > > > > > > Hi, > > > > > > > > > > I downloaded the entire MNI package. Although > > > I see all these MNI > > > files, I > > > > > still get the same error, file not found. Any > > > clues why this might be? > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > Arvind Gururajan > > > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > > just download and install the whole MNI > > > package. Much easier than > > > trying > > > > > > to install various pieces.... > > > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan > > > wrote: > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > I am very new to Freesurfer. Could > > > anybody please tell me which > > > > > specific > > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > > > > >> > > > > > > >> I tried the following > > > command. > > > > > > >> > > > > > > >> ./recon-all -smooth1 ZM > > > > > > >> > > > ######################################## > > > > > > >> program versions used > > > > > > >> $Id: recon-all-nmr,v 1.37 > > > 2004/01/06 22:21:48 tosa Exp $ > > > > > > >> $Id: mri_motion_correct2,v 1.7 > > > 2004/01/16 20:25:10 tosa Exp $fire > > > > > > >> mri_convert --version > > > > > > >> $ > > > > > > >> strings: rawtominc:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: minctracc:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: mincresample:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: mincaverage:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> $Id: talairach2,v 1.5 > > > 2003/08/28 21:45:48 tosa Exp $ > > > > > > >> mri_convert --version > > > > > > >> $ > > > > > > >> strings: mritotal:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> strings: nu_correct:: No such > > > file or directory > > > > > > >> strings: Command: No such file > > > or directory > > > > > > >> strings: not: No such file or > > > directory > > > > > > >> strings: found.: No such file > > > or directory > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> $ > > > > > > >> > > > ####################################### > > > > > > >> ERROR: Flag ZM > > > unrecognized. > > > > > > >> -smooth1 ZM > > > > > > >> > > > > > > >> > > > > > > >> The folder ZM has only one orig > > > file in the surf directory. There > > > are > > > > > no > > > > > > >> raw data(.COR files). Please > > > let me know your feedback. > > > > > > >> > > > > > > >> Sincerely, > > > > > > >> > > > > > > >> Arvind Gururajan > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > COLOR="#000000">_______________________________________________ > > > Freesurfer mailing list > > > <A > > > > > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu > > </ > > > A> > > > <A > > > > > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ > > /m > > > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > </pre> > > > </blockquote> > > > </body> > > > </html> > > > > > > --=-yST7vkqiza7BNyzh64R8-- > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 13 Jun '05

13 Jun '05

Nick, Thanks for the clear description. I repeated the exact installation and got the same errors. I noticed that the 'current' directory was wrongly placed in this path. /usr/pubsw/mni/current. Repeated the same steps again, but now installed in the right directory. Getting the following errors: [root@node1 noarch]# ./recon-all -smooth1 ZM ######################################## program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag ZM unrecognized. -smooth1 ZM Your feedback will be appreciated. Thanks, Arvind On 10 Jun 2005, Nick Schmansky wrote: > > --=-yST7vkqiza7BNyzh64R8 > Content-Type: text/plain > Content-Transfer-Encoding: 7bit > > Arvind > > I'm suspect that our instructions may be a bit confusing. The files to > download are not the netcdf and minc files from the MNI distribution > site, but rather the file mni.Linux.tar.gz from our site (where it says > 'Download MNI binaries for Linux and/or SunOS.', click on Linux). > Following the instructions, this will result in an installation of files > in the directory /usr/pubsw/packages/mni/current. Then, the line: > > source $FREESURFER_HOME/FreeSurferEnv.csh > > will add MINC_BIN_DIR to the path. > > Also, where the instructions say to type: > > ln -s `which perl` perl > > be sure you are using the ` key, which is the far upper left corner key > on the keyboard (not to be confused with the ' key). > > The important thing is to have perl in the /usr/pubsw/bin directory. If > its already there, then no need to create a link. > > Hope this helps. > > Nick > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > > > Hi Nick, > > > > I am running it on Linux platform. I followed the same instruction > > described here. > > http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html > > and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 > > > > I am not sure, if I created the symbolic link correctly. > > ln -s 5.8.0 perl - > > ln: `perl': File exists [ Same output even the first time] > > > > Also, there are no tools in the path, I manually created current/bin and > > current/lib. Is there a way to fix this, can I moved all the tools to these > > two directories? > > > > Your help is really appreciated. > > > > Arvind Gururajan > > > > > > > > On 10 Jun 2005, Nick Schmansky wrote: > > > Arvind, > > > > > > Hi. On what platform are you running? Linux? > > > > > > Did you follow the special installation instructions, involving making > > > the symbolic links? Lastly, are the tools in your path? > > > > > > If you are feeling brave, an alternative to installing the binaries is > > > to compile the MNI package from source on your platform, and install > > > those binaries. Instructions to do this are here: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > > > > > and the gzip file is here: > > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > > > > > > > Nick > > > > > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > > > > > Hi, > > > > > > > > I downloaded the entire MNI package. Although I see all these MNI > > files, I > > > > still get the same error, file not found. Any clues why this might be? > > > > > > > > > > > > Thanks, > > > > > > > > Arvind Gururajan > > > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > > just download and install the whole MNI package. Much easier than > > trying > > > > > to install various pieces.... > > > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I am very new to Freesurfer. Could anybody please tell me which > > > > specific > > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > > > > >> > > > > > >> I tried the following command. > > > > > >> > > > > > >> ./recon-all -smooth1 ZM > > > > > >> ######################################## > > > > > >> program versions used > > > > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > > > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire > > > > > >> mri_convert --version > > > > > >> $ > > > > > >> strings: rawtominc:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: minctracc:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: mincresample:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: mincaverage:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > > > > >> mri_convert --version > > > > > >> $ > > > > > >> strings: mritotal:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> strings: nu_correct:: No such file or directory > > > > > >> strings: Command: No such file or directory > > > > > >> strings: not: No such file or directory > > > > > >> strings: found.: No such file or directory > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> $ > > > > > >> ####################################### > > > > > >> ERROR: Flag ZM unrecognized. > > > > > >> -smooth1 ZM > > > > > >> > > > > > >> > > > > > >> The folder ZM has only one orig file in the surf directory. There > > are > > > > no > > > > > >> raw data(.COR files). Please let me know your feedback. > > > > > >> > > > > > >> Sincerely, > > > > > >> > > > > > >> Arvind Gururajan > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > --=-yST7vkqiza7BNyzh64R8 > Content-Type: text/html; charset=utf-8 > Content-Transfer-Encoding: 7bit > > <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN"> > <HTML> > <HEAD> > <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> > <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> > </head> > <BODY> > Arvind > > I'm suspect that our instructions may be a bit confusing. The files to > download are not the netcdf and minc files from the MNI distribution site, > but rather the file mni.Linux.tar.gz from our site (where it says 'Download > MNI binaries for <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a> > and/or <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a >. > ', > click on Linux). Following the instructions, this will result in an > installation of files in the directory /usr/pubsw/packages/mni/current. > Then, the line: > > source $FREESURFER_HOME/FreeSurferEnv.csh > > will add MINC_BIN_DIR to the path. > > Also, where the instructions say to type: > > ln -s `which perl` perl > > be sure you are using the ` key, which is the far upper left corner key on > the keyboard (not to be confused with the ' key). > > The important thing is to have perl in the /usr/pubsw/bin directory. If > its already there, then no need to create a link. > > Hope this helps. > > Nick > > > > On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: > <BLOCKQUOTE TYPE=CITE> > <PRE> > Hi Nick, > > I am running it on Linux platform. I followed the same > instruction > described here. > <A > HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html">http :/ > /surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a> > and downloaded these two files: NetCDF 3.5.0 and MINC > 1.0 > > I am not sure, if I created the symbolic link > correctly. > ln -s 5.8.0 perl - > ln: `perl': File exists [ Same output even the first > time] > > Also, there are no tools in the path, I manually > created current/bin and > current/lib. Is there a way to fix this, can I moved > all the tools to these > two directories? > > Your help is really appreciated. > > Arvind Gururajan > > > > On 10 Jun 2005, Nick Schmansky wrote: > > Arvind, > > > > Hi. On what platform are you running? Linux? > > > > > Did you follow the special installation > instructions, involving making > > the symbolic links? Lastly, are the tools in your > path? > > > > If you are feeling brave, an alternative to > installing the binaries is > > to compile the MNI package from source on your > platform, and install > > those binaries. Instructions to do this are > here: > > > > <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp:// su > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a> > > > > and the gzip file is here: > > > > <A > HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp:// su > rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a> > > > > > > Nick > > > > > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind > Gururajan wrote: > > > > > Hi, > > > > > > I downloaded the entire MNI package. Although > I see all these MNI > files, I > > > still get the same error, file not found. Any > clues why this might be? > > > > > > > > > Thanks, > > > > > > Arvind Gururajan > > > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > > just download and install the whole MNI > package. Much easier than > trying > > > > to install various pieces.... > > > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan > wrote: > > > > > > > > > Hello, > > > > > > > > > > I am very new to Freesurfer. Could > anybody please tell me which > > > specific > > > > > MNI tool, I need to install? > > > > > > > > > > > > > > >> > > > > >> I tried the following > command. > > > > >> > > > > >> ./recon-all -smooth1 ZM > > > > >> > ######################################## > > > > >> program versions used > > > > >> $Id: recon-all-nmr,v 1.37 > 2004/01/06 22:21:48 tosa Exp $ > > > > >> $Id: mri_motion_correct2,v 1.7 > 2004/01/16 20:25:10 tosa Exp $fire > > > > >> mri_convert --version > > > > >> $ > > > > >> strings: rawtominc:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: minctracc:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: mincresample:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: mincaverage:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> $Id: talairach2,v 1.5 > 2003/08/28 21:45:48 tosa Exp $ > > > > >> mri_convert --version > > > > >> $ > > > > >> strings: mritotal:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> strings: nu_correct:: No such > file or directory > > > > >> strings: Command: No such file > or directory > > > > >> strings: not: No such file or > directory > > > > >> strings: found.: No such file > or directory > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> $ > > > > >> > ####################################### > > > > >> ERROR: Flag ZM > unrecognized. > > > > >> -smooth1 ZM > > > > >> > > > > >> > > > > >> The folder ZM has only one orig > file in the surf directory. There > are > > > no > > > > >> raw data(.COR files). Please > let me know your feedback. > > > > >> > > > > >> Sincerely, > > > > >> > > > > >> Arvind Gururajan > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > > > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > > > > > _______________________________________________ > Freesurfer mailing list > <A > HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer(a)nmr.mgh.harvard.edu </ > A> > <A > HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https:/ /m > ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a> > </pre> > </blockquote> > </body> > </html> > > --=-yST7vkqiza7BNyzh64R8-- > >

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Re: [Freesurfer] dlcompat binaries needed.
by Nick Schmansky 13 Jun '05

13 Jun '05

Mark, Creating empty directories for the subjects and fsl/bin was the right solution to the warning messages you were seeing. I need to add stub directories with READMEs to the directory structure. The FreeSurferEnv.csh file (which I am guessing you 'source' in your .cshrc file) has some text on the environment variables it references, including SUBJECTS_DIR and FSL_DIR, which pertain to your question (remember to set these before sourcing FreeSurferEnv.csh). Here's a snippet from that file: ############################################################################# # Name: FreeSurferEnv.csh # Purpose: sets up the environment to run FreeSurfer and FS-FAST # Usage: # 1. Create an environment variable called FREESURFER_HOME and set it # to the directory in which FreeSurfer is installed. # 2. From a csh or tcsh shell or (.login): # source FreeSurferEnv.csh # 3. There are environment variables that should point to locations # of software or data used by FreeSurfer. If set prior # to sourcing, they will not be changed, but will otherwise be # set to default locations: # FSFAST_HOME # SUBJECTS_DIR # MINC_BIN_DIR # MINC_LIB_DIR # FSL_DIR # 4. If NO_MINC is set (to anything), then all the MINC stuff is ignored. # 5. If NO_FSFAST is set (to anything), then the startup.m stuff is # ignored # 6. The script will print the final settings for the above variables # as well as any warnings about missing directories. If # FS_FREESURFERENV_NO_OUTPUT is set, then no normal output will # be made (only error messages). # # The most convenient way to use this script is to write another # script that sets FREESURFER_HOME and possibly SUBJECTS_DIR for # your set-up, as well as NO_MINC, NO_FSFAST, or # FS_FREESURFERENV_NO_OUTPUT as appropriate, and then source this # script. Nick On Sat, 2005-06-11 at 00:21 -0400, Mark Pinsk wrote: > Hi Nick, > > Thanks for the Tiger installation. I just installed it on my ibook > just to see if it worked, and so far so good. I was able to get the > csurf GUI to pop up, so I'll have to run thru a subject on my G5 > desktop in the next few weeks after I get back from HBM. > > 1 question: > When I sourced my .cshrc file it could not find a 'subjects' directory > and a 'fsl/bin' directory within the freesurfer folder. > I went ahead and just created empty folders with those names so that > it wouldn't complain. > But for future reference, where can I define the location of my > subjects folder and of my FSL installation if they aren't within the > freesurfer folder? > > Thanks ! > Mark > > > On 6/10/05, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Mark, > > > > I don't think dlcompat is required to run freesurfer. I am able to run it > > on a tiger machine without it. > > > > There is a new freesurfer build for Tiger just posted on the ftp site. Its > > a .dmg file, which is a compressed installation package. After download, a > > .mpkg file will appear, and clicking on that will begin the installation. > > > > The 'full' installation includes freesurfer binaries, support libraries and > > the MINC toolkit, all newly created on tiger from source. All install in > > /usr/pubsw/packages, thus Administrator access is required. The install > > location is not relocatable, as freesurfer depends on some fixed paths. A > > Fink installation is not necessary, as the support-libs packages includes > > everything freesurfer needs: jpeg, tiff, glut, tcl/tk, tix, blt and gsl. > > > > The full install file is at: > > > > ftp://surfer.nmr.mgh.harvard.edu > > and the file is called freesurfer-Darwin-tiger-full.dmg > > > > > > This is a work-in-progress, so I'd appreciate any comments, especially if > > it works for you. > > > > Nick > > > > > > > > On Fri, 2005-06-10 at 16:11 -0400, Mark Pinsk wrote: > > > > > > Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger > > machine. > > > > Turns out that Fink is not longer offering the dlcompat library for > > download. > > > > Can anyone wrap those binaries up and send them to me, or post them > > for download by any chance? > > > > thanks so much! > > Mark > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

1 0

Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 10 Jun '05

10 Jun '05

Hi Nick, I am running it on Linux platform. I followed the same instruction described here. http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 I am not sure, if I created the symbolic link correctly. ln -s 5.8.0 perl - ln: `perl': File exists [ Same output even the first time] Also, there are no tools in the path, I manually created current/bin and current/lib. Is there a way to fix this, can I moved all the tools to these two directories? Your help is really appreciated. Arvind Gururajan On 10 Jun 2005, Nick Schmansky wrote: > Arvind, > > Hi. On what platform are you running? Linux? > > Did you follow the special installation instructions, involving making > the symbolic links? Lastly, are the tools in your path? > > If you are feeling brave, an alternative to installing the binaries is > to compile the MNI package from source on your platform, and install > those binaries. Instructions to do this are here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README > > and the gzip file is here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz > > > Nick > > > > On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote: > > > Hi, > > > > I downloaded the entire MNI package. Although I see all these MNI files, I > > still get the same error, file not found. Any clues why this might be? > > > > > > Thanks, > > > > Arvind Gururajan > > > > On 9 Jun 2005, Bruce Fischl wrote: > > > just download and install the whole MNI package. Much easier than trying > > > to install various pieces.... > > > > > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > > > > > Hello, > > > > > > > > I am very new to Freesurfer. Could anybody please tell me which > > specific > > > > MNI tool, I need to install? > > > > > > > > > > > >> > > > >> I tried the following command. > > > >> > > > >> ./recon-all -smooth1 ZM > > > >> ######################################## > > > >> program versions used > > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire > > > >> mri_convert --version > > > >> $ > > > >> strings: rawtominc:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> strings: minctracc:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> strings: mincresample:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> strings: mincaverage:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > > > >> mri_convert --version > > > >> $ > > > >> strings: mritotal:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> strings: nu_correct:: No such file or directory > > > >> strings: Command: No such file or directory > > > >> strings: not: No such file or directory > > > >> strings: found.: No such file or directory > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> $ > > > >> ####################################### > > > >> ERROR: Flag ZM unrecognized. > > > >> -smooth1 ZM > > > >> > > > >> > > > >> The folder ZM has only one orig file in the surf directory. There are > > no > > > >> raw data(.COR files). Please let me know your feedback. > > > >> > > > >> Sincerely, > > > >> > > > >> Arvind Gururajan > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

dlcompat binaries needed.
by Mark Pinsk 10 Jun '05

10 Jun '05

Hi, I just tried a fresh installation of freesurfer on a new OS X Tiger machine. Turns out that Fink is not longer offering the dlcompat library for download. Can anyone wrap those binaries up and send them to me, or post them for download by any chance? thanks so much! Mark

2 1

Mean & SD over ROI in a FIR analysis (several timepoints)
by Tommi Raij 10 Jun '05

10 Jun '05

We are trying to calculate mean and SD over all the spatial (vertex) points included in a single functionally defined ROI/label. Bottom line, the biggest problem is that we do not know which tool to use to read all timepoints/frames of the hemodynamic waveforms (of all the vertex points included in the label, one at a time) into matlab. For details, please see below. Problem 1: We tried to use mri_label_vals but this gives only one value per vertex point. However this is a FS-FAST FIR analysis with a time window of 16 frames/TRs (of which two are prestimulus) so we should get 16 values for each vertex point in order to draw a BOLD time course. So we need a reader that will produce the functional stat values for all the time points, separately for all vertices included in the ROI. Problem 2: We would need to subtract the mean prestimulus baseline values from all 16 time points in order to set a (mean) zero baseline. This is necessary to decrease the voxel-to-next-voxel variability that is large in fMRI data. This of course has to be done before calculating the mean and SD values over the ROI. We did use mkcontrast-sess -rmprestim - does this result in that the baseline is already subtracted in the values (for each vertex point separately)? There are typically about 600 single vertex points in a label so saving them manually one by one as ASCII and then combining them is not feasible. As a separate but complicating issue, we have 6 simple contrasts (condition N minus REST, with names such as A-REST, V-REST, etc) and 2 slightly more complicated contrasts (condition 1 plus condition 2 minus condition 3). Loading and overlaying the ROI mean +- SD curves for each contrast separately increases the work load 6-fold. We have multiple subjects in six different conditions, each with multiple ROIs, and 6 simple contrasts, leading to thousands of BOLD waveforms - any practical application should automatically load all 6 contrast HDR waveforms and overlay them in a single window (exactly as sliceview-sess, tkmedit, and tksurfer do when you load time course - except that in these programs the time courses are displayed for only a single voxel at a time). Any suggestions how this could be achieved? Example data/analysis can be found in /space/cognito/5/users/raij/avml_fmri/avml12_session_BRISI07_ISI1TR_BERT There are two analyses here - here we are interested in the FIR analysis: ISI1TR_BERT_ERFIRsm6pf5tpefsub ... and the variables are setenv SUBJECT avml12 setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri/ Any advice would be greatly appreciated! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129

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Re: [Freesurfer] (MNI tools)
by Arvind Gururajan 10 Jun '05

10 Jun '05

Hi, I downloaded the entire MNI package. Although I see all these MNI files, I still get the same error, file not found. Any clues why this might be? Thanks, Arvind Gururajan On 9 Jun 2005, Bruce Fischl wrote: > just download and install the whole MNI package. Much easier than trying > to install various pieces.... > > On Thu, 9 Jun 2005, Arvind Gururajan wrote: > > > Hello, > > > > I am very new to Freesurfer. Could anybody please tell me which specific > > MNI tool, I need to install? > > > > > >> > >> I tried the following command. > >> > >> ./recon-all -smooth1 ZM > >> ######################################## > >> program versions used > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire > >> mri_convert --version > >> $ > >> strings: rawtominc:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: minctracc:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: mincresample:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: mincaverage:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > >> mri_convert --version > >> $ > >> strings: mritotal:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> strings: nu_correct:: No such file or directory > >> strings: Command: No such file or directory > >> strings: not: No such file or directory > >> strings: found.: No such file or directory > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> $ > >> ####################################### > >> ERROR: Flag ZM unrecognized. > >> -smooth1 ZM > >> > >> > >> The folder ZM has only one orig file in the surf directory. There are no > >> raw data(.COR files). Please let me know your feedback. > >> > >> Sincerely, > >> > >> Arvind Gururajan > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

Strip and register check
by Fornito, Alexander 10 Jun '05

10 Jun '05

Hi, A couple of questions; 1 - The skull stripping feature has overstripped some of my brains, and using -wsmore doesn't completely fix the problem. Are there any other options? 2 - I'd like to check my registrations by mapping labels from the average back onto the individual's brain. What's the best way to do this? Thanks, Alex

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