Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

Re: Freesurfer Digest, Vol 28, Issue 32
by Sebastian Moeller 28 Jun '06

28 Jun '06

Hi Anil, On 26. Jun 2006, at 00:08 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 8 > Date: Sun, 25 Jun 2006 17:07:36 -0500 > From: "Anil Roy" <aroy85(a)gmail.com> > Subject: Re: [Freesurfer] recon-all error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <627ebe090606251507s57777571wbd816d66196fc4f5(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative-------------- next part > -------------- > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > ERROR: /usr/local/freesurfer/subjects/F200 exists, delete or re-run > with -force > [root@dhcp-129-105-146-220 freesurfer]# recon-all -force -i > /root/Desktop/F200.mnc -subjid F200 -sd /usr/local/freesurfer/subjects > -all > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > INFO: /usr/local/freesurfer/subjects/F200 exists with -i, but -force > specified. > Deleting any previous source volumes > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 root root 9126 Jun 25 15:42 > /usr/local/freesurfer/subjects/F200/scripts/recon-all.log > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > WM removal version > /usr/local/freesurfer/subjects/F200 > > mri_convert /root/Desktop/F200.mnc > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > > mri_convert /root/Desktop/F200.mnc > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > reading from /root/Desktop/F200.mnc... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Sun Jun 25 15:42:47 CDT 2006 > Found 1 runs > /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > WARNING: only one run found. This is OK, but motion > correction cannot be performed on one run, so I'll > copy the run to rawavg and continue. > > cp /usr/local/freesurfer/subjects/F200/mri/orig/001.mgz > /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > > /usr/local/freesurfer/subjects/F200 > > mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform > > mri_convert /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz --conform > reading from /usr/local/freesurfer/subjects/F200/mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from 4 to 0 (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to /usr/local/freesurfer/subjects/F200/mri/orig.mgz... > > mri_add_xform_to_header -c > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm > /usr/local/freesurfer/subjects/F200/mri/orig.mgz > /usr/local/freesurfer/subjects/F200/mri/orig.mgz > > INFO: extension is mgz > #-------------------------------------------- > #@# Nu Intensity Correction Sun Jun 25 15:43:04 CDT 2006 > > mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 > > /usr/local/freesurfer/subjects/F200/mri > /usr/local/freesurfer/bin//mri_nu_correct.mni > --i orig.mgz --o nu.mgz --n 2 > nIters 2 > $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > Sun Jun 25 15:43:04 CDT 2006 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by nicks@kani > (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 > tmpdir is ./tmp.mri_nu_correct.mni.3620 > /usr/local/freesurfer/subjects/F200/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3620/nu0.mnc > Can't find the talairach xform > '/usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm' > Transform is not loaded into mri > reading from orig.mgz... > Talairach transform > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm does > not exist ... > Cannot load tal xfm file > /usr/local/freesurfer/subjects/F200/mri/transforms/talairach.xfm > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to ./tmp.mri_nu_correct.mni.3620/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Sun Jun 25 15:43:10 CDT 2006 > nu_correct -clobber ./tmp.mri_nu_correct.mni.3620/nu0.mnc > ./tmp.mri_nu_correct.mni.3620/nu1.mnc > [root@dhcp-129-105-146-220.speech.northwestern.edu:/usr/local/ > freesurfer/subjects/F200/mri/] [2006-06-25 15:43:11] running: > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber > -nokeeptmp -tmpdir /usr/tmp/nu_correct_3670/ > ./tmp.mri_nu_correct.mni.3620/nu0.mnc > ./tmp.mri_nu_correct.mni.3620/nu1.imp > > /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared > libraries: libstdc++.so.5: cannot open shared object file: No such > file or directory Here is the part where it breaks; the freesurfer program you use most likely was compiled with gcc 3.x.x, while FC4 is using gcc 4.x.x. The result from the switch in compilers is that you only have a libstdc++.so.6. If you install the following rpm from your installation medium (or any source from the internet) compat-libstdc++-33-3.2.3-47.fc4.i386; it should work. One caveat, I never used FC4, so I might be way off. Ahoi & good luck Sebastian > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=32512) > nu_correct: crashed while running nu_estimate_np_and_em (termination > status=32512) > ERROR: nu_correct > Linux dhcp-129-105-146-220.speech.northwestern.edu > 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 > GNU/Linux > > recon-all exited with ERRORS at Sun Jun 25 15:43:11 CDT 2006 > -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] tesselating
by Chacko Cherian 27 Jun '06

27 Jun '06

yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum. --- Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > and does the filled.mgz look correct? Are the > hemisphere separately > labeled and the cerebellum gone? Also, please post > these to the list so > other people can answer! > > Bruce > > > On Thu, 22 Jun 2006, Chacko Cherian wrote: > > > Yes when I load the image in tkmedit I odnt have > any > > problems.Its perfectly clear and > coronal,horizonatal > > and sagittal are all correct. > > > > --- Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > > >> when you load it in tkmedit does it display > >> properly? That is, is the > >> coronal view really coronal? > >> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> > >>> Hello all, > >>> I ran an Analyze format image in > Fresurfer...just > >> the > >>> Morphometry and reconstruction tutorial..but > found > >>> that it's creating a filled.mgz volume but I'm > >> having > >>> a problem in tesselating and creating the > outputs > >>> lh.orig and rh.orig for the left and right > >>> hemispheres.It displays a very tiny piece of the > >>> volume. > >>> Could you please let me know how to troubleshoot > >> this > >>> problem.. > >>> THanks in advance. > >>> > >>> Chacko. > >>> > >>> > >>> > >>> Chacko Cherian > >>> M.S EE > >>> Graduate Assistant > >>> Department of Psychology > >>> Arizona State University. > >>> Tempe,AZ. > >>> > >>> > >>> > __________________________________________________ > >>> Do You Yahoo!? > >>> Tired of spam? Yahoo! Mail has the best spam > >> protection around > >>> http://mail.yahoo.com > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > > > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > > > > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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problems with fsaverage
by Doug Greve 27 Jun '06

27 Jun '06

I've recently found a problem with the left hemi of fsaverage. This problem unfortunately also extends to the left hemi of any average subject created with stable3. The right hemi is not affected. The problem was that the lh.sphere.reg was wrong (it was actually that of average7). This will cause some inaccuracies in the visualization of maps on the left hemi of fsaverage and other average subjects (but the statistics themselves should be ok). I've included jpegs of the cortical parcellations on the left hemi as they should be ("good") and as they are with the incorrect lh.sphere.reg ("bad"). The parcellations are not dramatically different, but the boundaries do shift around a bit, especially medially. I have fixed this error in stable, and the fix will be live upon the next stable update. It is already live in dev. Nick is also preparing a new tarball for distribution, and this will include this fix. If you have an average subject that you want to correct, you do not have to rebuild it. Rather, you can simply: cd youraveragesubject/surf cp lh.sphere.reg lh.sphere.reg.old # backup cp rh.sphere.reg lh.sphere.reg # copy rh.sphere to lh.sphere There should be no difference between lh.sphere.reg, lh.sphere, rh.sphere.reg, and rh.sphere (they are all 7th order icosahedron). If in the future, if you need to determine whether an average subject has the correct sphere.reg, just use the unix diff command to check for differences between lh.sphere.reg and rh.sphere.reg. I'm sorry that this error occured, and I hope it does not cause too much inconvenience. Please contact me if you have any questions. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mkbrainmask-sess
by Sebastian Moeller 26 Jun '06

26 Jun '06

Hi List, to follow up my mail from several days ago, all mkbrainmask-sess (v3.0.2 centos4 x86_64) really needs to be able to select the run from which to take the run-number are the following lines: case "-run" set run = $argv[1]; shift; breaksw somewhere between the label "parse_args:" and the command "goto parse_args_return". Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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converting register.mnc to register.dat
by Jeremy Young 26 Jun '06

26 Jun '06

Hi, Is it possible to convert register.mnc files to register.dat files or are they incompatible? I am trying to use register -rgb instead of tkregister to register functional data to anatomical data. Thanks! Jeremy

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viewing group analysis results in tkmedit (3D) while using spherical space intersubject morphing
by raij＠nmr.mgh.harvard.edu 26 Jun '06

26 Jun '06

Hi FreeSurfers, A small group analysis question of fMRI data (fixed effects). The target brain is "fsaverage". I have resampled and averaged the stat maps across subjects in _spherical_ space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / stxgrinder-sess. Viewing the results on a "fsaverage" surface with tksurfer works fine, thanks. Now I would like to also view the mean functional maps in 3D space (tkmedit) on the "fsaverage" brain. This does not seem to work - obviously because the results were calculated in spherical space and were never resampled back to 3D space. Is there a way to resample the group average from sperical space to 3D space so that it could be viewed in tkmedit? Or is the only way to achieve something like this to recalculate the analyses entirely in Talairach space without using the spherical space? To make the results actually comparable between 3D (tkmedit) and surface-based (tksurfer) viewing, I think I should use the same type of space for intersubject averaging - preferably spherical in both cases. Hence, if a tool such as sph2func-sess exists (could not find it in the wiki), or there is a workaround, any suggestions would be very much welcome. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Difficulties with segmentation
by Jeffrey Spielberg 26 Jun '06

26 Jun '06

Hi, I had a couple of questions regarding cortical/subcortical segmentation- 1. In our cortical segmentation we keep getting what look to be inaccurate segmentation of the rostral and caudal acc. It looks some of what should be labeled as one of those two areas is getting labelled corpus callosum or "unlabelled subcortical" instead, sometimes fairly large chunks. Does this indicate any problem earlier in the processing stream, and is there anything that can be done to prevent this? If not I saw that both tksurfer and tkmedit can be used to edit the segmentation, what would be the easiest way to do this? 2. When registering a freesurfer anatomical to Feat output (using reg-feat2anat) the registration seems to be somewhat inaccurate. Registering brainmask.mgz to our example_func using flirt has given us a better registration so far. Since reg-feat2anat seems to use flirt in its registration I was wondering what the difference might be resulting from. Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any way to have it use brainmask instead, as that seems to give better results? Thanks, Jeff

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Re: Re: [Freesurfer] Finding ROI and average
by Joongnam Yang 26 Jun '06

26 Jun '06

Thanks, Bruce & Kevin, What I meant is that 1. I have an overlay image (FSL functional image overlaid onto Freesurfer inflated image). So, the image has both functional and anatomical in it. 2. I found an area of interest in the overlay image and I'd like to get (functional) statistics of that particular area regarding amplitude of activation. 3. I am asking if such a method is available on TkSurfer or TkMedit, or I should do some other methods. Thanks always. Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 06/06/19 오후 2:57 >>> do you mean specifying it anatomically or functionall? You can do both. Anatomically you can use any of the cortical parcellation or subcortical segmentation units for this, or draw one yourself. On Mon, 19 Jun 2006, Joongnam Yang wrote: > Hi All, > > Is there a method of isolating an area of the overlay image (functional onto > anatomical) on Freesurfer as ROI and get the average of the amplitude of the > ROI? > > Any suggestions would be appreciated. > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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questions about group analysis
by Lars M. Rimol 26 Jun '06

26 Jun '06

Hi, I have three questions: 1) Where can I find information on what the different output files of mri_glmfit represent, i.e. ar1.mgh eres.mgh rstd.mgh rvar.mgh These can all be plotted (Load Overlay) since they are .mgh files but they seem to rarely show any blobs (except with extremely liberal thresholding). Can they be used for QA of the analyses? What to look for? 2) What does gamma.mgh represent? I assume the sig.mgh is some kind of p-value distribution, is that correct? 3) What is the difference between the "Calculate identity matrix" and "No registration needed" options when loading Overlay? Do I need any registration if I do the statistical analysis e.g. in Matlab (after having done mris_preproc and mris_surf2surf) and export the results back to FS as mgh files? Or can I just choose No registration needed, given that registration did take place in the mris_preproc and mris_surf2surf steps previous to Matlab analysis? -- yours, LMR

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Volume estimates i Freesurfer
by Kjell-Inge Gjesdal 26 Jun '06

26 Jun '06

Members How do I get the actual numbers for the structural volumes after I have done the cortical and subcortical segmentations? Is the "norm" command needed to get the correct values? What are the units (ml or qubic cm/mm)? Is it possible to get a printable list? Thanks Kjell-Inge Gjesdal Sunnmøre MR-centre Norway

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Freesurfer June 2006