Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

retinotopy
by Nurunisa Neyzi 28 Jun '06

28 Jun '06

Hi, during retinotopic mapping, still at the beginning, when I run the analysis (with the command sfa-sess), I get the error: ERROR: meanimg for mean image failed meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset -o rtopy/h-offset and I have h.bdhr and omnibus in my eccen and polar folders... and no h volume folder. (I have f.bhdr, fmc.bhdr, fmc.mcdat, my 32 f-stem and fmc-stem data, rtopy.par, inorm.log and mcparams2extreg.log in 001, 002, etc.) what can be going wrong? Thanks! Nurunisa

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Scale Bar
by Reza Rajimehr 28 Jun '06

28 Jun '06

Hi, Does anybody have any idea what the scale bar shows in Tksurfer? I have heard that the scalebar is 10mm for the human brain. I am working with the monkey brain. Is the length of the scale bar 1cm for the monkey brain as well? Thanks, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Thank you for the response. I may be overly forthcoming here, but when will the next stable release be available. Aju On Thu, 29 Jun 2006 Doug Greve wrote : > >We are still evaluating it, but it should be ready by our next stable release. > >doug > > > >Bruce Fischl wrote: > >>Doug put together a white matter parcellation that does this kind of thing, but I'm not sure what the status of it is. Doug? >>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >> >>>What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. >>> >>>Aju. >>> >>> >>>On Thu, 29 Jun 2006 Bruce Fischl wrote : >>> >>>>what would the white matter volume of a cortical region mean? >>>>On Wed, 28 Jun 2006, Ajith Kumar U wrote: >>>> >>>>>Hello All, >>>>> >>>>>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >>>>> >>>>>Thanks, >>>>> >>>>>Aju. >>>>> >>>>> >>>>>************************************************** >>>>>Mr.Ajith Kumar U >>>>>Junior Research Fellow, >>>>>Department of Audiology, >>>>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>>>Manasagangothri, >>>>>Mysore,570006 >>>>>INDIA. >>>>>Ph: +91 821 2514449 Ext 186 (O) >>>>> +91 821 2514449 Ext 224 (R) >>>>>Fax: +91 821 2510515 >>>>>Email: ajithajitkumar18(a)rediffmail.com >>>>>************************************************** >>>> >>>>_______________________________________________ >>>>Freesurfer mailing list >>>>Freesurfer(a)nmr.mgh.harvard.edu >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>>************************************************** >>>Mr.Ajith Kumar U >>>Junior Research Fellow, >>>Department of Audiology, >>>All India Institute of Speech and Hearing, Naimisham Camppus, >>>Manasagangothri, >>>Mysore,570006 >>>INDIA. >>>Ph: +91 821 2514449 Ext 186 (O) >>> +91 821 2514449 Ext 224 (R) >>>Fax: +91 821 2510515 >>>Email: ajithajitkumar18(a)rediffmail.com >>>************************************************** >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- 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 > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. **************************************************

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Re: Re: [Freesurfer] Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work. Aju. On Thu, 29 Jun 2006 Bruce Fischl wrote : >what would the white matter volume of a cortical region mean? >On Wed, 28 Jun 2006, Ajith Kumar U wrote: > >>Hello All, >> >>How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? >> >>Thanks, >> >>Aju. >> >> >>************************************************** >>Mr.Ajith Kumar U >>Junior Research Fellow, >>Department of Audiology, >>All India Institute of Speech and Hearing, Naimisham Camppus, >>Manasagangothri, >>Mysore,570006 >>INDIA. >>Ph: +91 821 2514449 Ext 186 (O) >> +91 821 2514449 Ext 224 (R) >>Fax: +91 821 2510515 >>Email: ajithajitkumar18(a)rediffmail.com >>************************************************** >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

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Total Volumes
by Ajith Kumar U 28 Jun '06

28 Jun '06

Hello All, How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file? Thanks, Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

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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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Freesurfer