Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

reg-feat2anat regsitration problems
by oxro03＠yahoo.com 14 May '07

14 May '07

Hi Doug & others, I am trying to use reg-feat2anat as it is described on the FSL web page: http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html However, I always seem t get a very bad registration. I tried using different values for --maxangle --cost mutualinfo --bins, but maintained --dof always at 6 for rigid body registration of the T1 and EPI, but didn't gt any good results. Initially I thought it might be because reg-fea2anat does not use a skull-stripped T1, but when I run Feat using the T1.mgz (converted to .nii.gz) as the main structural image for Registration (and the MNI brain as standard space), both with 'Full Search' option and dof = 6, the registration (with FEAT) works well. Is there anything else I can try to make it work with reg-feat2anat. Why wouldn't the registration work on my data with reg-feat2anat given that it works with Feat? Any comments or suggestions would be very appreciated. best, Sandy --------------------------------- Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out.

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surf-sess error
by Lee, Jung Min 14 May '07

14 May '07

Hi, I was able to use surf-sess command (modified in our group) to take pictures (rgb) of the brain; however, several days ago, I was kept getting errors (even errors with commands that worked fine before). it keep saying tksurfer.new: Command not found., then quit. Would you help me out? Machine: Roma /space/roma/1/users/caplan/plaus2 Env: Standard environment Subjects_Dir: /space/thor/1/users/west/subjects [roma:plaus2] (nmr-std-env) /space/roma/1/users/caplan/plaus2/scripts/surf-sess-rgb_wfile \ ? -analysis plaus2_corr \ ? -space sph \ ? -spacedir sph20 \ ? -subject west_margaret \ ? -s isxavg-plaus2_corr \ ? -contrast implaus_plaus_8-12sum \ ? -map sig \ ? -fthresh 1.3 \ ? -fmid 2.0 \ ? -fslope 1 \ ? -df dir \ ? -isxavg random \ ? -avgcurv \ ? -offset 0 \ ? -wfile /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w \ ? -hemi lh \ ? -rgbname plaus2_corr_implaus_plaus_8-12sum_300 cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /dev/null ----------------------------------------------------------------- ---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- INFO: You are about to use the NEW version of tksurfer. INFO: If you want to use the OLD version, re-run surf-sess INFO: with the -old flag. ---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- ------------------------------------------------------ ------------------------------------------------------ Session: isxavg-plaus2_corr ---- ------ lh hemisphere ------ sig-0-west_margaret west_margaret nowsource west_margaret equal wfile is /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w ------------ tcl file ----------- set val /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w sclv_read_binary_values 0 set curv lh.avg_curv read_binary_curv; set curvflag 1; source /usr/local/freesurfer/stable/lib/tcl/readenv.tcl file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb open_window sclv_set_current_field 0 puts "Taking Snapshots..." make_lateral_view redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_lat.rgb save_rgb rotate_brain_x 90 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_ven.rgb save_rgb make_lateral_view rotate_brain_y 180 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_med.rgb save_rgb exit --------------------------------- ---------------------------------------------------------- /autofs/space/roma_001/users/caplan/plaus2/isxavg-plaus2_corr/bold/plaus2_corr/s ph20-rfx/implaus_plaus_8-12sum tksurfer.new -west_margaret lh inflated -tcl /tmp/surf-sess-22861.tcl ---------------------------------------------------------- tksurfer.new: Command not found. Mon May 14 12:43:08 EDT 2007 I am also attaching the /surf-sess-rgb_wfile under command line. Thanks a lot! -Jung Min ********************************************** Jung Min Lee Neurology/Neuropsychology Martinos Center for Biomedical Imaging Massachusetts General Hospital Tel: 617-726-0303 (work) 617-780-1900 (cell) e-mail: jlee63(a)partners.org <mailto:jlee63@partners.org> jmlee(a)nmr.mgh.harvard.edu <mailto:jmlee@nmr.mgh.harvard.edu> **********************************************

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can't load sig.mgh in dev tksurfer
by Catherine Hartley 14 May '07

14 May '07

Hi, I'm having a problem with the development version of tksurfer. When I try to load a sig.mgh file as an overlay, I get the following error: % surfer: couldn't load /Applications/freesurfer/subjects/reruns/ glmleft/ReappCSplusContrast/sig.mgh sclv_read_from_volume: error in FunD_New Thanks, Cate

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question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'
by Ruiwang Huang 14 May '07

14 May '07

Dear All I meet a problem when I run the command mris_wm_volume to calculate the white matter volume for each hemisphere. The error message is coplied here >> mris_wm_volume >> mris_wm_volume: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Does any one know how to solve the problem? (My PC installed Suse9.3) Many thanks in advance Rhuang

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reg- feat2anat error
by Furlong, Carolyn 14 May '07

14 May '07

Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn

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Re: [Freesurfer] question about 'mris_wm_volume: errorwhileloading shared libraries: libstdc++.so.6'
by Ruiwang Huang 14 May '07

14 May '07

Dear Nick Thanks a lot. Here is the output of ' ldd `which mris_wm_volume` linux-gate.so.1 => (0xffffe000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x40019000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x40038000) libz.so.1 => /lib/libz.so.1 (0x40088000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x40099000) libstdc++.so.6 => not found libm.so.6 => /lib/tls/libm.so.6 (0x400eb000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x4010e000) libc.so.6 => /lib/tls/libc.so.6 (0x40116000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4022f000) /lib/ld-linux.so.2 (0x40000000) Any suggestions please? Rhuang On Monday 14 May 2007 17:53, Nick Schmansky wrote: > Ruiwang, > > It looks like you are already running what I thought would be the > correct version (rh9 is redhat 9). Can you send me the output of this > command? > > ldd `which mris_wm_volume` > > Nick > > On Mon, 2007-05-14 at 17:43 +0200, Ruiwang Huang wrote: > > Dear Nick > > > > Many thanks for your message. > > > > Here is the output after my typing > > > > >> cat $FREESURFER_HOME/build-stamp.txt > > >> freesurfer-Linux-rh9-stable-pub-v3.0.3 > > > > Do I need update the freesurfer on my PC? > > > > > > Ruiwang > > > > On Monday 14 May 2007 17:26, you wrote: > > > Rhuang, > > > > > > I'm guessing that you're using our Centos freesurfer distribution > > > (type: cat $FREESURFER_HOME/build-stamp.txt to find out). You'll > > > want to use our RedHat 9 freesurfer distribution with Suse9.3. > > > > > > Nick > > > > > > On Mon, 2007-05-14 at 17:05 +0200, Ruiwang Huang wrote: > > > > Dear All > > > > > > > > I meet a problem when I run the command > > > > mris_wm_volume > > > > to calculate the white matter volume for each hemisphere. > > > > > > > > The error message is coplied here > > > > > > > > >> mris_wm_volume > > > > >> mris_wm_volume: error while loading shared libraries: > > > > >> libstdc++.so.6: > > > > > > > > cannot open shared object file: No such file or directory > > > > > > > > Does any one know how to solve the problem? (My PC installed Suse9.3) > > > > > > > > Many thanks in advance > > > > > > > > Rhuang > > > > > > > > _______________________________________________ > > > > 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 --

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quick scatterplot label question
by Morgan Hough 14 May '07

14 May '07

Once I have defined a label in tksurfer and I select *Tools -> *Group* -> Graph Marked Vertices Avg to open a scatterplot window, how do I change the y axis label from the default "external" label. I assume that I need to set this beforehand in the fsgd file but I wasn't sure how. Thanks in advance. Cheers, -Morgan *

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(no subject)
by hankee 14 May '07

14 May '07

hi,I have some question to ask, First,now I want to add four parts of the occipital lobe's gray matter volume(Lateral Occipital,Lingual,Cuneus,Pericalcarine) to evaluate occipital lobe development,can I do like this? second, I also want to use the occipital lobe's cortical thickness to evaluate development,but four parts of the occipital's cortical thickness is different,so I add the four parts of the cortical thickness and divide 4,after that I get the average value,then use this average value to do statistics analysis,can I also do like this? Thank you very much! hankee

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Re: [Freesurfer] Make_average_subject error
by Furlong, Carolyn 14 May '07

14 May '07

Thanks Doug, I have tried your suggestion and set the command make_average_subject running again. I has been going for several hours but there is no visible change/activity on the console, is this unusual?. Also, there are only 13 subjects, how long would you expect this process to take per subject? Best wishes Carolyn ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wed 5/9/2007 6:21 PM To: Furlong, Carolyn Cc: Freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Make_average_subject error you may be using a version that does not have this option. Try using these doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… Furlong, Carolyn wrote: Hi all, I tried running it again with --no-symlink but this error came up ERROR: Flag --no-symlink unrecognized. any advice? Best wishes Carolyn ________________________________ _______________________________________________ Freesurfer mailing list 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

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labels for split parcellation
by Catherine Hartley 13 May '07

13 May '07

Hi, I've used mris_divide_parcellation to generate split the automatic parcellation into subregions. When I view the resulting annotation in tksurfer, the label names do not correspond to the subdivision names, so I am unable to tell which division is which (ie, which is rostralanteriorcingulate_div4, as none of them have this name). Is there a way to display these new label names? Thanks, Cate

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