Freesurfer

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30076 discussions

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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(no subject)
by hankee 12 May '07

12 May '07

Hi, In freesurfer software,some file's name is *.mgz,what does the mgz abbreviate? Thanks. hankee，duhanjian(a)sohu.com 2007-05-05

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Difficulties with segmentation follow-up
by Jeffrey Spielberg 11 May '07

11 May '07

Hi, I sent a message to the forum last June regarding a problem with segmentation of the acc we were running into. We kept having areas of the rostral and caudal acc labeled as corpus callosum or "unlabelled subcortical". I got a reply that this was being worked on and I was wondering if this is now fixed in 3.0.4, and if not if there is any timeline for releasing a fix? Thanks, Jeff

2 3

Editing Segmentation Results
by Jared Conley 11 May '07

11 May '07

I am new to FreeSurfer and am attempting to segment T1 images using the "recon-all...autorecon2" command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using I think either 3D Slicer or the tkmedit program. (I would prefer to use 3D Slicer if possible since this is the program with which I am more familiar). Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared

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Re: [Freesurfer] mris_anatomical_stats
by Catherine Hartley 11 May '07

11 May '07

On May 11, 2007, at 1:38 PM, Catherine Hartley wrote: > Hi Jenni, > > This doesn't work either: > > [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats > mm103184 lh inflated -f mm103184/stats/ > lh.aparc.splitcingulate.stats -a mm103184/label/ > lh.aparc.splitcingulate.annot > > Any suggestions? > > Thanks, > Cate > > On May 11, 2007, at 1:33 PM, Jenni Pacheco wrote: > >> Hi Cate, >> >> I think you have to use the -f flag to specify an output file, >> otherwise it just prints to the screen. >> >> mris_anatomical_stats >> usage: mris_anatomical_stats [options] <subject name> <hemi> >> [<surface name>] >> >> This program measures a variety of anatomical properties >> >> valid options are: >> >> -i <low thresh> <hi thresh> - only consider thicknesses in >> the specified range. >> -l <label file> - limit calculations to specified label >> -t <thickness file> - use specified file for computing >> thickness statistics >> -a <annotation file> - compute properties for each label >> in the annotation file separately >> -b - tabular output >> -f tablefile - table output to a file (different format than -b) >> -log <log> - will write the stats into a file named <log> >> -nsmooth <#> - will smooth the thicknessmap # of iterations >> before using it >> >> >> >> Jenni >> On Fri, 11 May 2007, Catherine Hartley wrote: >> >>> Hi, >>> >>> I'm trying to get the anatomical statistics for a new >>> parcellation, ? h.aparc.splitcingulate.annot, I've created using >>> mris_divide_parcellation. I've tried using mris_anatomical_stats >>> with various argument structures (specifying output filenames, >>> not specifiying output filenames) and can't seem to get it to >>> write a ?h.aparc.splitcingulate.stats file. >>> >>> It generates and outputs summary statistics, but it does not >>> write a .stats file to the stats directory: >>> >>> [catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats >>> mm103184 lh inflated -a mm103184/label/lh.aparc.splitcingulate.annot >>> reading volume /Applications/freesurfer/subjects/reruns/mm103184/ >>> mri/ wm.mgz... >>> reading input surface /Applications/freesurfer/subjects/reruns/ >>> mm103184/surf/lh.inflated... >>> reading input surface /Applications/freesurfer/subjects/reruns/ >>> mm103184/surf/lh.pial... >>> reading input surface /Applications/freesurfer/subjects/reruns/ >>> mm103184/surf/lh.white... >>> done. >>> computing second fundamental form... ... done. >>> total white matter volume = 516178 mm^3 >>> total surface area = 81462 mm^2 >>> total gray matter volume = 230187 mm^3 >>> average cortical thickness = 2.175 mm +- 0.836 mm >>> average integrated rectified mean curvature = 0.025 >>> average integrated rectified Gaussian curvature = 0.096 >>> folding index = 9766.477 >>> intrinsic curvature index = 937.896 >>> [catemac:freesurfer/subjects/reruns] cate% >>> >>> Thanks for your help! >>> >>> -Cate >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >

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bus error when loading annotation
by Catherine Hartley 11 May '07

11 May '07

Hi, When I attempt to load a custom annotation file (that I created using mris_divide_parcellation) within tksurfer, I get a bus error which seems to result from a problem with the colortable: % reading colortable from annotation file... CTABreadFrom: could not allocate -2 bin table Cannot allocate memory Bus error I'm working on an Intel Mac. Thanks, Cate

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