Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

(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 >>> >>> >>> >

4 6

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

1 0

mris_anatomical_stats
by Catherine Hartley 11 May '07

11 May '07

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

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Fwd: [Freesurfer] mris_divide_parcellation
by Catherine Hartley 11 May '07

11 May '07

> From: Catherine Hartley <cate(a)nyu.edu> > Date: May 10, 2007 7:10:19 PM EDT > To: Doug Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mris_divide_parcellation > > then i get: Exec format error. Binary file not executable. > > [catemac:/Applications] cate% cd freesurfer/bin > [catemac:/Applications/freesurfer/bin] cate% chmod a+x > mris_divide_parcellation > [catemac:/Applications/freesurfer/bin] cate% mris_divide_parcellation > tcsh: /Applications/freesurfer/bin/mris_divide_parcellation: Exec > format error. Binary file not executable. > [catemac:/Applications/freesurfer/bin] cate% > > > > On May 10, 2007, at 6:58 PM, Doug Greve wrote: > >> try >> >> chmod a+x mris_divide_parcellation >> >> Catherine Hartley wrote: >> >>> Thanks! However when i try to execute the command, i get a >>> message saying "Permission denied". Any ideas? >>> >>> Thanks, >>> Cate >>> >>> On May 10, 2007, at 5:30 PM, Doug Greve wrote: >>> >>>> >>>> here you go ... >>>> >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> mris_divide_parcellation >>>> >>>> Catherine Hartley wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm hoping to get a hold of the function >>>>> mris_divide_parcellation which automatically subdivides the >>>>> cortical parcellations for a region into sub-regions. It's >>>>> not a part of the current Freesurfer release but would it be >>>>> possible to get a copy of the development version? >>>>> >>>>> Thanks, >>>>> Cate >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> >>> >> >> -- >> 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 >> >> >

2 2

mris_divide_parcellation
by Catherine Hartley 10 May '07

10 May '07

Hi, I'm hoping to get a hold of the function mris_divide_parcellation which automatically subdivides the cortical parcellations for a region into sub-regions. It's not a part of the current Freesurfer release but would it be possible to get a copy of the development version? Thanks, Cate

2 3

converting .xfm to register.dat
by s032441＠student.dtu.dk 10 May '07

10 May '07

Dear All Im trying to make a register.dat file by using tkregister2 --mov func.mnc --xfm your.xfm --s yoursubjectname --reg register.dat , but I get the following error message: tkregister2 --mov TDU__Blind_bef_JensenBruun_stat_TDU-Sens_TDU.mnc --xfm pet2tal.xfm --s jensen_ole_b --reg register.dat INFO: reading xfm file pet2tal.xfm, trying as MINC xfm regio_read_mincxfm: No such file or directory Could read pet2tal.xfm Does anyone know what to do? Thanks, Carsten

2 1

Does 'color scale bar' show the cortical thickness or [-log10(p)]?
by Ruiwang Huang 10 May '07

10 May '07

Dear All, I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure? Many thanks in advance Rhuang

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Freesurfer