Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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

1 0

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

3 2

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

3 9

mris_thickness_diff computation method?
by David Perlman 09 May '07

09 May '07

In the documentation of mris_thickness_diff it says "This program computes the difference of two surface data sets defined on the two surface mesh. Result = data2 - data1 (in sense of closest vertex)." Also, on the thickness repeatability page, it states that the output of mris_thickness_diff is sampled on the first surface. Just want to make sure I'm understanding this correctly: this means that mris_thickness_diff does NOT resample the data onto a common mesh to do vertex-wise subtraction, but rather, for each vertex in surface1, it finds the spatially closest vertex in surface2 and then subtracts the data2 at that point from data1 at the original point. So I assume this means that using mris_thickness_diff, even if you have two thickness data files which are sampled on the *same* mesh, if they are physically not aligned in space for whatever reason, you will get very wrong results? (I think I had this problem earlier and didn't understand what was going on.) One more question about the thickness repeatability page. How will the results obtained in this way differ from results obtained by aligning the surfaces with mri_surf2surf and simply doing a vertex- wise subtraction using matlab? -- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer