Freesurfer

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30131 discussions

No variation in white matter volume between groups as well as hemispheres
by Jürgen Hänggi 25 Mar '09

25 Mar '09

Dear FS experts We analyzed two groups of six subjects each and recognized that the mean total white matter volume (as reported in aseg) is identical between the two groups as well as between the two hemispheres: group1: mean/sd: lh 244.2/32.3 cm3; rh 244.2/32.3 cm3 group2: mean/sd: lh 244.2/32.3 cm3; rh 244.2/32.3 cm3 However, when looking at the individual subjects there is variation between the individuals as well as the left and the right hemisphere. Any ideas? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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New Tutorial Attachments
by Jeff Sadino 24 Mar '09

24 Mar '09

Hello, I wanted to review the FreeSurfer attachments on the wiki's tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Whenever I try to click on an attachment, it brings me to a page and says: Attached FilesNo attachments stored for FsTutorial/April2009CourseSchedule You are not allowed to attach a file to this page. I see the page was recently updated for the new class. Are the powerpoints still available to view somewhere? Mahalo, Jeff Sadino _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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corpus callosum mask
by Al-Radaideh Ali 24 Mar '09

24 Mar '09

Dear FreeSurfer Experts, I wonder if Freesurfer saves the mask of corpus callosum or not. If so, could you please tell me where it is saved or how can I get a cc mask? Many thanks Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Thickness Repeatibility of a roi
by Campanella Martina 23 Mar '09

23 Mar '09

Hi, We would like to test the thickness repeatibility in a particular region of interest from 6 scans of the same subject in the same session and from the same subject in 6 different sessions to compute the overall statistics of them. We are trying to follow the protocol described in the wiki page about Thickness Repeatibility (http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility) but we're encountering some problems. We defined with tksurfer tools the label corresponding to the roi intended, afterwards we converted it in an annotation. The tutorial suggests the use of mris_thickness_diff but we have 6 scans, rather than only 2. So what can we do? Anyway we tried to find the thickness difference map using the first scan as the reference surface and the others as the input surfaces but, since we'd like to analyze the thickness deviation standard in a specific region, we used the option flag -annotation and the results seem wrong: we tried to use several annot files, specifing different label names but we found always the same error: total 0 vertices involved in thickness comparison. Any suggestions for our data? Thanks, Elisa Molinari, Martina Campanella

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RE: [Freesurfer] merging rh and lh surfaces
by ppj＠netfilter.com.br 22 Mar '09

22 Mar '09

I think Bruce or Douglas can explain better. However, the reason for both hemispheres being separated is that you need to mantain an S2 topological space. Sent from my Nokia phone @E71 -----Original Message----- From: slew(a)nmr.mgh.harvard.edu Sent: 19/03/2009 19:07:48 Subject: [Freesurfer] merging rh and lh surfaces Hi, I would like to have a single surf file that composed of both right and left pial surf. Is there a way to do it in freesurfer? Best. seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: RE: [Freesurfer] Voxel size smaller than 1x1x1mm?
by "Falk Lüsebrink" 21 Mar '09

21 Mar '09

Hi Nick, yes I have been trying to use the -noaseg flag, but as recon-all did exit with an error I thought this process might be needed, so I haven't tried anything else. The error message I received was: #-------------------------------------------- #@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands.... 20 segments, 4813 filled 10270 bright non-wm voxels segmented. 5589 diagonally connected voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320. Regards, Falk -------- Original-Nachricht -------- > Datum: Sat, 21 Mar 2009 10:08:24 +0100 > Von: "Falk Lüsebrink" <falk.luese(a)gmx.net> > An: falk.luese(a)gmx.net > Betreff: RE: [Freesurfer] Voxel size smaller than 1x1x1mm? > Falk, > > Probably you should try adding the -noaseg flag to recon-all, as the > aseg step relies on having 'conformed' volume data to register to the > atlas. The -noaseg flag skips creation and usage of the subcortical > atlas. > > Nick > > > On Wed, 2009-03-11 at 13:16 +0100, Falk Lüsebrink wrote: > > Hi again, > > > > so I did use the -cm flag to conform the voxels to its minimum size of > .8mm > > iso (which is also the native size of my data set) during the > mri_convert > > process and used the -noconform flag for the mri_normalize stage during > > autorecon1 to prevent further conformation to 1mm. > > > > But now recon-all exits with an error at stage 12 > > (http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) The error message > I > > got is as follows: > > #-------------------------------------------- > > #...@# Intensity Normalization2 Wed Mar 11 08:38:44 CET 2009 > > /home/falk/freesurfer/subjects/claus/mri > > > > mri_normalize -f home/falk/freesurfer/subjects/claus/tmp/control.dat > > -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz > > > > using control points from file > > /home/falk/freesurfer/subjects/claus/tmp/control.dat... > > not interpolating and embedding volume to be 256^3... > > using segmentation for initial intensity normalization reading from > > norm.mgz... > > mri_normalize: aseg volume aseg.mgz must be conformed using MR volume > > brainmask.mgz to mask input volume... > > Linux xxxxxx 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 > > x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Wed Mar 11 08:38:55 CET 2009 > > --------------------------------------------- > > > > Does anyone know what to do? > > > > Regards, > > Falk > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > > Sent: Friday, March 06, 2009 1:26 PM > > To: Falk Lüsebrink > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Voxel size smaller than 1x1x1mm? > > > > Hi Falk, > > > > yes, you can use the "conform to min" (-cm I think) switch in recon-all. > > Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard > > for whole brain morphometry because of dielectric effects. Good luck. > > > > Bruce > > On > > Fri, 6 Mar 2009, Falk Lüsebrink wrote: > > > > > Hi Freesurfers, > > > > > > I'm currently doing my bachelors thesis in medical engineering and I'm > > > trying to measure the cortical thickness of scans acquired by a 7T > MRT. > > > > > > A colleague of mine has used Freesurfer (v4.0.5) before and mentioned > that > > > high resolution scans with a voxel size smaller than 1x1x1mm (like > > > .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of > > autorecon > > > - I think during the mri_convert process. > > > > > > Is it possible to keep the native size or does Freesurfer need to > change > > the > > > voxel size to 1mm in order to do the segmentation correctly? > > > > > > Regards, > > > Falk > > > > > > _______________________________________________ > > > 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 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: > http://www.gmx.net/de/go/multimessenger01 -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger01

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RE: [Freesurfer] Voxel size smaller than 1x1x1mm?
by Nick Schmansky 20 Mar '09

20 Mar '09

Falk, Probably you should try adding the -noaseg flag to recon-all, as the aseg step relies on having 'conformed' volume data to register to the atlas. The -noaseg flag skips creation and usage of the subcortical atlas. Nick On Wed, 2009-03-11 at 13:16 +0100, Falk Lüsebrink wrote: > Hi again, > > so I did use the -cm flag to conform the voxels to its minimum size of .8mm > iso (which is also the native size of my data set) during the mri_convert > process and used the -noconform flag for the mri_normalize stage during > autorecon1 to prevent further conformation to 1mm. > > But now recon-all exits with an error at stage 12 > (http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) The error message I > got is as follows: > #-------------------------------------------- > #@# Intensity Normalization2 Wed Mar 11 08:38:44 CET 2009 > /home/falk/freesurfer/subjects/claus/mri > > mri_normalize -f home/falk/freesurfer/subjects/claus/tmp/control.dat > -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz > > using control points from file > /home/falk/freesurfer/subjects/claus/tmp/control.dat... > not interpolating and embedding volume to be 256^3... > using segmentation for initial intensity normalization reading from > norm.mgz... > mri_normalize: aseg volume aseg.mgz must be conformed using MR volume > brainmask.mgz to mask input volume... > Linux xxxxxx 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 > x86_64 GNU/Linux > > recon-all exited with ERRORS at Wed Mar 11 08:38:55 CET 2009 > --------------------------------------------- > > Does anyone know what to do? > > Regards, > Falk > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Friday, March 06, 2009 1:26 PM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Voxel size smaller than 1x1x1mm? > > Hi Falk, > > yes, you can use the "conform to min" (-cm I think) switch in recon-all. > Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard > for whole brain morphometry because of dielectric effects. Good luck. > > Bruce > On > Fri, 6 Mar 2009, Falk Lüsebrink wrote: > > > Hi Freesurfers, > > > > I'm currently doing my bachelors thesis in medical engineering and I'm > > trying to measure the cortical thickness of scans acquired by a 7T MRT. > > > > A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that > > high resolution scans with a voxel size smaller than 1x1x1mm (like > > .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of > autorecon > > - I think during the mri_convert process. > > > > Is it possible to keep the native size or does Freesurfer need to change > the > > voxel size to 1mm in order to do the segmentation correctly? > > > > Regards, > > Falk > > > > _______________________________________________ > > 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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problem with tksurfer:no open gl window
by Battistella Giovanni 20 Mar '09

20 Mar '09

Dear freesurfer users, I've just installed freesurfer on my PC and I tried testing it using the sample subject. tkmedit works fine, but with tksurfer I see the window where the image should appear but no image. the error I have is: no open gl window. I'm using Ubuntu 8.10 version with a Intel Q45 graphic card. Somebody can help me solving the problem? thank you in advance, giovanni

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mri_surfcluster
by Yigal Agam 20 Mar '09

20 Mar '09

Hi, When I run mri_surfcluster on a surface with 12 timepoints, how do I know when each of the reported clusters occurred? Thanks, Yigal

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Outline files convert
by Flavio Seixas 20 Mar '09

20 Mar '09

Hi All, I've got from IBSR (Internet Brain Segmentation Repository) MR images and their subcortical structures segmented manually. The segmented images are saved in Outline (.OTL) format. How could I convert from .OTL to .IMG or .NII (Analyze) format using mri_convert? Are there any examples? I would appreciate any help. There are one image to each of image slice, as shown bellow: IBSR_01_seg_18.otl IBSR_01_seg_46.otl IBSR_01_seg_73.otl IBSR_01_seg_100.otl IBSR_01_seg_19.otl IBSR_01_seg_47.otl IBSR_01_seg_74.otl IBSR_01_seg_101.otl IBSR_01_seg_20.otl IBSR_01_seg_48.otl IBSR_01_seg_75.otl IBSR_01_seg_102.otl IBSR_01_seg_21.otl IBSR_01_seg_49.otl IBSR_01_seg_76.otl IBSR_01_seg_103.otl IBSR_01_seg_22.otl IBSR_01_seg_4.otl IBSR_01_seg_77.otl IBSR_01_seg_104.otl IBSR_01_seg_23.otl IBSR_01_seg_50.otl IBSR_01_seg_78.otl IBSR_01_seg_105.otl IBSR_01_seg_24.otl IBSR_01_seg_51.otl IBSR_01_seg_79.otl IBSR_01_seg_106.otl IBSR_01_seg_25.otl IBSR_01_seg_52.otl IBSR_01_seg_7.otl IBSR_01_seg_107.otl IBSR_01_seg_26.otl IBSR_01_seg_53.otl IBSR_01_seg_80.otl IBSR_01_seg_108.otl IBSR_01_seg_27.otl IBSR_01_seg_54.otl IBSR_01_seg_81.otl IBSR_01_seg_109.otl IBSR_01_seg_28.otl IBSR_01_seg_55.otl IBSR_01_seg_82.otl IBSR_01_seg_10.otl IBSR_01_seg_29.otl IBSR_01_seg_56.otl IBSR_01_seg_83.otl IBSR_01_seg_110.otl IBSR_01_seg_2.otl IBSR_01_seg_57.otl IBSR_01_seg_84.otl IBSR_01_seg_111.otl IBSR_01_seg_30.otl IBSR_01_seg_58.otl IBSR_01_seg_85.otl IBSR_01_seg_112.otl IBSR_01_seg_31.otl IBSR_01_seg_59.otl IBSR_01_seg_86.otl IBSR_01_seg_113.otl IBSR_01_seg_32.otl IBSR_01_seg_5.otl IBSR_01_seg_87.otl IBSR_01_seg_114.otl IBSR_01_seg_33.otl IBSR_01_seg_60.otl IBSR_01_seg_88.otl IBSR_01_seg_115.otl IBSR_01_seg_34.otl IBSR_01_seg_61.otl IBSR_01_seg_89.otl IBSR_01_seg_116.otl IBSR_01_seg_35.otl IBSR_01_seg_62.otl IBSR_01_seg_8.otl IBSR_01_seg_117.otl IBSR_01_seg_36.otl IBSR_01_seg_63.otl IBSR_01_seg_90.otl IBSR_01_seg_118.otl IBSR_01_seg_37.otl IBSR_01_seg_64.otl IBSR_01_seg_91.otl IBSR_01_seg_119.otl IBSR_01_seg_38.otl IBSR_01_seg_65.otl IBSR_01_seg_92.otl IBSR_01_seg_11.otl IBSR_01_seg_39.otl IBSR_01_seg_66.otl IBSR_01_seg_93.otl IBSR_01_seg_120.otl IBSR_01_seg_3.otl IBSR_01_seg_67.otl IBSR_01_seg_94.otl IBSR_01_seg_12.otl IBSR_01_seg_40.otl IBSR_01_seg_68.otl IBSR_01_seg_95.otl IBSR_01_seg_13.otl IBSR_01_seg_41.otl IBSR_01_seg_69.otl IBSR_01_seg_96.otl IBSR_01_seg_14.otl IBSR_01_seg_42.otl IBSR_01_seg_6.otl IBSR_01_seg_97.otl IBSR_01_seg_15.otl IBSR_01_seg_43.otl IBSR_01_seg_70.otl IBSR_01_seg_98.otl IBSR_01_seg_16.otl IBSR_01_seg_44.otl IBSR_01_seg_71.otl IBSR_01_seg_99.otl IBSR_01_seg_17.otl IBSR_01_seg_45.otl IBSR_01_seg_72.otl IBSR_01_seg_9.otl Thank you, Flavio

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