Freesurfer March 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
79 discussions

errors with segmentation
by Joan Fisher 25 Mar '07

25 Mar '07

Hi all -- I've had problems recently with the subcortical segmentation, where it calls the caudate the hippocampus and the putamen is labeled the amygdala, etc. I'm wondering if the WM/GM volumes can still be accurate (which it looks like based on wm.mgz) when the identification of these structures is so far off. Also, the aseg.stats file was generated but contains no data, even though autorecon2 and 3 completed with no reported errors. What can I do to get the aseg.stats information? Running it again didn't fix the problem. Please let me know if there's an alternate way to get the WM and GM volumes for each hemisphere, even if the aseg.stats isn't working. Many thanks, Joan Fisher This is what aseg.stats looks like: # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.11.2.5 2006/04/13 18:57:07 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 007 # sysname Darwin # hostname joan-fishers-powerbook58.local # machine Power Macintosh # user joanfisher # anatomy_type volume # # SUBJECTS_DIR /Users/joanfisher/subjects # subjectname 007 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2007/19/02 18:02:57 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1447820, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1447820.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1158492, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1158492.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105720.605166, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2007/24/02 08:19:55 # ColorTable /Applications/freesurfer/FreeSurferColorLUT.txt # ColorTableTimeStamp 2007/14/00 12:14:41 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2007/23/02 14:29:21 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2007/23/02 14:29:21 # ExcludeSegId 0 # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader normMean # TableCol 6 FieldName Intensity normMean # TableCol 6 Units MR # TableCol 7 ColHeader normStdDev # TableCol 7 FieldName Itensity normStdDev # TableCol 7 Units MR # TableCol 8 ColHeader normMin # TableCol 8 FieldName Intensity normMin # TableCol 8 Units MR # TableCol 9 ColHeader normMax # TableCol 9 FieldName Intensity normMax # TableCol 9 Units MR # TableCol 10 ColHeader normRange # TableCol 10 FieldName Intensity normRange # TableCol 10 Units MR # NRows 1 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 666 -1414545516 -0.0 """""" nnnnnn|QV|QVÇW\ÇW\ólqólq€∞¥€∞¥™Ì™™Ì™¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨ØÛØØÛØØÛØØÛØØÛØØÛØ´Ó´´Ó´™Ì™™Ì™≠Ò≠≠Ò≠™Ì™™Ì™‡µ∫‡µ∫÷´Ø÷´ØøîôøîôÄÄÄÄÄÄRRRRRR 0.0000 0.0000 -0.0000 -0.0000 225831059456.0000

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Destrieux atlas
by skloeppe＠uke.uni-hamburg.de 25 Mar '07

25 Mar '07

Hi all, I was wondering if the more details atlas by Christophe Destrieux has already been published. I only found an abstract in the internet and therefore would prefer another citation. Thanks, Stefan -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Rolf A.K. Stahl

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{Disarmed}
by hankee 23 Mar '07

23 Mar '07

hi,I have some question to ask.First,I use flash black and white checkboard as stimulate,blocked design which presents off(30second)-on(30s)-off(30s)-on(30s)-off(30s)-on(30s) pattern,so such stimulation lasts 3 minutes,TR=3s.In order to create the sem_assoc_s001_r100.dat file,I write the optseq command as bellow:optseq -ntp 60 -npercond 3 -tpercond 30 -o sem_assoc-s,I don't why whether is right or not? Besides that another command shows bellow:mkanalysis-sess -analysis sem_assoc -TR 3 -paradigm sem_assoc.par -designtype blocked -funcstem fmc -inorm -fwhm 4 -nconditions 1 -timewindow 30 -tprestim 31,I also do't know whether right or not? Second,the surf-sess command produce the surface,But the active area is very tiny,compare to the SUMA.the picture is in the attachment. how to adjust its colour and size? Thank you very much!!!

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Re: [Freesurfer] Complex value color scales.
by Kevin Teich 23 Mar '07

23 Mar '07

> I am trying to display phase information on the cortical surface using tksurfer, > but am running into problems with the scale bar. Specifically when plotting > scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice > looking (continulus) cortical maps, with the correct scale values, but the > color bar is showing up inconsistent (two colors). Is there any way to correct > this problem, or access the actual color values being projected to the cortical > mesh? Unfortunately, the scale bar isn't really meant to be used with the complex color wheel. There is no way to get a nice legend for the color wheel. However, if you select View->Information->Angle, you can see the actual value that is being passed into the color function, so you can mouseover a color on the surface and see what value is mapped to it. I know it's not great, but maybe it will help a bit. -- Kevin Teich

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Re: Freesurfer Digest, Vol 37, Issue 21
by Sebastian Moeller 23 Mar '07

23 Mar '07

Not being Roland and al... On 23. Mar 2007, at 18:49 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Thu, 22 Mar 2007 15:18:05 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Re: Freesurfer Digest, Vol 37, Issue 16 > To: Paul Aparicio <aparicio(a)mit.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.0703221517330.3420(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > no, definitely don't use COR. I think you can use mri_convert -i[ijk]s. > Rudolph: can you elaborate on how to do this? here is what I use to accomplish this (in a csh script): set targ_dir = /path/to/your/input_volumes set targ_file_name = example.mgz set conformed_vol = the_name_of_the_volume_with_faked_resolution.mgz mri_convert -i ${targ_dir}/${targ_file_name} -o ${targ_dir}/${conformed_vol} -iis 1 -ijs 1 -iks 1 CAVEAT this expects isometric input scans, otherwise it gets a bit more elaborate...: this is what I used in the days of non-isometric scanning. It will express all resolutions as multiples of the minmum so that resampling later (by running mri_convert -cm ...) will do something reasonable. You still have to make sure, that you have <= 256 voxels per dimension... ahoi & hope it helps Sebastian ##### silly script to follow...###### #! /bin/csh! # run number from the dicom file zero padded to three digits set run = 008 # number of the first dicom file to contain data for this run (actually any dicom file for a run should do'?) set first_dicom = 34840259 # the session to work on set session_dir = 050610Lupo set dicom_dir = 06131042 set user_id = moeller # where does the dicom data live set src_dir = /space/data/raw_data/20${session_dir}/ set src_file = $src_dir/$first_dicom # where to put the cor files set targ_base_dir = /space/data/${user_id}/cooked/anatomicals/$session_dir/mri mkdir $targ_base_dir # the next one has to match the run number from the dicom information... set targ_dir = $targ_base_dir/orig # get the dimensions (read from unpack.log) # let's do it like freesurfer does (no error checkin though) set first_two_dims = `mri_probedicom --i $src_file --t 28 30` # tag 28 30 is of form 0.453125\0.453125, so split the critter at the back slash #echo $first_two_dims set first_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\"); print a[1]}'` #echo $first_dim set second_dim = `echo "$first_two_dims" | awk '{split($0, a, "\\"); print a[2]}'` #echo $second_dim # the slice resolution either in tag 18 50 or 18 88 set third_dim = `mri_probedicom --i $src_file --t 18 50` #echo $third_dim # get the shortest dimension, all this requires gnu bc to be installed set min_dim = `echo "min = $first_dim; if (min > $second_dim) { min = $second_dim }; if (min > $third_dim) { min = $third_dim }; min" | bc -l` set iis = `echo "scale=6; $first_dim / $min_dim" | bc -l` set ijs = `echo "scale=6; $second_dim / $min_dim" | bc -l` set iks = `echo "scale=6; $third_dim / $min_dim" | bc -l` #for unpacking at raw resolution mri_convert -i $src_file -o $targ_dir -it siemens_dicom -ot mgh #-iis $iis -ijs $ijs -iks $iks #end of script... ################################################### -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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maximum number of ROI in atlas
by Leila BH 23 Mar '07

23 Mar '07

Hello, I am modifying the 35-entries atlas by subdividing some parcels into N rois. Is there any limitation of the number of regions in an Atlas? Or an annotation file? Because when I have more than 300 region of interest in the atlas, the display of some region failed (gray) and the corresponding label became none. Do you know why? Leila

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Parts of tempral lobes not included
by deepa preeti 23 Mar '07

23 Mar '07

Hi Bruce: I appreciate if you could suggest how to intervene manually to fix this topology error - parts of superior & middle temporal regions not included in orig surface but included in brainmask & wm.mgz. Any suggestions is much appreciated. Thanks, Deepa. -- Deepa Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute 100 High St. Buffalo, NY 14203 Work: 716-859-7038 E-Mail: dramasamy(a)bnac.net

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FW: MINC Startup
by Alex Fornito 22 Mar '07

22 Mar '07

Hi, We've just installed version 3.05 for Mac and get the error below when running -autorecon1. I've noticed this error has been posted to the list a few times, but it always seems to have been resolved internally. Any help is much appreciated. Thanks, Alex Can't locate MNI/Startup.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/ darwin /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level/Network/Library /Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6/Library/Perl/5.8.1.) at /usr/ local/freesurfer/lib/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/lib/mni/bin/nu_correc t line 37. ERROR: nu_correct

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parts of temporal lobe not included
by deepa preeti 22 Mar '07

22 Mar '07

Hi Bruce: I looked at the brainmask.mgz and wm.mgz - obviously the pial is not included in superior & middle temporal regions in the brainmask.mgz and in the wm.mgz. The wm intensities are ranging from 96 - 106 in the missing superior & middle temporal regions in the brainmask.mgz. I have attached the brainmask.mgz, wm.mgz, aseg.mgz & aseg+aparc.mgz, all with pial, white and orig surfaces overlaid. As mentioned earlier, I had control points added in wm of excluded temporal regions and ran this command again ( to fix pial surface ) : recon-all -autorecon2-cp -autorecon3 -subjid subject The final image did not include the excluded temporal region after opening up in: tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white But gave me different values for entire regions in lh & rh aparc and aparc.a2005.stats - cov >1% in all regions. For example, Before adding control point After adding control point COV lh superior temporal(mm2) 3487 3102 8.3% rh superior temporal (mm2) 3434 3370 4.9% lh middle temporal(mm2) 3902 3001 18.5% rh middle temporal (mm2) 3046 3528 10.4% Another question: if you run this command > recon-all -autorecon2-cp -autorecon3 -subjid subject < Do we run the entire subcortical segmentation as well? I appreciate your suggestions. Deepa. Deepa Preeti Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute Department of Neurology Buffalo General Hospital 100 High St. Buffalo, NY 14203 Work: 716-859-7038 E-Mail: dramasamy(a)bnac.net

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Re: Freesurfer Digest, Vol 37, Issue 16
by Paul Aparicio 22 Mar '07

22 Mar '07

Hi Bruce, regarding the high res recon, you mention that you can change the info w/o changing the data using mri_convert, and this should keep mri_normalize from conforming the data to 1mm voxels? Do you know the commands that accomplish this? I have tried changing the file to COR format and editing the file to do as you suggest, the change it back to mgz, but mri_normlaize still conforms the volume to 1mm? Thanks Paul On Tue, 20 Mar 2007 freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." >

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Freesurfer March 2007