Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 discussions

calculate the deformation in the anatomical configurition space after spherical registration
by Zhong Jidan 02 Jan '10

02 Jan '10

Hi Freesurfer experts, I have a 3D fiducial surface ('anatomical' surface configuration), based on this fiducial surface ,let's say, "template", I generated some simulated fiducial surface with some deformation, let's say "subject". So here I know the "deformation vectors" for each vertex between the template and the subject in the original 3D fiducial surface "space". Then I use FreeSurfer to generate the spheres and do spherical registration from those subjects to the template. I want to check how these " deformation vectors " I got from Freesurfer are different from my generated "deformation vectors". But the problem for me is, after Freesurfer registration, the " deformation vectors" is based on the spherical space. While my generated "deformation vectors" are in the 3d fiducial surface space, it's not comparible for these two vectors. I want to know whether I can put the deformed subject sphere back into the fiducial surface representation. In that way, I can calculate the difference in the fiducial space. If getting the deformed subject sphere into the fiducial surface space is not possible, could you give me some suggestions about how to calculate the difference of the deformation vectors which are not in the same space? Generating the deformation vectors in the spherical space is the last thing I want to do because you never know how it likes in the real fiducial surface representation. Thank you. Jidan On Mon, May 4, 2009 at 8:48 PM, Zhong Jidan <jidanz(a)gmail.com> wrote: > Hi, > > I have a question about the sphere registration. The registration of > surface is spherical registation, so the outpput of the surface is > also a sphere. When we have the inflated and smoothwm, we can convert > the surface into sphere using mris_sphere, but reversely, how to > convert the deformed sphere in the form of white surface or pial > surface? > > Also, if I want to use the surface between the white and pial surface > to do registration, do I need to make the sphere myself? > > Thanks, > > > -- > Regards, > > Jidan > -- Regards, Jidan

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bad segmentation ?
by Gonzalo Rojas Costa 01 Jan '10

01 Jan '10

Hi: I have some questions about the segmentation of a patient with a cortical displasia: why the aparc+aseg.tif labeled "none" in the segmentation of the cortical displasia section (red cross in T1.tif) and the other segmentation method (aseg.tif) labeled ok that area ?... How can I fix it ?... How can I fix the cortical thickness of that section ?... Sincerely, Gonzalo Rojas Costa

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aseg.stats
by Hui J Yu 30 Dec '09

30 Dec '09

Dear Freesurfer Experts, I have ran recon-all on a T1 SPGR image of a control subject without error. The outputs look reasonable (visually). However, the numbers I got from aseg.stats do not make sense (they are way off). Any thoughts? # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject AH --surf-wm-vol --ctab /mrbin/freesurfer.cver/ASegStatsLUT.txt # sysname Linux # machine x86_64 # anatomy_type volume # # SUBJECTS_DIR /freesurfer.v4.50/subjects # subjectname CTRL # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2009/12/28 13:45:15 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1403481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1403481.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1021869.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1034494, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1034494.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1218358.332484, mm^3 # SegVolFile mri/aseg.mgz # SegVolFileTimeStamp 2009/12/28 20:51:43 # ColorTable /freesurfer.cver/ASegStatsLUT.txt # ColorTableTimeStamp 2009/08/11 08:24:37 # InVolFile mri/norm.mgz # InVolFileTimeStamp 2009/12/28 14:25:34 # InVolFrame 0 # PVVolFile mri/norm.mgz # PVVolFileTimeStamp 2009/12/28 14:25:34 # surface-based-volume mm3 lh-cerebral-white-matter 192622.906250 # surface-based-volume mm3 rh-cerebral-white-matter 198347.390625 # surface-based-volume mm3 tot-cerebral-white-matter 390970.296875 # 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 49 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 187032 187032.0 Left-Cerebral-White-Matter 102.5864 7.8948 42.0000 128.0000 86.0000 2 3 216661 216661.0 Left-Cerebral-Cortex 75.4785 9.6262 20.0000 120.0000 100.0000 3 4 5897 5897.0 Left-Lateral-Ventricle 46.5982 12.1178 21.0000 103.0000 82.0000 4 5 111 111.0 Left-Inf-Lat-Vent 53.2529 9.1730 31.0000 75.0000 44.0000 5 7 18124 18124.0 Left-Cerebellum-White-Matter 86.7241 5.8041 34.0000 108.0000 74.0000 6 8 48971 48971.0 Left-Cerebellum-Cortex 67.2554 9.0672 20.0000 94.0000 74.0000 7 10 5893 5893.0 Left-Thalamus-Proper 94.6949 7.5163 51.0000 115.0000 64.0000 8 11 2861 2861.0 Left-Caudate 89.1393 6.8791 54.0000 112.0000 58.0000 9 12 4485 4485.0 Left-Putamen 92.3673 5.6768 59.0000 107.0000 48.0000 10 13 1403 1403.0 Left-Pallidum 99.4880 9.0969 38.0000 117.0000 79.0000 11 14 848 848.0 3rd-Ventricle 53.1839 14.1313 9.0000 88.0000 79.0000 12 15 1595 1595.0 4th-Ventricle 43.9798 10.9321 19.0000 84.0000 65.0000 13 16 20022 20022.0 Brain-Stem 87.3585 9.3424 0.0000 111.0000 111.0000 14 17 3923 3923.0 Left-Hippocampus 79.3928 7.2511 47.0000 105.0000 58.0000 15 18 1332 1332.0 Left-Amygdala 75.6713 6.1980 53.0000 93.0000 40.0000 16 24 1112 1112.0 CSF 61.4318 13.1568 10.0000 115.0000 105.0000 17 26 603 603.0 Left-Accumbens-area 85.5804 4.0438 71.0000 102.0000 31.0000 18 28 3514 3514.0 Left-VentralDC 96.1436 8.7264 52.0000 112.0000 60.0000 19 30 42 42.0 Left-vessel 74.2500 7.1572 60.0000 87.0000 27.0000 20 31 1041 1041.0 Left-choroid-plexus 60.1743 12.6617 30.0000 94.0000 64.0000 21 41 193652 193652.0 Right-Cerebral-White-Matter 102.1858 8.4199 29.0000 128.0000 99.0000 22 42 218080 218080.0 Right-Cerebral-Cortex 74.1964 9.5593 24.0000 112.0000 88.0000 23 43 7313 7313.0 Right-Lateral-Ventricle 45.4438 12.3664 21.0000 96.0000 75.0000 24 44 186 186.0 Right-Inf-Lat-Vent 55.9329 9.9081 29.0000 80.0000 51.0000 25 46 17040 17040.0 Right-Cerebellum-White-Matter 89.3756 5.6165 41.0000 108.0000 67.0000 26 47 50180 50180.0 Right-Cerebellum-Cortex 68.7090 9.1593 15.0000 95.0000 80.0000 27 49 5702 5702.0 Right-Thalamus-Proper 94.7338 7.4958 52.0000 113.0000 61.0000 28 50 2742 2742.0 Right-Caudate 86.3893 7.4517 49.0000 109.0000 60.0000 29 51 4351 4351.0 Right-Putamen 92.2726 5.7435 62.0000 114.0000 52.0000 30 52 1267 1267.0 Right-Pallidum 99.1728 9.1982 47.0000 117.0000 70.0000 31 53 3650 3650.0 Right-Hippocampus 79.5501 7.5132 50.0000 109.0000 59.0000 32 54 1420 1420.0 Right-Amygdala 76.6007 5.3777 46.0000 94.0000 48.0000 33 58 618 618.0 Right-Accumbens-area 87.6877 5.1789 69.0000 108.0000 39.0000 34 60 3270 3270.0 Right-VentralDC 95.6004 10.3447 49.0000 114.0000 65.0000 35 62 40 40.0 Right-vessel 71.4286 7.5935 51.0000 86.0000 35.0000 36 63 857 857.0 Right-choroid-plexus 61.1068 11.6978 30.0000 89.0000 59.0000 37 72 58 58.0 5th-Ventricle 68.8148 9.9054 53.0000 97.0000 44.0000 38 77 2823 2823.0 WM-hypointensities 79.6001 12.5822 30.0000 106.0000 76.0000 39 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 40 79 0 0.0 Right-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 41 80 82 82.0 non-WM-hypointensities 65.6207 16.5103 29.0000 96.0000 67.0000 42 81 0 0.0 Left-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 43 82 0 0.0 Right-non-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 44 85 188 188.0 Optic-Chiasm 76.3684 13.4378 46.0000 100.0000 54.0000 45 251 797 797.0 CC_Posterior 111.4135 8.5269 77.0000 123.0000 46.0000 46 252 344 344.0 CC_Mid_Posterior 102.7219 11.1890 60.0000 118.0000 58.0000 47 253 358 358.0 CC_Central 103.9541 9.0602 69.0000 114.0000 45.0000 48 254 366 366.0 CC_Mid_Anterior 104.4078 9.1388 77.0000 120.0000 43.0000 49 255 629 629.0 CC_Anterior 107.1212 9.0856 60.0000 122.0000 62.0000

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Conform to 0.8mm
by Oya, Hiroyuki 30 Dec '09

30 Dec '09

Dear Experts, We obtain structural MPRAGE T1 with 0.8 x 0.8 x 1.0mm voxel size (3 volumes). Is is possible to conform the volume to 0.8mm for all the processing (recon-all)? Thank you very much. Hiroyuki

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Conform to 0.8mm
by Oya, Hiroyuki 30 Dec '09

30 Dec '09

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Pallidum too bright
by Lena Palaniyappan 29 Dec '09

29 Dec '09

While running recon-all autorecon3 I got the following error message. mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Left_VentralDC based on Right_VentralDC = 1.17 x + 0 estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.21 x + 0.0 Left_Pallidum too bright - rescaling by 1.004 (from 1.000) to 106.4 (was 106.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Darwin pmc10113.nottingham.ac.uk 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Sat Dec 26 19:10:16 GMT 2009 On visual inspection using tkmedit , I couldn¹t see any obvious differences in brightness. Is there any way this could be manual edited and rerun? _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH 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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RES: How can I install freesurfer for Windows(XP, 32bit)?
by "Pedro Paulo de Magalhães Oliveira Junior" 29 Dec '09

29 Dec '09

In the dowload section there's a version for Virtualbox Use it with Virtualbox for Windows Enviado do meu celular Nokia -----Msg original----- De: So-young Choe Enviado: 29/12/2009 00:35:01 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] How can I install freesurfer for Windows(XP, 32bit)? Dear freesurfers Hello, I am new this freesurfer, and I am struggling setting up freesurfer to my Window XP (32 bit) on my laptop. Freesurfer wiki site only provide installation tip for Linux and Mac. How can I set up freesurfer to Window? Thank you in advance. -- So-young Choe Personality and Emotion Lab Psychology department Seoul National University, San 56-1 Shillim-dong, Gwanak-gu Seoul, South Korea +82-2-880-6446

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How can I install freesurfer for Windows(XP, 32bit)?
by So-young Choe 28 Dec '09

28 Dec '09

Dear freesurfers Hello, I am new this freesurfer, and I am struggling setting up freesurfer to my Window XP (32 bit) on my laptop. Freesurfer wiki site only provide installation tip for Linux and Mac. How can I set up freesurfer to Window? Thank you in advance. -- So-young Choe Personality and Emotion Lab Psychology department Seoul National University, San 56-1 Shillim-dong, Gwanak-gu Seoul, South Korea +82-2-880-6446

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license problem - please help
by tracy butler 28 Dec '09

28 Dec '09

I've pasted the error message (and all the preceding command lines) below. I'm using the latest version of ubuntu in virtualbox. I made the .license file w/ pico, and it looks fine to me, but it's just not working. Thanks for any help! tracy tracy@covet:~$ tcsh covet:~> setenv FREESURFER_HOME /usr/local/freesurfer covet:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni covet:~> more /usr/local/freesurfer/.license tab2006(a)med.cornell.edu 8222 *CTAeXNprjJ6 covet:~> tkmedit bert orig.mgz OpenGL Warning: Failed to connect to host. Make sure 3D acceleration is enabled for this VM. -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. --------------------------------------------------------------------------

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Help with freeview on Mac OS X
by Ginsburg, Daniel 28 Dec '09

28 Dec '09

Hi All, I am attempting to build and run freeview on Mac OS X 10.6.1 and am having problems with freeview crashing on startup. From gdb, the crash is the following: Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_PROTECTION_FAILURE at address: 0x00000000 0x00000000 in ?? () (gdb) backtrace #0 0x00000000 in ?? () #1 0x02b148c0 in vtkOpenGLRenderWindow::OpenGLInit () #2 0x02b391a9 in vtkCarbonRenderWindow::CreateAWindow () #3 0x02b37fa4 in vtkCarbonRenderWindow::WindowInitialize () #4 0x02b36435 in vtkCarbonRenderWindow::Start () #5 0x02a9d1db in vtkRenderWindow::DoStereoRender () #6 0x02a9d3a9 in vtkRenderWindow::DoFDRender () #7 0x02a9d832 in vtkRenderWindow::DoAARender () #8 0x02a9bc54 in vtkRenderWindow::Render () #9 0x00130417 in wxVTKRenderWindowInteractor::OnPaint (this=0x1d05aa00) at wxVTKRenderWindowInteractor.cpp:409 I am on Mac OS X 10.6.1 and build the freesurfer tree using the following settings: CFLAGS=-m32 CXXFLAGS=-m32 LDFLAGS=-m32 ./configure --disable-Wall --disable-Werror --prefix=/chb/freesurfer/ x86_64-Darwin/packages/freesurfer/dev/ --with-wxwidgets-dir=/usr/pubsw/ packages/wxWidgets/wxMac-2.8.10/ I have the /usr/pubsw tree mapped to /space/lyon/9/pubsw/MacOS10.5- i686 on the NMR network (for what it's worth, I have also tried building all of freesurfer with all of the dependent libraries installed locally and ran into the same issue). When I try running the same executable on a Mac OS X 10.5.8 machine I get the following different error: LSOpenFromURLSpec() failed with error -10810 for the file /chb/ freesurfer/x86_64-Darwin/packages/freesurfer/dev/bin/Freeview.app. I have not had any luck resolving the errors on either system. Some help from someone who has successfully run freeview on the Mac would be greatly appreciated. Thank you! -- Dan

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Freesurfer December 2009