Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

Transform orig.mgz image to native space
by Flavio Seixas 26 May '09

26 May '09

Hi Hii, I'm beginner Freesurfer user. I segmented brain subcortical structures using Freesurfer (recon-all). The process was concluded ok. How could I convert aseg.mgz and orig.mgz back to native space? I've tried "mri_convert orig.mgz orig.nii -ot nii --apply_inverse_transform transforms/talairach.xfm", but didn't work. Anyone could help me? I would appreciate any suggestion. Thank you, Flávio.

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when recon-all stoped
by Paula Diniz 26 May '09

26 May '09

Hi I was running recon-all -all when the computer was turned off. I can restart the recon-all in the point that it stopped?How? Thanks 2009/5/15 Paula Diniz <paula.rejane(a)gmail.com> > Hello! > > I have to convert the aseg.mgz file to a minc file, but I lost the > structure values reference. > Where I can find a convertion table or how I make to recover the structures > values reference? > > Thanks! > -- > ================================== > Paula Rejane Beserra Diniz > Bacharel em Informática Biomédica > Mestre em Neurociências > Doutoranda em Neurociências > Universidade de São Paulo > Hospital das Clínicas - Ribeirão Preto > ================================== > -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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RES: [Freesurfer] when recon-all stoped
by Pedro Paulo de Magalhaes Oliveira Junior 26 May '09

26 May '09

recon-all -s subjid -make all Enviado do meu celular Nokia -----Msg original----- De: Paula Diniz Enviada: 26/05/2009 17:47:04 Para: Freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] when recon-all stoped Hi I was running recon-all -all when the computer was turned off. I can restart the recon-all in the point that it stopped?How? Thanks 2009/5/15 Paula Diniz <paula.rejane(a)gmail.com> > Hello! > > I have to convert the aseg.mgz file to a minc file, but I lost the > structure values reference. > Where I can find a convertion table or how I make to recover the structures > values reference? > > Thanks! > -- > ================================== > Paula Rejane Beserra Diniz > Bacharel em Informática Biomédica > Mestre em Neurociências > Doutoranda em Neurociências > Universidade de São Paulo > Hospital das Clínicas - Ribeirão Preto > ================================== > -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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segmentation fault when running mris_anatomical_stats
by John Drozd 26 May '09

26 May '09

Hello, I am running the reconall steps individually for a firts try. I noticed that I get a segmentation fault when I run mris_anatomical_stats as whown below: [jdrozd@trumpet mri]$ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh INFO: assuming MGZ format for volumes. computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz... reading input surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading input pial surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial... reading input white surface /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name Segmentation fault john

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Re: question about eTIV calculation
by John Drozd 26 May '09

26 May '09

Hello, I have a question about the eTIV intracranial volume calculation. My question is: Does the eTIV intracranial volume include everything interior to the outer pial surface (excluding the skull, eyes, neck and dura), and does it also include the CSF? That's all. Thank you for your time. john drozd

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tkmedit crash loading x_skull.surf files
by Jesse Friedman 26 May '09

26 May '09

tkmedit is crashing when I try to load a particular subject's inner_skull.surf or outer_skull.surf surfaces. These files were created by the MNE software, so my apologies if this question would be better suited to mne_support. If I load from the command line I get the messages below in the terminal, and tkmedit never opens. If I load the T1 without the surface from the command line and then load the surface in the gui, tkmedit quits and I get the same message in the terminal. [vantz:bem] (nmr-std-env) tkmedit RMSCH018 T1 -surface $SUBJECTS_DIR/RMSCH018/bem/outer_skull.surf Setting subject to RMSCH018 (null): vertex 0 x coordinate nan! Does anyone know what the problem is? Thanks, Jesse bugr info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.3.1b-20090522 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: vantz SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects PWD: /space/ventzl/36/users/RespMon12C/subjects/RMSCH018/bem ssh vantz setenv SUBJECTS_DIR /space/ventzl/36/users/RespMon12C/subjects cd /space/ventzl/36/users/RespMon12C/subjects/RMSCH018/bem -- Jesse Friedman, B.A. Massachusetts General Hospital Martinos Center, Manoach Lab Psychiatric Neuroimaging 149 13th Street #2613 Charlestown, MA 02129 Phone: (617) 726-1908 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu

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mris_ca_label
by xforever＠ucla.edu 26 May '09

26 May '09

Dear Freesurfer Experts, I was able to use mris_ca_train to produce a atlas (.gcs) file with all the labels I am interested in, and I also modified the surface_labels.txt in the freesurfer folder so only the labels I am interested are listed on the txt file. however, when I try to use mris_ca_label to apply the label onto the different brain. The names of each label doesn't transfer, I'd get names like parcellation 20 30 150. Is there anyway to fix this? sincerely, Andy S

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RES: [Freesurfer] focal cortical dysplasia
by Pedro Paulo de Magalhaes Oliveira Junior 26 May '09

26 May '09

In the article section of FreeSurfer wiki there is a paper about cortical thickness in PMG. In that study we also analyzed, but still not published, cortical dysplasia cases. In some cases we made manual interventions (look at FreeSurfer wiki on recon-all process.) to fix small segmentation errors. Take a look on this. If you need more help drop me a note. Enviado do meu celular Nokia -----Msg original----- De: Heath Pardoe Enviada: 26/05/2009 05:57:24 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] focal cortical dysplasia Hi, I've run the standard recon-all processing stream on a subject with a fairly large (~ few cms) focal cortical dysplasia near the central sulcus. On the MR scan the intensity's somewhere between gm & wm, although it is clearly visible. The wm surface has pretty much missed the whole thing though. I was wondering if there are any parameters I can adjust to potentially improve sensitivity to this kind of pathology? I can send some images if that helps. Thanks Heath -- Heath Pardoe, PhD Brain Research Institute Neurosciences Building Austin Health Banksia Street Heidelberg West, Victoria, 3081, Australia Phone: (+61 3) 9496 2576 Fax: (+61 3) 9496 4071 Email: h.pardoe(a)brain.org.au _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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focal cortical dysplasia
by Heath Pardoe 26 May '09

26 May '09

Hi, I've run the standard recon-all processing stream on a subject with a fairly large (~ few cms) focal cortical dysplasia near the central sulcus. On the MR scan the intensity's somewhere between gm & wm, although it is clearly visible. The wm surface has pretty much missed the whole thing though. I was wondering if there are any parameters I can adjust to potentially improve sensitivity to this kind of pathology? I can send some images if that helps. Thanks Heath -- Heath Pardoe, PhD Brain Research Institute Neurosciences Building Austin Health Banksia Street Heidelberg West, Victoria, 3081, Australia Phone: (+61 3) 9496 2576 Fax: (+61 3) 9496 4071 Email: h.pardoe(a)brain.org.au

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licensing question
by John Drozd 25 May '09

25 May '09

*Hello, I have a question regarding the second statement in the Clinical Use section of your registration web page. "Clinical Use: This software may not and should never be used for clinical purposes. Software used for clinical purposes may require regulatory documentation and associated filings." Does the statement "**Software used for clinical purposes may require regulatory documentation and associated filings." mean that a version of FreeSurfer can be used for clinical work? Thank you for your time, john drozd *

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Freesurfer May 2009