Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Equivalent labels
by FIDEL ALFARO ALMAGRO 12 Jan '11

12 Jan '11

Hi Freesurfer experts, I would like to know what are the equivalent labels to - Gyrus Intralmibic - Sulcus semmi annularis In the label file FreeSurferColorLUT.txt. I have checked the paper "Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature" but the information there is not useful (e.g. indusium griseum does not appear in that file). Thanks and best regards. Fidel.

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Nipype 0.3.4 release
by Chris Filo Gorgolewski 12 Jan '11

12 Jan '11

Dear all, I'm very happy to announce new release of nipype - the pipelining framework that allows you to combine FSL, SPM, FreeSurfer, Nipy and other neuroimaging packages. Among other changes (see the full list below) this release brings support for surface transformations, flash processing and flirt matrix in BBRegister. You can get the newest version of nipype from https://github.com/nipy/nipype/zipball/0.3.4 and soon from NeuroDebian repository ( http://http://neuro.debian.net/ ). Full documentation with examples can be found at http://nipy.sourceforge.net/nipype/documentation.html Changes since 0.3.3: * API: hash values for float use a string conversion up to the 10th decimal place. * API: Iterables in output path will always be generated as _var1_val1_var2_val2 pairs * ENH: Added support to nipy: GLM fit, contrast estimation and calculating mask from EPI * ENH: Added support for manipulating surface files in Freesurfer: - projecting volume images onto the surface - smoothing along the surface - transforming a surface image from one subject to another - using tksurfer to save pictures of the surface * ENH: Added support for flash processing using FreeSurfer * ENH: Added support for flirt matrix in BBRegister * ENH: Added support for FSL convert_xfm * ENH: hashes can be updated again without rerunning all nodes. * ENH: Added multiple regression design for FSL * ENH: Added SPM based Analyze to Nifti converter * ENH: Added increased support for PyXNAT * ENH: Added support for MCR-based binary version of SPM * ENH: Added SPM node for calculating various threshold statistics * ENH: Added distance and dissimilarity measurements * BF: Diffusion toolkit gets installed * BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples) on all options specific to different subsampling levels On behalf of the nipype team, Chris Gorgolewski

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How to transform surfaces back to original MRI space
by A.Janssen＠neuro.umcn.nl 12 Jan '11

12 Jan '11

Hello FS experts, I am a new FS user and I could use some help concerning translating surfaces. I have completed the FS pipeline using my own data with the autorecon all command. I now want to combine the .pial and .wm surfaces with the rest of my data. Therefore I have to translate the surfaces back to their original location in the MRI (scanner) space. I already looked at the talairach.lta and talairach.xfm files, but I haven't found the solution yet. Can someone give me some advice on how to do this? Does the transformation include one, or several steps? Thanks. Best, Arno Janssen Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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fsgd file for 3 groups and 4 covariates
by Jose Luis Cantero Lorente 12 Jan '11

12 Jan '11

Dear all, I have a data set with a diagnosis factor (three groups) and four covariates, the fsgd.txt file is pasted below: <!-- /* Font Definitions */ @font-face {font-family:Cambria; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:auto; mso-font-pitch:variable; mso-font-signature:3 0 0 0 1 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Cambria; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi; mso-ansi-language:EN-US; mso-fareast-language:EN-US;} @page Section1 {size:595.0pt 842.0pt; margin:70.85pt 3.0cm 70.85pt 3.0cm; mso-header-margin:35.4pt; mso-footer-margin:35.4pt; mso-paper-source:0;} div.Section1 {page:Section1;} GroupDescriptorFile 1 Title Thickness-subj Class control Class EHM Class NEHM variables zAge zGender zCTlh zCFF Input c_12 control 0.15 1 -0.66 0.24 Input c_13 control -0.64 1 1.02 -0.09 Input c_14 control 0.28 2 1.14 1.93 Input ehm_1 EHM 0.81 2 0.22 1.17 Input ehm_10 EHM 1.47 2 -0.34 -0.15 Input ehm_16 EHM 1.34 1 -2.18 -0.09 Input nehm_10 NEHM 0.81 2 -0.8 1.11 Input nehm_11 NEHM -0.77 1 -0.06 0.59 Input nehm_13 NEHM -0.64 1 0.63 0.09 ... The contrast to test whether intercepts are different between groups (ANOVA) would be: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 whereas if I want to test for slope differences between groups for the zCFF variable I should write: 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 An example of post hoc contrast for the former case would be 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 and for the latter 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 I just need confirmation that everything is fine (or wrong). Thanks in advance for your help. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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which volume to edit?
by Yang Liu 11 Jan '11

11 Jan '11

Hi Freesurferers, I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time. For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works. So, which one should I work on? brian.mgz or brainmask.mgz? Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it. How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently. Thank you. Yang

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Invitation to connect on LinkedIn
by Stefan Du Plessis via LinkedIn 11 Jan '11

11 Jan '11

LinkedIn ------------Stefan Du Plessis souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Stefan Accepter l'invitation de Stefan Du Plessis http://www.linkedin.com/e/-qq80um-git9d09s-34/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Stefan Du Plessis http://www.linkedin.com/e/-qq80um-git9d09s-34/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ SAVEZ-VOUS que présenter vos compétences sur LinkedIn augmente votre crédibilité professionnelle et peut vous amener des propositions de postes ou de missions ? Répondre à des questions de la rubrique Réponses vous permet de faire valoir votre expertise auprès d'une communauté mondiale de professionnels. http://www.linkedin.com/e/-qq80um-git9d09s-34/abq/inv-24/ -- (c) 2010, LinkedIn Corporation

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surface area vs. areal expansion
by Ecker, Christine 11 Jan '11

11 Jan '11

Dear FreeSurfer experts, I would like to compare surface area in a vertex-by-vertex fashion across two subject groups. There has been some discussion already on the mailing list and it seems that areal expansion is a better measure than simply surface area for doing so. I also remember reading that when the data is converted from native space to a template (e.g. fsaverage), the values are automatically transformed to areal expansion measures, which have been used previously in some genetic studies (e.g. Rimol et al. (2010) or Joyner et al. (2009)). Please could you let me know if the output of –qcache (e.g. lh.area.pial.fsaverage.mgh) contains the area values (i.e. average area across triangles touching vertex) or areal expansion values - I believe these values are also compared in qdec. Many thanks, Christine

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a segfault error after reinstallation of ati videocard driver on CentOS 5.5 x86_64
by Alexander Lebedev 11 Jan '11

11 Jan '11

Dear Freesurfer users, Has anybody tried to run FS with ati video cards? I am asking because I am completely stuck with it... At the beginning everything was good except the bad brain displaying with "$rh pial" command (FS displays only a small piece of it). I decided to reinstall my videocard driver - and now I cant start even "$tkmedit" getting a "segfault error". I am providing you my report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.32.1.el5 x86_64 --------------------------------------------------------------------- 1) subject name: bert 2) the entire command-line executed: [root@localhost subjects]# setenv FREESURFER_HOME /usr/local/freesurfer [root@localhost subjects]# source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- 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 FSL_DIR /usr/local/fsl [root@localhost subjects]# tkmedit bert orig.mgz 3) the error message generated: =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : ================================================= I have also attached my "xdebug_tkmedit" and "xorg.conf" files. Any help would be very appreciated... Thank you beforehand. -- Sincerely Yours, Alexander Lebedev, I.P. Pavlov State Medical University, 197022, Lev Tolstoy str. 6/8, Saint Petersburg, Russian Federation. tel.:+7-921-441-79-42 e-mail: awlman(a)rambler.ru Skype ID: alexander.vl.lebedev

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contrasts using DODS
by Jose Luis Cantero Lorente 11 Jan '11

11 Jan '11

Hello, -  we are analyzing cortical thickness data from three groups and want to study whether there are between-group differences after removing the effects of three covariates. We are assuming different intercepts and different slopes (DODS) and would like to be sure that the contrasts performed for the ANOVA and for the post hoc comparisons are correct: ANOVA 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 e.g., post-hoc analysis for testing group1 > group2 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 I would appreciate your help with this matter. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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intensity values of original T1 rounded to next integer
by Micheli, C. 11 Jan '11

11 Jan '11

Dear Freesurfers The command: mri_convert orig.mgz conv.mgz --conform generates a conform volume but the intensity values are rounded to the next integer. Do you know how to avoid this? Best Cristiano

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