Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

MRI_concat
by Rita Loiotile 13 Jan '11

13 Jan '11

For a series of nifti fMRI images does it matter in what order I list the images for my input? Or does MRI_concat get the time series info from the files themselves? Sent from my iPhone

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 26
by Bevil R. Conway 13 Jan '11

13 Jan '11

I will be out of the country from Jan. 10 - Jan 18, 2011, and will not have access to email. For issues concerning my laboratory, please contact my lab manager, Rosa Lafer-Sousa (rlaferso(a)wellesley.edu) Thank-you and I'll be in touch when I get back. Bevil

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Continuation of my futile attempts at configuring ATI videocard driver for Freesurfer=)
by Alexander Lebedev 13 Jan '11

13 Jan '11

Dear Freesurfers, I keep fighting with my 64bit-CentOS in order to configure my videocard (ATI Radeon Sapphire HD 5750) for FS. At last I got rid of "segfault error". And now there is another error (after tkmedit command): ============================================================= X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 19 (X_GLXQueryServerString) Serial number of failed request: 15 Current serial number in output stream: 15 ============================================================= I assume there is a problem with OpenGL... I have searched in archives, googled but unfortunately haven't found useful information on this topic. Do you have any idea how to solve this problem? My "xorg.conf"-file includes following: ============================================================= # Xorg configuration created by system-config-display Section "ServerLayout" Identifier "single head configuration" Screen 0 "aticonfig-Screen[0]-0" 0 0 InputDevice "Keyboard0" "CoreKeyboard" EndSection Section "Module" EndSection Section "InputDevice" Identifier "Keyboard0" Driver "kbd" Option "XkbModel" "pc105" Option "XkbLayout" "us" EndSection Section "Monitor" Identifier "aticonfig-Monitor[0]-0" Option "VendorName" "ATI Proprietary Driver" Option "ModelName" "Generic Autodetecting Monitor" Option "DPMS" "true" EndSection Section "Device" Identifier "Videocard0" Driver "vesa" EndSection Section "Device" Identifier "aticonfig-Device[0]-0" Driver "fglrx" BusID "PCI:7:0:0" EndSection Section "Screen" Identifier "Screen0" Device "Videocard0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection Section "Screen" Identifier "aticonfig-Screen[0]-0" Device "aticonfig-Device[0]-0" Monitor "aticonfig-Monitor[0]-0" DefaultDepth 24 SubSection "Display" Viewport 0 0 Depth 24 EndSubSection EndSection ================================================================= Thank you beforehand. -- Best Regards, Alexander Lebedev.

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Re: [Freesurfer] Freesurfer Digest, Vol 83, Issue 24
by Bevil R. Conway 12 Jan '11

12 Jan '11

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zero intensities within brainmask.mgz
by Xinian Zuo 12 Jan '11

12 Jan '11

Hi, FSers, Sorry for sending again. I am using FS5. 0 to extract brain mask for other analyses. I found there were always some zero intensities within voxels of some CSF, thus lead to a brain mask with some small holes inside after binary operation. Is there a way of filling them? Thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

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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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Freesurfer January 2011