Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

freeview error
by Rujing Zha 31 Dec '13

31 Dec '13

Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button "configure overlay". Then freeview were suspended. The CPU ran "100%",and memory ran "23%". There was nothing to do but terminated it manually in the command console by "ctrl + c". I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is "NVIDIA GeForce 8600 GT", and CPU is "Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz", and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha

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Obtaining the center of mass coordinates of a label file
by Omar Singleton 31 Dec '13

31 Dec '13

Dear Freesurfer Community, Does anyone know of a way to get the coordinates of the center of mass of a FreeSurfer label? Is there any way of doing this? Thanks! Best, Omar

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citation for smoothing method
by YUMI MAEDA 30 Dec '13

30 Dec '13

Hi, I have a question about citation for smoothing methods. In the following link, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer there are statement " ....This data was smoothed in the volume at 5mm, but when preparing for a group surface-based analysis, we recommend that you smooth on the surface prior to group analysis and not smooth in the volume at all (or less than the voxel size) ...." Is there any reference paper that I can cite when I write a manuscript? thank you very much. YUMI

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mri_mask output problem
by Caspar M. Schwiedrzik 30 Dec '13

30 Dec '13

Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar

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freeview error
by Rujing Zha 30 Dec '13

30 Dec '13

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transfer the Parcellation to MNI
by 宋银南 29 Dec '13

29 Dec '13

Dear all, I want to extract the ROI defined by Desikan-Killiany Atlas and save it as a mask on the MNI space. I try to extract the vertex coordinates by the freesurfer_read_surf and transfer them to MNI. But which surface should I use? And maybe some better method. Thank you for the freesurfer, it is really very good. Best Wishes! Yinnan Song from Peking , China

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EM Registration error
by Mark Plantz 29 Dec '13

29 Dec '13

Hello freesurfers, Does anyone know the physical meaning of the "transform matrix" and the "quasinewton matrix" outputted during "EM Registration" of auto-recon2? For some odd reason, both of them are identity matrices (one's along the diagonal). I am almost certain that should not be the case. Here is some context: ************************************************ Computing MAP estimate using 1658 samples... ************************************************ * dt = 5.00e-06, momentum=0.80, tol=1.00e-05* * l_intensity = 1.0000* * Aligning input volume to GCA...* * Transform matrix 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;* * nsamples 1658 Quasinewton: input matrix* * 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;* * THE SEARCH DIRECTION IS NOT A DESCENT DIRECTION IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 0 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = -0.0 tol 0.000010* * Resulting transform:* * 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;* * pass 1, spacing 8: log(p) = -4.8 (old=-5.1)* * transform before final EM align:* * 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;* Thank you and happy holidays! - Mark

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PhD Positions, Brainnetome Center, CASIA
by Yong Liu 29 Dec '13

29 Dec '13

Dear list, *Job1: PhD Positions are available in Neuroimaging and Brainnetome* Applications close: *Jan. 15, 2014*. *CAS-TWAS President’s Fellowship Programme Download <http://www.brainnetome.org/images/job/PhD_Positions_CASIA.zip>* The role The development of the brain is characterised by the formation of connections between neurons. One of the largest fibre tracts in the brain is the corpus callosum, which connects neurons in the left and right cerebral hemispheres. We are using molecular and genetic approaches as well as state-of-the-art imaging technologies to discover how the brain is wired up during development. This work has direct implications for understanding how the brain functions and the pathophysiological mechanism of psychiatric disorders, by integrating the multi-level network features obtained with various functional and anatomical brain imaging technologies on different scales. Five PhD positions are available at Brainnetome Center of CASIA to utilise neuroimaging technologies to discover mechanisms of brain wiring. These positions will be supported by CAS-TWAS President’s Fellowship Programme for PhD Candidates from Developing Countries and other grants. They involve developing neuroimage analysis methods and tools and applying them to neuroscience and clinical problems. In this role the students will develop skills in developing computational algorithms and computer programming in neuroimage analysis that could be utilised in both basic research and clinical areas. The person Applicants should meet the requirements of “CAS-TWAS President’s Fellowship Programme for PhD Candidates from Developing Countries” and have MSc degree in one of the following fields: mathematics, physics, neuroimaging, computer science, electronic engineering, neurobiology, psychology, cognitive neuroscience, psychiatry, and neurology. Outstanding C/C++ programming skills in Linux are highly desired. Enquiries Please contact Professor Tianzi Jiang at jiangtz(a)nlpr.ia.ac.cn. In order to complete the form application process, please fill in the - Fellowship form<http://www.brainnetome.org/images/job/PhD_Positions_CASIA.zip> Applications close: *Jan. 15, 2014*. Please visit our homepages www.brainnetome.org Sincerely, Yong -- Best wishes. -------------------------------------------------------------------- Liu Yong Brainnetome Center National Laboratory of Pattern Recognition (NLPR) Institute of Automation, Chinese Academy of Sciences (CASIA) http://www.brainnetome.org/yongliu

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import from caret
by Colin Reveley 28 Dec '13

28 Dec '13

Hi - I actually sent this a couple of weeks back, but only just noticed it was bounced back because I used the wrong address. Happy new year! Date: Sat, 14 Dec 2013 09:57:27 +0000 Subject: import from CARET Hi - If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer? The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure. The surface will be aligned to the volume in the sense that it's co-ordinates work with respect to that header/origin. What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer. Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET. That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). that should be fine. Also, there will be no ?h.orig surface, and the mesh is arbitrary wrt the MRI data (not derived from it in any way). I don't know if that matters. The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Pretty much. It's some scaling, translating, conforming and format conversions. connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools hope can help Colin Reveley

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FW: FreeSurfer Installation
by Tyler Farren 27 Dec '13

27 Dec '13

Hello, my name is Tyler Farren and I am from the Carnegie Mellon University Psychology Department. I recently installed FreeSurfer on a cluster and it seemed to install properly. However, when I attempt to go through the steps on the testing page, nothing seems to work. I am running CentOS 6.2. I get the following errors: $ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red X Error: BadValue (integer parameter out of range for operation) 2 Extension: 147 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x40 Abort $ tkmedit bert orig.mgz GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found. $ tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found. [tfarren@psych-o freesurfer]$ tkmedit bert mri/orig.mgz GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found. $ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /home/cresdata/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/cresdata/freesurfer checking for nofix files in 'pial' Reading image info (/home/cresdata/freesurfer/subjects/bert) Reading /home/cresdata/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /home/cresdata/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) Window type not found! surfer: failed, trying double buffered window Window type not found! surfer: failed, no suitable display found $ qdec ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x273e9900): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x273e9900): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x273e9900): Could not find a decent visual X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 147 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x40 Serial number of failed request: 4812 Current serial number in output stream: 4812 Please let me know if you can help with this. Thanks! Tyler Farren

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