Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

qdec Font Error
by Jeff Sadino 24 Mar '10

24 Mar '10

Hello, When I get to the last step of qdec 1.2, when I choose the "Description" under "Scalers" on the "Display" tab, I get a couple of errors relating to fonts: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkFreeTypeUtilities.cxx, line 1659 vtkTextProperty (0x217178e0): Unable to create font ! (family: 0, bold: 1, italic: 1, length: 36128) ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Rendering/vtkOpenGLFreeTypeTextMapper.cxx, line 366 vtkOpenGLFreeTypeTextMapper (0x21717710): Render - No font I installed vtk 5.2.0, and also the newest vtk, but neither one worked. I also installed all of the windows fonts on my Linux. Haven't looked at OpenGL yet. Am I just missing the right font, or is there a deeper problem? btw, Freesurfer 4.3.1 is installed on a server that I log into. Thank you again! Jeff Sadino

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Research fellow/Postdoc in Pain Research, University of Michigan, Ann Arbor, MI
by alexandr＠nmr.mgh.harvard.edu 24 Mar '10

24 Mar '10

Research fellow/Postdoc in Pain Research, University of Michigan, Ann Arbor, MI The Headache and Orofacial Pain Effort (H.O.P.E.) requests applications for Research fellow/Postdoc at the University of Michigan Ann Arbor. The research ranges from neuroimaging (e.g. PET, MRI-based morphometry, fMRI, DTI, connectivity) to non-invasive brain stimulation for primary headaches and orofacial pain. Knowledge of Linux/UNIX operating systems as well as programming experience is required, as is a good level of comfort with novel computer applications. Previous research experience, including neuroimaging methods and analyses (e.g. Freesurfer, SPM) and statistics, is highly desirable. A background in pain and/or psychology neuroscience is an asset. We are also seeking applicants with well-developed organizational and interpersonal skills, and strong self-motivation to work in a highly innovative, altruistic, and mentoring environment. Hence, the applicant should feel comfortable working with chronic pain patients (e.g. migraineurs, trigeminal neuralgia and TMJD patients) and a multidisciplinary group of clinical and research collaborators. As part of the H.O.P.E. team, responsibilities will include facilitating experiments with subject handling, but mainly data acquirement and analysis. The stipend is commensurate with experience and training. Applications may be submitted at any time; however due to the competitiveness of this position, you are advised to apply early. H.O.P.E. is a multidisciplinary collaborative effort at University of Michigan to investigate the brain as a research and therapeutic target for headaches and orofacial pain disorders. Together with collaborators at University of Michigan and other academic institutions, we use state-of-the-art neuroimaging techniques to study neuroplasticity, and to investigate novel therapeutic approaches and mechanisms in chronic trigeminal pain disorders. Initially a curriculum vitae and letter of intent should be sent to: Alexandre F. M. DaSilva, DDS, DMedSc Director, Headache and Orofacial Pain Effort (H.O.P.E.) TM Assistant Professor, University of Michigan Ann Arbor Biologic & Material Sciences, School of Dentistry Laboratory: The Molecular & Behavioral Neuroscience Institute (MBNI) 205 Zina Pitcher Pl, room 1021 Ann Arbor, MI 48109-5720 Office: 734 615-3807 Fax: 734 763-3453 adasilva(a)umich.edu University of Michigan is one of the top public universities of the world, a diverse institution of higher learning, fostering excellence in research. http://research.umich.edu/

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Segmentation fault during skull-stripping
by Michael Waskom 24 Mar '10

24 Mar '10

Hi Bruce, Nick, I'm getting a segmentation fault that's crashing recon-all at the start of the watershed during skull-stripping. I've tried this three times, once starting the unpacking stream fresh from the raw dicoms, and it keeps happening at exactly the same place. I've been reconstructing brains of other subjects in the same directory all the while, so I don't think it's a permissions issue of any sort. Full recon-all log is atatched, but here's the section where it crashes: *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=116 y=166 z=95 r=51 first estimation of the main basin volume: 585576 voxelsSegmentation fault Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010 And here's the OS data from the bugr script: FREESURFER_HOME: /software/Freesurfer/4.4.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-20-generic x86_64 Do you have any idea what might be going wrong? Thanks! Mike

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DISPLAY error
by Lindsay Ercole 24 Mar '10

24 Mar '10

Hello All, I am running Mac OS 10.5.8. I can set all of my environment variables and then when I enter the line for calling up a session, I get: GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:0.0 I try to set this to my IP address of the computer, and I still get: GLUT: Fatal Error in tkmedit.bin: could not open display: (my ip):0.0 FS v. 4.0.1 is what we are running. The system did an overnight automatic update, and I think this is what has now caused our display issues, since they were not presenting yesterday (or the day prior). Thanks, Lindsay

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Re: [Freesurfer] extract thickness values for vertex
by Pedro Paulo de Magalhães Oliveira Junior 24 Mar '10

24 Mar '10

Maybe your fsaverage directory is not in the default place I've updated the wiki page # Script created December 2007 by Pedro Paulo Jr. # Use with Freesurfer 4.x # Updated: 24/03/2010 set FSAVERAGE_DIR = "../../fsaverage" #set fsaverage dir cd #your directory where qdec data are stored. set numsubject = 17 #your value for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc done ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.br --- Novo Netfilter Small Business Em 24 de março de 2010 06:30, Prapti Gautam <Prapti.Gautam(a)anu.edu.au>escreveu: > I run mri_glmfit the usual way, as detailed in the GroupAnalysis tutorial.. > I couldn't get the script to run either with qdec or mri_glmfit output > directory, so figured it must be a permission issue with fsaverage? > > > > -----Original Message----- > From: Pedro Paulo de Magalhães Oliveira Junior [mailto: > ppj(a)netfilter.com.br] > Sent: Wed 3/24/2010 7:27 PM > To: Prapti Gautam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] extract thickness values for vertex > > Maybe I need to change that script. > > How do you usually run you glmfit analysis? > > 2010/3/24, Prapti Gautam <Prapti.Gautam(a)anu.edu.au>: > > Dear FreeSurfers, > > > > > > Is there a way to extract thickness values for individual subjects for a > > vertex that are obtained after analyses with mri_glmfit? I have seen a > > script that does this with qdec - but most of the analyses I run are on > > mri_glmfit, so was wondering if the script on the user contribution > > section needs to be modified for mri_glmfit. I ran the script where the > > output files are located and get the following error: > > > > > > > > > > > > ERROR: failure writing ./media...../fsaverage/surf/lh.1.mgh > > > > > > > > Reading group avg surface area 864 cm^2 from file > > > > > > > > mghRead( /media/...../fsaverage/suf/lh.1.mgh, -1) : could not open file > > > > > > > > > > > > > > > > Is this simply a permission issue with the fsaverage folder? > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > Prapti > > > > > > > > > > > > > > > > > > > -- > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.4 www.Netfilter.com.br > --- Novo Netfilter Small Business > > > >

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extract thickness values for vertex
by Prapti Gautam 24 Mar '10

24 Mar '10

Dear FreeSurfers, Is there a way to extract thickness values for individual subjects for a vertex that are obtained after analyses with mri_glmfit? I have seen a script that does this with qdec - but most of the analyses I run are on mri_glmfit, so was wondering if the script on the user contribution section needs to be modified for mri_glmfit. I ran the script where the output files are located and get the following error: ERROR: failure writing ./media...../fsaverage/surf/lh.1.mgh Reading group avg surface area 864 cm^2 from file mghRead( /media/...../fsaverage/suf/lh.1.mgh, -1) : could not open file Is this simply a permission issue with the fsaverage folder? Thanks for your help, Prapti

2 1

gaussian and mean curvature error
by Ana Catarino 23 Mar '10

23 Mar '10

Hello, I'm trying to do a gaussian curvature and mean curvature analysis using qdec but I get the following error message: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh Can anyone help? Thank you, Ana Catarino

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Retinotopy with FsFast
by p.kok＠fcdonders.ru.nl 23 Mar '10

23 Mar '10

Hello everyone, I used FsFast to do retinotopy analysis as described at https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I have data for both a clockwise and a counter-clockwise rotating wedge, and when I do retinotopy on these separately, it seems to work fine, but when I put both runs in one retinotopy analysis (as 001 and 002), they seem to cancel each other out and the results looks rubbish; sliceview-sess shows very little activation and the surf-sess polar maps don't make sense. Do you have any idea what might be the problem here? Of course I defined opposite directions for both runs in the rtopy.par files. Some 'problems' with my data which might give you a clue as to what's going on: - I don't have eccentricity runs, so I copied polar data in a 'fake' eccentricity run. Doesn't seem to be the problem, since retinotopy works fine for the clockwise and counterclockwise runs separately. - My wedge starts at the top right of the screen, so I need to state an angle offset when watching the results in tksurfer (-0.125) in order for the colour coding to make sense (blue = horizontal meridian, right?) - Although the movement of the wedge fits perfectly with the scans in the clockwise run (each wedge lasts one TR and starts exactly at the start of a scan), there is a slight offset for the counterclockwise run; wedges still last exactly one TR but the first wedge doesn't start exactly at the start of a scan. This doesn't seem to cause problems when I analyse the runs separately, but could it explain why the activations seem to cancel each other out when I combine them in one analysis? I would appreciate any suggestions. Thanks, Peter Kok

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DTI group analysis
by Ryan 23 Mar '10

23 Mar '10

Hello all, In trying to perform a group analysis on volumetric and DTI data (with test4d.nii.gz file created by fslmerge), I encounter an error. Any help is greatly appreciated. Also, can anyone tell me what programs they prefer to use for DTI group analysis? It seems QDEC isn't helpful if you need volumetric analyses. bash-3.2$ mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir gdfReadHeader: reading /Applications/freesurfer2/subjects/glm/gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 64.2 Class Means of each Continuous Variable 1 gender_male 52.5000 2 gender_female 72.0000 INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.138.2.3 2008/08/27 13:33:05 greve Exp $ cwd /Applications/freesurfer2/subjects/4964-59 cmdline mri_glmfit --y test4d.nii.gz --fsgd /Applications/freesurfer2/subjects/glm/gender_age.fsgd dods --C /Applications/freesurfer2/subjects/glm/lh-Avg-thickness-age-Cor.mtx --glmdir lh.gender_age.glmdir sysname Darwin hostname ryan-mcgarrys-mac-pro.local machine i386 user ryanmcgarry FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer2/subjects/4964-59/test4d.nii.gz logyflag 0 usedti 0 FSGD /Applications/freesurfer2/subjects/glm/gender_age.fsgd glmdir lh.gender_age.glmdir DoFFx 0 Creating output directory lh.gender_age.glmdir Loading y from /Applications/freesurfer2/subjects/4964-59/test4d.nii.gz Matrix condition is 1765.88 Pruning voxels by frame. Found 279419 voxels in mask Saving mask to lh.gender_age.glmdir/mask.mgh search space = 2.23535e+06 ERROR: dimension mismatch between y and X. y has 2 inputs, X has 5 rows. I also ran bugr and the following output was produced: FREESURFER_HOME: /Applications/freesurfer3 Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386

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DTI group analysis
by Ryan 23 Mar '10

23 Mar '10

1 0

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Freesurfer March 2010