Freesurfer

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17 participants
30086 discussions

combining aseg and seg_edited files for an atlas
by N/A N/A 10 Jul '14

10 Jul '14

Hi Freesurfer forum, I have never used the forum before but I am a long time user of Freesurfer and I am currently working on making a new atlas for the cerebellum. However I am having a problem loading my *seg_edited.mgz* files into the *rebuild_gca_atlas.csh* script. So I renamed my *aseg.mgz* file to *seg_edited* and that worked but my resulting image is not great. I think it did not work with my original *seg_edited* file because the atlas needed cortex data to complete the process and my original *seg_edited* file did not have and my *aseg* does. I would like to try and combine my *aseg* file and my original *seg_edited* files together but I realized that no one has apparently asked about doing that before on your forums. Is there anyway to combine those files? I would appreciate any advise on the matter! Thank you, Alexarae Bryon FIU student

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Group analysis tutorial
by Joshua S 10 Jul '14

10 Jul '14

Hi all, I was following the group analysis tutorial when I got an error when trying to view the uncorrected significance map with freeview. I used the command "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d". I removed the annot_outline=1, because it gave an error. Sig.mgh would not load, and I would get the attached image. I tried to manually add sig.mgh through add surface, but the program immediatley closed, and I got the message in the attached error.log. Text below. Thank you for any help, Josh Did not find any volume geometry information in the surface �Tgreading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Did not find color table in track volume. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named farklemt.nmr.mgh.harvard.edu by dc325 Wed Jul 2 11:35:56 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

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Categorical covariates with more than two levels on qdec
by Isotalus, Hanna 10 Jul '14

10 Jul '14

Subject: Categorical covariates with more than two levels on qdec Categorical covariates with more than two levels on qdec Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for the imaging site but qdec only allows me to covary for categorical variables if they have two levels (and I have eight). I am also using age (continuous) and gender (categorical, two levels) as covariates. Is there a way of using the imaging site as a covariate using qdec? Do you have any suggestions on how I should proceed? Is treating imaging site as a continuous variable acceptable? Best wishes, Hanna

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Compiling data from lobesStrict
by krista kelly 10 Jul '14

10 Jul '14

Hi all, I'm trying to extract cortical thickness data from each lobe per participant. Here are the commands I used so far: 1) create annotation file for lobes: mri_annotation2label --subject $s --hemi lh --lobesStrict lh.lobesStrict.annot 2) extract lobe labels: mri_annotation2label --subject $s --hemi lh --annotation lobesStrict --outdir $s/label 3) create stats file for each lobe per participant: mris_anatomical_stats -a $s/label/lh.lobesStrict.annot -b -f $s/stats/lh.lobesStrict.stats PROBLEM: I'm stuck now on how to compile all of the data into one file. I've tried: aparcstats2table --subjects <subjectlist> --parc lobesStrict.annot --hemi lh –meas thickness --tablefile lh.lobesStrict.thickness.stats.txt I've also tried: asegstats2table --subjects <subjectlist> --subdir=stats --statsfile lh.lobesStrict --tablefile lh.lobesStrict.thickness.stats.txt None of these work. Can someone please tell me what I'm doing wrong? Thanks! Krista

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Choi2012 convert to FSL MNI152 2mm
by Kathy L. Pearson 10 Jul '14

10 Jul '14

To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have tried both of the mri_vol2vol commands below. The results as shown in freeview are offset by several voxels from the original. Is there a transform or an intermediate step that can make this work -- or a different command? Also, is there a recommended way to extract each individual value (here 1 ... 7) to create separate masks in FSL 2mm space? Thanks for any advice, Kathy Pearson #!/bin/bash input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o output1.nii.gz --no-save-reg --interp nearest --precision uchar mri_vol2vol --targ $input --mov $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz --no-save-reg --interp nearest --precision uchar # Compare results freeview $input output1.nii.gz output2.nii.gz&

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Research position at Columbia University Medical Center {Disarmed}
by binod thapa-chhetry 09 Jul '14

09 Jul '14

The Molecular Imaging and Neuropathology Division at Columbia University Medical Center is seeking a full-time image analyst to begin working immediately. The position involves assisting in the processing of brain imaging data, including positron emission tomography (PET) and structural and functional magnetic resonance imaging (MRI). Some background in brain imaging data processing is highly desired, as well as exceptional programming and other computer skills. Applicants should have experience coding in relevant languages, including Matlab, Python, unix command line scripting, HTML and PHP. A bachelor's degree in a scientific subject and and a strong academic record are required. Candidates invited to an interview will be asked to provide references, which will be contacted. Please fill out the official application at this link (https://jobs.columbia.edu/applicants/Central?quickFind=142939) as soon as possible. We are currently interviewing candidates and seek to fill the position within the next week.

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Tracula -qa flag
by qtnguyen＠nmr.mgh.harvard.edu 09 Jul '14

09 Jul '14

Dear Freesurfer experts, I'm trying to run Tracula -prep after sourcing Freesurfer 5.3. The file "<subjid>/dmri/dwi_motion.txt" is not included in the output. I then ran: trac-all -qa -c dmrirc and got the error message: flag -qa unrecognized Do you know what could have gone wrong? Do I have to download the updated Tracula version from here: http://ftp.nmr.mgh.harvard.edu/fswiki/Tracula ? Thank you, Trang

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LGI error
by Alan Francis 09 Jul '14

09 Jul '14

Hi Marie & FreeSurfers: I am running the LGI command on a group of brains and I am getting an error message. MATLAB opens up and begins to run when this error appears: < M A T L A B (R) > Copyright 1984-2011 The MathWorks, Inc. R2011b (7.13.0.564) 64-bit (maci64) August 13, 2011 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... closing volume... {Undefined function 'fspecial' for input arguments of type 'char'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); } I tried setting the environment using : setenv MATLABPATH /Applications/MATLAB_2011/bin setenv PATH ${MATLABPATH}/bin:${PATH} However this did not help. Any advice? thanks, Alan

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Freesurfer longitudinal GLM Design question
by Salil Soman 09 Jul '14

09 Jul '14

Hi, I have been following the tutorial from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial and here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel And I believe I am running into problems with my GLM design. I have a set of subjects with 2 time points each (all about 0.1 years apart). All I wish to do is see what areas are significantly changed in volume, after correcting for multiple comparisons (fdr or montecarlo). Could anyone suggest how I should setup the Design in QDEC?. I have included years and age in my cross.qdec.table.dat file (made from my long.qdec.table.dat file as described the tutorial, and have the measures of long.thickness-avg, long.thickness-rate, long.thickness-pc1 and long.thickness-spc avaialble (again from the tutorial). Any advice would be greatly appreciated. Sal

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Request to post message on freesurfer
by maluu＠ucalgary.ca 08 Jul '14

08 Jul '14

> Hello, > > My name is May, and I am the lab coordinator for the Clinical > Neuroscience > of Schizophrenia Lab at the University of Calgary in Calgary, Canada. I > was hoping to post a message to all the members of freesurfer. Please > let > me know if I will be able to post this message: > > Post-Doctoral Scholar in Mental Health Research > > Department of Psychology at University of Calgary, Calgary, Canada > invites > application for a post-doctoral fellowship beginning in Fall/Winter 2014 > (start date depends on individual requirements) to work with Dr. Vina > Goghari, PhD, R.Psych. > > The scholar will become a part of a research laboratory, which focuses on > elucidating the biological bases of dysfunction in schizophrenia and > bipolar disorder. Our laboratory brings together multiple methodologies, > including structural and functional MRI, behavioural genetics (i.e., > family studies), cognitive and affective experimental psychology, and > clinical assessment. The position will in part involve working with a > team > on a grant investigating neuroimaging and blood markers in bipolar > disorder. The person will also become part of the larger mental health > and > neuroscience community including the Mathison Centre for Mental Health > and > Education and Hotchkiss Brain Institute. > > Candidates should have a Ph.D. in clinical, cognitive, or biological > psychology or a related field focusing on mental health or neuroimaging. > Knowledge and experience working with psychological disorders and/or > neuroimaging is an asset; however, individuals wanting to transition to > that field are also encouraged to apply. Review of applications will begin immediately and will continue until the > position is filled, with an ideal employment start in Fall/Winter of > 2014. > To apply for the position, please send a CV, statement of background and > interest, and a list of three referees to Vina Goghari > (vmgoghar(a)ucalgary.ca) International applicants are also encouraged to > apply. Salary is competitive $50, 000 for two-years plus benefits. > > >

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