Freesurfer

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17 participants
30099 discussions

Convert label file to STL file‏
by Mat yuki 10 Jul '14

10 Jul '14

Dear Freesurfer Experts, I'm trying to convert .label file to .stl file. In more detail of my purpose, I want to get separate stl files of whole brain. Now, I want to make stl files of label files which made from ?h.aparc.a2009s.annot. First, I tried to convert lh.pial to lh.pial.stl, I've got it (this was just check how mris_convert works). Second, I copied lh. white file from surf dir into label dir. Then, I runed next command: cd <subjid>/label mris_convert --label lh.bankssts.label bankssts lh.white lh.bankssts.label.stl And got the error message: ERROR: unknown file annot file type specified for output: lh.bankssts.label.stl Do you know what could have gone wrong? Thank you, Yuki.

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ACPC alignment in freeview?
by Tracy Riggins 10 Jul '14

10 Jul '14

Hello Freesurfer experts: I am wondering if I can do ACPC alignment in freeview. Perhaps using Tools> Transform volume and then rotating using landmarks. Is this indeed possible? If so, can anyone provide guidance on the 3 landmarks to select (would it be anterior commissure superior & posterior edges & posterior commissure) and how to map these landmarks to coordinate axis vectors? I would appreciate it. Thanks in advance, Tracy Riggins

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Save automatically masks drawn in Freeview
by Dorian P. 10 Jul '14

10 Jul '14

Hi users and developers, I am currently using Freeview to draw about 25 masks per subject for 60+ subjects. After generating the volume in Freeview, giving them the proper name, and drawing the ROI, I need to save them one by one, giving also the extension .nii to have the file as niftii. This procedure is very time consuming and prone to errors (filenames need to be precise). Is there a way to save the generated masks automatically, perhaps by selecting the volumes all at once, pressing save, and the software automatically saves them with the same name given in Freeview and with the extension .nii? Any suggestion is welcome, even if it requires hacking the software somewhere... Using Ubuntu 12.04 and Freesurfer 5.0.3. Thank you. Dorian TJU

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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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