Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

Yeo 2011 Functional Cortical Parcellations
by Bronwyn Overs 24 Oct '18

24 Oct '18

Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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masking cortical thickness
by N Saf 11 Oct '18

11 Oct '18

External Email - Use Caution Dear Freesurfer Experts, I wonder how can I show the cortical thickness surface on just one region of my interest in Freeview. assume that I want to see the thickness surface of one of the regions in DKTatlas. does it work if I make a binary mask of that specific region on aparcDKTatlas.annot and then multiply it to the ?h.thickness surface ?? any help will be appreciated. Best Regards, Nazanin

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Morphing Buckner2011 MNI152 to subject's space {Disarmed}
by Peled, Noam 05 Oct '18

05 Oct '18

Dear group, I'm trying to morph the Buckner2011<http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011> cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange. Thanks, Noam

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freeview problem on Linux RHEL 7-4 libGLU.so.1
by Avner Meoded 01 Oct '18

01 Oct '18

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in /usr/local/fsl/bin/FSLeyes/libGLU.so.1 any idea ho to solve this problem Thanks avner

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FreeSurfer 6.0.0 CentOS 7 compatibility
by Vanzo, Davide 25 Sep '18

25 Sep '18

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if the current stable release works correctly on CentOS 7 or not? Thank you. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu

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QAtools tkmedit snapshots are black
by Ehsan Adeli 13 Sep '18

13 Sep '18

External Email - Use Caution Hello, I tried to create snapshots with tkmedit, but the output snapshot files are all black. This is the command: export SUBJECTS_DIR=./ tkmedit blubber norm.mgz tkmedit shows the image correctly, but when taking a snapshot it is all black. No error messages are displayed. I was wondering if anybody else had a similar issue and if there is any solutions to that. Thank you very much, in advance. Sincerely, Ehsan Adeli, Ph.D., Stanford University

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FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error
by Sean Ma 07 Sep '18

07 Sep '18

External Email - Use Caution Hi Eugenio, I'd like to report a Matlab runtime Java error when running the Hippocampal subfield on FS6.0-dev (Jun 27, 2018) after a successful completion of `recon-all`. Matlab 2014b runtime has been successfully expanded at /MCRv84. The error I've encountered follows. Any suggestions on how I can overcome this error? Thanks for your pointers! Best, Sean Ma University of Michigan ================================== [tehsheng@b-fmri FS6results]$ segmentHA_T1.sh b30002_02712 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Mon Jul 2 15:16:41 EDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv84//runtime/glnxa64:/opt/freesurfer6/MCRv84//bin/glnxa64:/opt/freesurfer6/MCRv84//sys/os/glnxa64::/opt/freesurfer6/MCRv84//sys/opengl/lib/glnxa64: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) @#@FSTIME 2018:07:02:15:16:41 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 32.59 S 0.39 U 5.00 P 16% M 205368 F 82 R 43627 W 0 c 54 w 1963 I 24008 O 82888 L 0.00 0.07 0.89 @#@FSLOADPOST 2018:07:02:15:17:13 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.15 0.11 0.87 Linux b-fmri.edu 2.6.32-696.28.1.el6.x86_64 #1 SMP Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Mon Jul 2 15:17:13 EDT 2018 For more details, see the log file /mnt/blab/Sean_Working/FS6results/b30002_02712/scripts/hippocampal-subfields-T1.log

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[TRACULA] eddy_correct /affine registration matrices / motion/ eddy currents
by Daumail, Loic Jean 28 Aug '18

28 Aug '18

Dear FreeSurfer experts, I would like to understand better the principle of eddy_correct: -in which way the eddy currents caused by motion are set apart from the eddy currents caused by fast switching diffusion-encoding gradients? -and then, how are the affine registration matrices reflecting motion computed by eddy_correct considering the previous issues? -does eddy_correct even computes these affine registration matrices(dwi.ecclog)? or is it another tool of dmri_motion? Thanks, Loïc Daumail Graduate intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST

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error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz
by Montserrat Domingo Ayllón 28 Aug '18

28 Aug '18

External Email - Use Caution Hi everybody! I have an error in one of my subjects preprocessing error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz In the dlabel folder of this subject, the mni folder has the half of the items that the rest of subjects have (2036 vs 4568). It is a subject with severe atrophy, therefore, I don't know if the trac-preproc has exited with errors due to this atrophy or because of other facts that I'm not able to detect. Thank you in advance, Montse

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Follow-Up: Longitudinal Processing - Retaining Manual Edits
by KALEY E ELLIS 27 Aug '18

27 Aug '18

External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the a filter was used on the raw images to adjust for hyperintensities in the images due to using a multi-channel coil. At this point, our bases have already been processed and consist of three timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. Since we have invested many resources into the manual editing process, we want to try to retain all the manual edits that have been done to the base. We still have the original scan and the filtered scan for each subject. We have some ideas on how we might be able to retain the edits, but would you be able to provide input regarding whether this seems reasonable? Your feedback is greatly appreciated! Plan A: 1) Create a new T3 cross-sectional with the correct nifti 2) Run recon-all on the existing base Q: Will this retain the previous manual edits AND incorporate the new cross-sectional image? Plan B: 1) Create a new T3 cross-sectional with the correct nifti 2) Create a new base Q: Is it possible to transfer data from old manual edits to a new base? If so, how? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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Freesurfer July 2018