Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 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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Midline errors
by Maxime Perron 16 Oct '18

16 Oct '18

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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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Re: [Freesurfer] Surface Area in Toddlers/Children
by Douglas Greve 18 Sep '18

18 Sep '18

The flag to preserve area is not being turned on there. You can try running mris_preproc separately for area and including the --jac flag. If that does not work, you can download version6 and just use it to run mris_preproc On 8/10/18 4:41 PM, Derek Sayre Andrews wrote: > > External Email - Use Caution > > Hi Douglas, > > Of course, please find attached a copy of the recon-all.log file. > > Best, Derek > > PS: Apologies for the direct email in order to get you the attachment > > cid:image001.png@01D430A0.A5153C80 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas > Greve <dgreve(a)mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 11:12 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > Yes. -qcache actually calls mris_preproc. At one point, FS did not > preserve total area when mapping to fsaverage. I fixed it a while > ago, but maybe something was still off in 5.1 > > On 8/10/18 2:06 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Hi Douglas, > > Thank you for the response. > > I did not use mris_preproc to prepared the data. > > The data was mapped to fsaverage using recon-all with -qcache. I > then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into > MATLAB using SurfStatReadData > <http://www.math.mcgill.ca/keith/surfstat/> and summed them across > each vertex. > > Would the terminal output of recon-all -qcache be helpful? > > Best, Derek > > cid:part2.2B5BCEFF.1D6DDEE5@mgh.harvard.edu > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of > Douglas Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> > *Reply-To: *Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, August 10, 2018 at 10:25 AM > *To: *"freesurfer(a)nmr.mgh.harvard.edu" > <mailto:freesurfer@nmr.mgh.harvard.edu> > <freesurfer(a)nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children > > It should be preserving total surface area. Can you send your > mris_preproc command line and the terminal output? It might be > something with 5.1 as well. > > > > On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: > > * External Email - Use Caution * > > Dear Freesurfer Developers and Experts, > > I have been exploring various vertex wise (mass univariate) > effects using freesurfer measures of cortical thickness and > surface area in a cohort of toddlers/children aged 25-70 months. > > When looking at the effect of age on surface area using > individuals’ measures mapped to fsaverage and smoothed at 15mm > fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread > negative effect of age (i.e. decreased surface area with age). > Given the age group of the cohort this seems implausible. > Plotting the sum of each individuals > lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the > relationship: > > cid:image001.png@01D42FCE.C197B360 > > However, plotting the lh+rh total surface area returned by > mris_anatomical_stats reveals a much more plausible > relationship between surface area and age: > > cid:image002.png@01D42FCE.C197B360 > > My working hypothesis is that the significantly smaller brain > sizes of our cohort compared to fsaverage, and the fact(?) > that -qcache does not preserve global surface area, is causing > an “over adjustment” in our cohorts smallest brains when > mapped to fsaverage. > > Thus, my questions are three fold > > 1. Is the mapping of our significantly smaller brains to > fsaverage a potential explanation for the results we are > seeing in our mass univariate analyses of surface area? > > 2. If this is the case, would this effect be limited to > surface area or also extend to other freesurfer measures > including cortical thickness, lGI, sulcal depth etc. > > 3. How would you recommend approaching vertex wise analyses > in a cohort of this age? Create a study specific average > subject using make_average_subject to map onto? > > Thank you for your insight and guidance! > > Best, Derek > > PS: All processing was performed using freesurfer v5.1 > > cid:image003.png@01D42FCE.C197B360 > > *Derek Sayre Andrews, PhD* > > Postdoctoral Scholar > > Department of Psychiatry and Behavioral Sciences > > The M.I.N.D Institute > > University of California Davis > > > Telephone: +1 916 703 0360 > Email: dandrews(a)UCDavis.edu <mailto:dandrews@UCDavis.edu> > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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fsaverage6 ?h.cortex.flat.patch files
by Dinicola, Lauren 14 Sep '18

14 Sep '18

Hi all, We are hoping to visualize flat maps of surface data sampled to fsaverage6. Do 'flat.patch' files exist already for fsaverage6? Thank you for any help, Lauren DiNicola

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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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Freesurfer August 2018