Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 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>

2 5

Midline errors
by Maxime Perron 16 Oct '18

16 Oct '18

3 15

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

3 6

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

3 3

Re: [Freesurfer] Overlay electric field distribution on pial surface
by Meusen - Klooster, D.C.W. 03 Oct '18

03 Oct '18

External Email - Use Caution Dear Prof. Fischl, Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize. bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1 tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150 Best, Debby ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface Hi Debby you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks cheers Bruce On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote: > > External Email - Use Caution > > Dear all, > I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS > induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my > other images. I have a .nii file of the electric field distribution, registered to T1, representing > field strengths in every voxel. Visualization in freeview looks okay, but visualization using > tksurfer does not really give the right results (most of the brain is yellow... no field > distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I > would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how > to accomplish this? > Thank you very much in advance. > Best, > Debby > >

3 4

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 01 Oct '18

01 Oct '18

External Email - Use Caution If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes. If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others. This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700 Do the raw images look like that too? From: <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>>> on behalf of Matthew Grecsek <m...(a)grecsek.com<mailto:m...@grecsek.com <m...(a)grecsek.com>>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution Yes, a part of the brain appears missing. See attached screenshot. I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks! a.y

2 6

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

2 1

cannot stat volumesAmygdala.txt
by John Papatriantafyllou 30 Sep '18

30 Sep '18

External Email - Use Caution dear Freesurfers, after processing hippocampal subfields i cannot get amygdala stats. Instead i get the following massage *cannot stat volumesAmygdala.txt* Any suggestions? John PS i run freesurfer under neurodebian system on pc with windows 10

2 3

Re: [Freesurfer] amygdala segmentation atlas influence
by Iglesias Gonzalez, Eugenio 30 Sep '18

30 Sep '18

External Email - Use Caution Dear Raj, A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But this is a direction I’m still interested in, and which I’m planning to revisit in the future. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily K Clarke <ekc23(a)duke.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 26 September 2018 at 15:15 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu> Subject: [Freesurfer] amygdala segmentation atlas influence External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

1 0

Re: [Freesurfer] ERROR: dimension mismatch between X and
by Backhausen, Lea 29 Sep '18

29 Sep '18

External Email - Use Caution Thank you so much for your help - it's working now. ---------------------------------------- Lea Backhausen Wissenschaftliche Hilfskraft Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de _____________________________________________________________________________________ Date: Thu, 27 Sep 2018 15:24:01 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: dimension mismatch between X and contrast To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <09411cf0-185b-26c6-9ad0-479edb2d6e2c(a)mgh.harvard.edu> Content-Type: text/plain; charset="Windows-1252" You have 3 groups and 2 covariates, so you will have 3*(2+1)=9 regressors, in this order ADHD-offset COM-offset TD-offset ADHD-Age COM-Age TD-AGE ADHC-IQ COM-IQ TD-IQ You will need to have a single value for each regressor in your contrast matrix, meaning that you should have 9 values. You have 10 values, thus the error. On 09/27/2018 09:39 AM, Backhausen, Lea wrote: > > ????????External Email - Use Caution > > Dear FreeSurfer experts, > > I get this error message when running group analysis on cortical > thickness using glmfit: > ERROR: dimension mismatch between X and contrast > Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols > > Please find attached the FSGD file, the contrast file and the terminal > output below. > > I want to do ANCOVA with three groups (ADHD, COM and TD) controlling > for the effects of age and IQ. > So I assume the regressors would be ADHD COM TD age IQ and my contras > matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two > tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V. > > Can anybody help me out? Where am I wrong? Why does glmfit assume X > has 9 cols? > > Any help would be much appreciated, thank you in advance! > > Best > Lea > > > Terminal Output: > mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd > FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx > --surf fsaverage rh --cortex --glmdir > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 Age 13.6015 1.73148 > 1 IQ 107.288 11.1649 > Class Means of each Continuous Variable > 1 ADHD? 13.7193 104.3478 > 2 COM? 12.8657 105.3929 > 3 TD? 14.0119 112.3784 > INFO: gd2mtx_method is dods > Reading source surface > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/fsaverage/surf/rh.white > Number of vertices 163842 > Number of faces??? 327680 > Total area???????? 65020.839844 > AvgVtxArea?????? 0.396851 > AvgVtxDist?????? 0.717994 > StdVtxDist?????? 0.193566 > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS cmdline mri_glmfit.bin --y > rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd > FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx > --surf fsaverage rh --cortex --glmdir > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > sysname? Darwin > hostname edr06188.dip.tu-dresden.de > machine? x86_64 > user???? Lea > FixVertexAreaFlag = 1 > UseMaskWithSmoothing???? 1 > OneSampleGroupMean 0 > y > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh > logyflag 0 > usedti? 0 > FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd labelmask > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/fsaverage/label/rh.cortex.label > maskinv 0 > glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > Loading y from > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh > ?? ... done reading. > INFO: gd2mtx_method is dods > Saving design matrix to > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat > Computing normalized matrix > Normalized matrix condition is 1027 > Matrix condition is 4.07619e+06 > Found 149926 points in label. > Pruning voxels by thr: 1.175494e-38 > Found 149926 voxels in mask > Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh > Reshaping mriglm->mask... > search space = 74490.844410 > ERROR: dimension mismatch between X and contrast > Contrasts/ADHD_COM_TD_age_IQ.mtx?????? X has 9 cols, C has 10 cols > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 6 Date: Thu, 27 Sep 2018 15:38:38 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Best way to update Freeview To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4CBE100D-0B0E-4B8D-B21B-4520523B668D(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Arkadiy, this should be fixed now. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 26, 2018 at 6:01 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Best way to update Freeview Hi everyone, I was able to download Freeview- the link now works. However I am having an issue with starting this version. bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/ bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_6.0/ FSFAST_HOME /Applications/freesurfer_6.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Volumes/DrEmetBrown/ MNI_DIR /Applications/freesurfer_6.0/mni bash-3.2$ freeview dyld: Library not loaded: @rpath/QtWidgets.framework/Versions/5/QtWidgets Referenced from: /Applications/freesurfer_6.0//Freeview.app/Contents/MacOS/Freeview Reason: image not found Abort I am running a Mac OS HighSierra (10.13.6). It seems that people had similar issues in the past, but not quiet like this one. I would love to hear any tips on how to fix it. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2018