Freesurfer

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30132 discussions

training set
by javier quilis 13 Apr '20

13 Apr '20

External Email - Use Caution Hello everyone, I'm trying to do a study of a comparison between the automated methods to analyze structural MRI from FSL and Freesurfer. I am interested in the training set used by Freesurfer to do the brain segmentation and I can not find a detailed description of it. Is there any source where this set is described? Thanks in advance. Bests, Javier Quilis

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Trac-all Error
by Hua, Jessica 13 Apr '20

13 Apr '20

External Email - Use Caution Hi FreeSurfer, I am running trac-all prepocessing using a configuration file. I tried preprocessing a couple of participants, and I keep getting this error: #------------------------------------- #@# Tensor fit Sat Apr 11 21:29:36 PDT 2020 dtifit -k /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dwi.nii.gz -m /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvecs -b /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/bvals -o /Volumes/HuaExternal/DTI_FS/S11018a_LGI/dmri/dtifit libc++abi.dylib: terminating with uncaught exception of type std::logic_error: Mat::operator(): index out of bounds Abort This is my configuration file: set dtroot = /Volumes/HuaExternal/DTI_FS set subjlist = ( S11018a_LGI ) set dcmroot = /Volumes/HuaExternal/DTI set dcmlist = ( S11018a.nii ) set bvecfile = /Volumes/HuaExternal/DTI/bvecsSPACE.txt set bvalfile = /Volumes/HuaExternal/DTI/bvals.txt set runlist = (1) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 set mnitemp = /Volumes/HuaExternal/DTI/MNI152_T1_1mm_brain.nii.gz set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) Do you know what is going wrong, and how I would fix this issue? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Hello Respected Community,
by Safi Ullah . 12 Apr '20

12 Apr '20

External Email - Use Caution Hello Respected Community, I generated a label file using the command mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173 --l midbrain.label the content of the label file is probably in RAS format. My question is how to locate a point in freeview using the given coordinates of the label file? i.e the label file content is as follows -1 4.000 -20.750 33.750 0.0000000000 -1 3.500 -20.750 33.750 0.0000000000 I am unable to locate 4.0, -20.750, 33.750 in the volume shown through freeview. I also want to find out the overlapping planes of two label files, for which I need to convert the label file into voxal coordinates (or may be there is any other simpler way, i dont know) Any help shall be highly appreciated. Regards, Safi <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] Freeview_Linux_Subsystem
by fsbuild 11 Apr '20

11 Apr '20

External Email - Use Caution Hello Kristian, I have been looking at this as well, and my understanding is things are not configured “out of the box” for an X-Windows client like freeview running under the Windows Linux subsystem to work with the 3rd party Xming software running on the windows side..  For me, the freeview window is partially drawn in the X-window, but its graphics are not entirely drawn or rendered.  I will post more information when I know something more. There is however a virtual machine with Ubuntu linux you can run on windows that has been tested and comes installed with both the freesurfer 6 and the new freesurfer 7 beta release, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R. On Apr 11, 2020, at 06:02, Kristian Stefanov <Kristian.Stefanov(a)glasgow.ac.uk> wrote:        External Email - Use Caution        Dear developers,I’m running into an issue using freeview. I have installed freesurfer on a Linux subsystem for Windows (Ubuntu 18.04 LTS) according to the guidelines (https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport) including Xming. The frresurfer commands work without a problem (e.g. recon all), however, freeview does not display anything even though I can successfully load volumes and surfaces (see attached image). I do not have any problems with FSLeyes or tkmedit. Any advise on what could be causing this issue?  Many thanks, Kristian Stefanov Kristian Stefanov,Research AssistantImaging Centre of Excellence (ICE)University of GlasgowTel: +44 (0) 0141 541 6859 <freeview_issue.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hippocampal subfields
by ioana cracana 11 Apr '20

11 Apr '20

External Email - Use Caution Hello, I'm doing a study about hippocampal atrophy and I'm using the Segmentation of Hippocampal subfields tool. There were some minor errors and I edited them using Freeview, voxel edit tool. I would like to generate a new [lr]h.hippoSfVolumes-T1.v10.txt file using the edited [lr]h.hippoSfLabels-T1.v10.mgz in order to see the new results. What command do i have to use? Is there another way to edit the hippocampal subfields?And how do i see the results? I'm using Freesurfer v6.0.0. on macOS Mojave. Thanks, Ioana

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Freeview_Linux_Subsystem
by Kristian Stefanov 11 Apr '20

11 Apr '20

External Email - Use Caution Dear developers, I’m running into an issue using freeview. I have installed freesurfer on a Linux subsystem for Windows (Ubuntu 18.04 LTS) according to the guidelines (https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport) including Xming. The frresurfer commands work without a problem (e.g. recon all), however, freeview does not display anything even though I can successfully load volumes and surfaces (see attached image). I do not have any problems with FSLeyes or tkmedit. Any advise on what could be causing this issue? Many thanks, Kristian Stefanov Kristian Stefanov, Research Assistant Imaging Centre of Excellence (ICE) University of Glasgow Tel: +44 (0) 0141 541 6859

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Re: [Freesurfer] Permutation with Non-Orthogonal Matrices
by Hua, Jessica 10 Apr '20

10 Apr '20

External Email - Use Caution I had a question regarding the output for permutation. perm.th40.abs.y.ocn.dat -- the average value of each subject in each cluster Is this average value the raw value of each subject, or does this also account for my covariates (age, sex, and ICV)? --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Error running recon-all
by David Schwantner 10 Apr '20

10 Apr '20

External Email - Use Caution Thank you in advance for the assistance! I am running the following command: recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all The log is at https://github.com/dschwant/mri_to_3d/blob/master/202004090853_error_recon-…, and the nii file is at https://github.com/dschwant/mri_to_3d/blob/master/202004_DS_Brain_MRI/1131_… . Here is the tail of the log. As you can see, I am running it in Ubuntu 18.04.4 under the Windows Subsystem for Linux. ... searching rotation angles z=[-9 5], y=[-22 -8] searching scale 1 Z rot 5.3 global minimum found at slice 139.0, rotations (-14.14, -1.42) final transformation (x=139.0, yr=-14.141, zr=-1.420): 0.96940 0.02478 -0.24423 8.04082; -0.02403 0.99969 0.00605 -41.07934; 0.24430 0.00000 0.96970 18.40543; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07 15:22:00 PST 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DS_T2 exited with ERRORS at Thu Apr 9 11:19:24 DST 2020 ... Is it just not enough "details" in the nifti file? I am trying the next larger one now. ---------------------------- David - dschwant(a)gmail.com ----------------------------

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Error running "recon-all"
by David Schwantner 10 Apr '20

10 Apr '20

External Email - Use Caution Thank you in advance for the assistance! I am running the following command: recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all I have attached the log file. Here is the tail. As you can see, I am running it in Ubuntu 18.04.4 under the Windows Subsystem for Linux. ... searching rotation angles z=[-9 5], y=[-22 -8] searching scale 1 Z rot 5.3 global minimum found at slice 139.0, rotations (-14.14, -1.42) final transformation (x=139.0, yr=-14.141, zr=-1.420): 0.96940 0.02478 -0.24423 8.04082; -0.02403 0.99969 0.00605 -41.07934; 0.24430 0.00000 0.96970 18.40543; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux LT499318 4.4.0-17763-Microsoft #864-Microsoft Thu Nov 07 15:22:00 PST 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DS_T2 exited with ERRORS at Thu Apr 9 11:19:24 DST 2020 ... What other information would be helpful in determining what I need to do to make this work? ---------------------------- David Schwantner dschwant(a)gmail.com (858) 518-7263 ----------------------------

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Re: [Freesurfer] mri_glmfit-sim FWHM error
by Douglas N. Greve 09 Apr '20

09 Apr '20

Did you down load all the files in the patch? I think the new mri_surfcluster is there On 4/8/2020 8:51 AM, s7675854(a)stud.uni-frankfurt.de wrote: > External Email - Use Caution > Hi again, > I already took a few more steps and set up PALM/ fspalm. It's working > fine, up to the point where it does the actual cluster analysis. As > part of the script, the command > mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 > --subject fsaverage --hemi lh --annot aparc --sum resilience. > clustertable.summary --no-fixmni --surf white --ocn resilience.ocn.mgz > oannot ./resilience.ocn.annot --sig2pmax --bonferroni-max2 > is generated. However, the last two flags (--sig2pmax > --bonferroni-max2) are not recognized, so it crashes. Indeed, they do > not appear as possible flags in the mri_surfcluster --help section, so > how and why do they get here...? > Just to see what happens, I ran the mri_surfcluster... command without > the last 2 flags, which only gave me another error: "could not read > fsp_clustere_tstat_fwep.mgz as type" > > Do you have an idea what I could do about this? > Thanks a lot, > Doro > > Zitat von s7675854(a)rz.uni-frankfurt.de: > >> Hi Douglas, >> >> I just saw that permutation wasn't working for me because I use >> continuous covariates/ a non-orthogonal design. You just answered to >> a similar question in the mailing list yesterday and suggested to add >> "--perm-resid", but this flag does not exist for the mri_glmfit-sim >> command, does it? Do I have to install PALM to be able to run >> permutation on my design or is there any way around that? >> >> Thanks again, >> >> Doro >> Zitat von "Douglas N. Greve" <dgreve(a)mgh.harvard.edu>: >> >>> On 4/6/2020 10:57 AM, s7675854(a)stud.uni-frankfurt.de wrote: >>>> External Email - Use Caution >>>> Hi Douglas, >>>> >>>> thanks a lot for your quick response. I wanted to use Monte Carlo sim >>>> as all other analyses in our project include a monte carlo simulation >>>> and I try to keep things consistent. Am I getting you right - there is >>>> no way to run a monte carlo simulation with LGI data? And why exactly >>>> would you not recommend it in this case (even if it worked)? >>> Yes, you can do the MCZ simulation yourself with mri_mcsim, >>> something like >>> mri_mcsim --o /your/space/mcsim/fsaverage/lh/cortex --base mc-z >>> --save-iter --surf fsaverage lh --nreps 1000 --fwhm 37 >>> Then run mri_glmfit-sim as you did before, but specify --mczsim-dir >>> /your/space/mcsim >>> >>>> >>>> I did try permutations with freesurfer in the past, but it never >>>> really worked out for me, to be honest. They kept running for ages and >>>> I stopped them after 6-7 days... >>> Not sure what happened, but if you want to debug it, I can help >>> >>>> >>>> Thanks in advance, >>>> >>>> Doro >>>> Zitat von "Douglas N. Greve" <dgreve(a)mgh.harvard.edu>: >>>> >>>>> The problem is that mri_glmfit-sim is looking for a entry in the >>>>> table that does not exist. The table only goes up to a smoothness >>>>> level of 35. LGI data tend to bed very smooth. I would strongly >>>>> recommend that you use permutation instead. See >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… >>>>> >>>>> >>>>> On 4/6/2020 7:42 AM, s7675854(a)stud.uni-frankfurt.de wrote: >>>>>> External Email - Use Caution >>>>>> Dear Freesurfer experts, >>>>>> >>>>>> I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI >>>>>> data (fwhm10), but get an error due to the estimated fwhm kernel. >>>>>> The folder corresponding to the fwhm value (-->37) does not exist, I >>>>>> guess because it's a pretty unusual value...? >>>>>> >>>>>> DoSim = 0 >>>>>> UseCache = 1 >>>>>> DoPoll = 0 >>>>>> DoPBSubmit = 0 >>>>>> DoBackground = 0 >>>>>> DiagCluster = 0 >>>>>> gd2mtx = dods >>>>>> fwhm = 36.855100 >>>>>> ERROR: cannot find >>>>>> /apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd >>>>>> >>>>>> >>>>>> I've seen mails describing similar issues in the archive and from >>>>>> your explanation I more or less understand that you cannot define >>>>>> this value as it is estimated in the process...? However, I did not >>>>>> see if there is a solution to this problem. What could I do about it >>>>>> now? >>>>>> >>>>>> I attached the logfiles and would be very grateful for your help, >>>>>> >>>>>> thanks a lot and stay healthy, >>>>>> >>>>>> Doro >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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