Freesurfer

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30086 discussions

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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Aseg file issue
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 09 Apr '20

09 Apr '20

External Email - Use Caution Dear Freesurfer experts, I'm having some difficulty importing my aseg stats data onto QDEC. The error which I'm getting is seen below (please open the JPEG file). Any ideas on why this is happening? Thank you!

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Fwd: Is it possible to load flatmaps in freeview and draw ROI's on them?
by Devavrat Vartak PhD 09 Apr '20

09 Apr '20

External Email - Use Caution Hello Freesurfer developers, Thank you for developing Freesurfer! I am postdoc at UC Berkeley and I am using Freesurfer 6.0 to create flat maps on which I draw my ROI's. The flat maps/patches are created in TKSURFER. However, I typically use Freeview to visualise my volumes and inflated surfaces, overlay data etc. I am trying to open flatmap maps in freeview but I am not able to. I was wondering if it was possible to load flatmaps in freeview and draw ROI's on them and overlay my data? OS: MacBook OS Thank you. Best, Devavrat -- Devavrat Vartak, PhD Postdoctoral Researcher Helen Wills Neuroscience Institute and School of Optometry Mailing address: 360 Minor Hall #2020 University of California, Berkeley Berkeley, CA, 94720-2020 USA Website: www.dvartak.com Email: dvartak(a)berkeley.edu devavratvartak(a)gmail.com

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Overlap of vertices in downsampled data
by Ersin Ersözlü 09 Apr '20

09 Apr '20

External Email - Use Caution Hi FreeSurfer experts, We calculated the differences with downsampled -fsaverage6- thickness data between our groups using 'PALM' on the vertex level and got .mgz files as overlays wit h log-p values for each contrast. Now, we would like to test the overlap. We computed a ratio of overlap through 'mri_compute_overlap' within log-p overlay files but it showed labels (-s option) such as unknown and white matter. Is there a way to differentiate vertices that are in cortical regions? And could this labeling be correct? Medical doctoral student University of Munich (LMU) Ersin Ersözlü

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mri_convert input files
by Setiaman, N. 09 Apr '20

09 Apr '20

External Email - Use Caution Hi, I would like to convert my raw scans to nifty. The scans are made on a Philips scanner. I was able to retrieve most of them as DICOM files, but some of them are only available as PAR/REC. Does mri_convert also handle PAR/REC or can I only convert the DICOMS with this tool? Best, Nikita ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Tracula: tract length meaning
by Nazife Ayyıldız 08 Apr '20

08 Apr '20

External Email - Use Caution Dear Tracula experts, I want to compare two groups according to the length statistics from Tracula overall.stats outputs. I just need comprehensive explanations what "tract length" statistics mean and how they are derived and what their reliability is. I checked but I couldn't find detailed information. Are they suitable to use in group comparisons? If so, which one is more suitable to use: average, center, min or max length? I saw in some articles that they used average_length of a tract. If I want to use length statistics do you suggest taking any control variables? I read a message from Anastasia in the archive-list saying that we should be aware that these measures are in their individual DWI spaces. If I understood correctly, I shouldn't use them directly. Should I control the head sizes of the individuals then? How would you do if you wanted to do this kind of comparative analysis? I would really appreciate it if you answer. Thank you very much in advance! Best regards, Nazife -- -Nazife Ayyıldız-

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Re: [Freesurfer] Permutation with Non-Orthogonal Matrices
by Hua, Jessica 07 Apr '20

07 Apr '20

External Email - Use Caution Thanks for your help! I downloaded the patch, and the analysis is now running. Hopefully, I will not run into any other issues with the permutation. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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