Freesurfer April 2020

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Install Freesurfer on Ubuntu
by Stephan 06 Apr '20

06 Apr '20

External Email - Use Caution Hi, ist there an official guideline how to install Freesurfer on Ubuntu? Best, Stephan

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vertex number to MNI coordinates
by Marina Fernández 06 Apr '20

06 Apr '20

External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to know the MNI coordinates to which a vertex of a surface corresponds? 2. I have projected the surfaces of the subjects onto the average subject from this dataset. Can I know the MNI coordinates corresponding to a vertex of the average subject of my dataset? Or do I need to project it onto the fsaverage to know the correspondence to de MNI space? 3. I know that the average surface is constructed by computing the MNI305 coordinate at each vertex, But how can I obtain the MNI152 coordinates (instead of MNI305) to which a vertex corresponds? (if it is possible). Thank you very much in advance. Best regards, Marina

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Re: [Freesurfer] Ubuntu image asking for user credentials on startup
by fsbuild 06 Apr '20

06 Apr '20

External Email - Use Caution Hello Vi, I will send the password to your email. - R. On Apr 6, 2020, at 13:22, rudolfrentier <1q2s3c4f5t6h7m8k9o0o(a)gmx.net> wrote:      External Email - Use Caution        Hi!I wanted to try out FreeSurfer and followed the install guide fromhttps://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded2020-04-06 1:29 AM CEST).However, upon startup of the virtual machine, the Ubuntu installationasks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtualmachine should just boot up to Desktop without requiring a password.Is there a default password I am supposed to use (I tried leaving thepassword field blank, "freesurfer", "FreeSurfer", "developer" but noneof those worked)?Thanks,Vi<FreeSurfer login prompt 2020-04-06 191708.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu image asking for user credentials on startup
by rudolfrentier 06 Apr '20

06 Apr '20

External Email - Use Caution Hi! I wanted to try out FreeSurfer and followed the install guide from https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-04-06 1:29 AM CEST). However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (see screenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password. Is there a default password I am supposed to use (I tried leaving the password field blank, "freesurfer", "FreeSurfer", "developer" but none of those worked)? Thanks, Vi

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Re: [Freesurfer] mri_glmfit-sim FWHM error
by Douglas N. Greve 06 Apr '20

06 Apr '20

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 > > >

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Re: [Freesurfer] Hippocampal subfield volumes.
by Devika K 06 Apr '20

06 Apr '20

External Email - Use Caution Hi, I want to extract hippocampal subfield volume from longitudinal samples. I ran recon-all-all with longitudinal pipeline for all those samples in FreeSurfer 6.0. How I need to process further (Commands that I need to follow). Would you please help me out? Regards Devika K

2 1

(no subject)
by Peng Liu 06 Apr '20

06 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am trying to customize a colour map of my own, with five colours and scale from -12.5 to 12.5, since when using Heat (with default options), the scale is correct but it is shown in only four colours. However after I created the .lut file (attached below), when loading it into freeview, the colour scale is from 0 to 6. [image: image.png] Does this mean I should also include scale information in the .lut file? Any help would be much appreciated. Peng Liu

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Permutation with Non-Orthogonal Matrices
by Hua, Jessica 06 Apr '20

06 Apr '20

External Email - Use Caution Hi FreeSurfer Experts, Reposting this message. I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the following script: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --sim perm-resid 1000 3.0 --sim-sign abs --cwp 0.05 --2spaces I am getting the following error message: ERROR: Flag abs unrecognized. And when I tried to put the "abs" after "1000 3.0," I got the error message saying that I needed to specify the --sim-sign. Could you please let me know how I need to edit my script? I have already run mris_preproc and mri_glmfit. Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

2 1

mri_glmfit-sim FWHM error
by s7675854＠stud.uni-frankfurt.de 06 Apr '20

06 Apr '20

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

2 1

Customizing colour map
by Peng Liu 06 Apr '20

06 Apr '20

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Freesurfer April 2020