Re: [Freesurfer] Permutation with Non-Orthogonal Matrices

did you download the patch as described here ("If You're Not at an Organized Course")? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 4/6/2020 6:45 PM, Hua, Jessica wrote: External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran

[Freesurfer] Permutation with Non-Orthogonal Matrices

External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid

Re: [Freesurfer] Install Freesurfer on Ubuntu

External Email - Use Caution Hello Stephan, There is some information here about packages to install in order to run freesurfer - see highlighted "apt-get install" commands. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements I think you will also need to install these

Re: [Freesurfer] Install Freesurfer on Ubuntu

External Email - Use Caution Hi Stephan, please have a look at the "FreeSurfer Download and Install” page within the FreeSurfer documentation: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall HTH,

Re: [Freesurfer] vertex number to MNI coordinates

answers below, but overall, take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 4/6/2020 4:06 PM, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to

[Freesurfer] Install Freesurfer on Ubuntu

External Email - Use Caution Hi, ist there an official guideline how to install Freesurfer on Ubuntu? Best, Stephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] vertex number to MNI coordinates

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

Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}

External Email - Use Caution Apologies for the late reply, hectic times. Please find the requested files here: https://uwmadison.box.com/s/vod1t4vlycd9baom42qqqwkc6unj9aui Let me know how else I can help! T From:

Re: [Freesurfer] Ubuntu image asking for user credentials on startup

External Email - Use Caution Hello Vi, I will send the password to your email. - R. On Apr 6, 2020, at 13:22, rudolfrentier 1q2s3c4f5t6h7m8k9...@gmx.net wrote:External Email - Use Caution Hi!I wanted to try out FreeSurfer and followed the install guide

Re: [Freesurfer] mri_glmfit-sim FWHM error

External Email - Use Caution thanks a lot! I will run both over night - if the permutation issue does not come up again, I agree that it would be the better option... Best, Doro Zitat von "Douglas N. Greve" : > On 4/6/2020 10:57 AM, s7675...@stud.uni-frankfurt.de wrote: >>

Re: [Freesurfer] Hippocampal subfield volumes.

Dear Devika, The command is longHippoSubfieldsT1.sh. You can find the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

Re: [Freesurfer] mri_glmfit-sim FWHM error

On 4/6/2020 10:57 AM, s7675...@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

Re: [Freesurfer] (no subject)

External Email - Use Caution Thank you so much. I shall modify my other scripts then. Peng On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang wrote: > I don’t think look up table works with negative indices. It was mainly > designed for label volumes. > > Ruopeng > > On Apr 6, 2020,

Re: [Freesurfer] (no subject)

I don’t think look up table works with negative indices. It was mainly designed for label volumes. Ruopeng > On Apr 6, 2020, at 10:35 AM, Peng Liu wrote: > > External Email - Use Caution > > > Hi Ruopeng, > > Thank you for your reply. > > I have also tried NIH and JET,

Re: [Freesurfer] Permutation with Non-Orthogonal Matrices

try this mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces On 4/4/2020 11:31 PM, Hua, Jessica wrote: External Email - Use Caution HiFreeSurferExperts, Reposting this message. I am trying to correct for multiple comparisons by

Re: [Freesurfer] mri_glmfit-sim FWHM error

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

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Ruopeng, Thank you for your reply. I have also tried NIH and JET, but with negative scale, the entire image will turn into one same color as if there is some error. Meanwhile the reason of me trying to create .lut map is because I want five

Re: [Freesurfer] (no subject)

Hi Peng, Your lookup table only contains indices between 0 to 6. In any case I would not use look up table to display negative scales. Have you tried any other color maps like JET or NIH which has more colors? Best, Ruopeng > On Apr 6, 2020, at 6:30 AM, Peng Liu wrote: > > External

[Freesurfer] mri_glmfit-sim FWHM error

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

[Freesurfer] Customizing colour map

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

[Freesurfer] (no subject)

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