Re: [Freesurfer] Gray matter volume image per group

External Email - Use Caution Dear Doug, Thanks for the fast reply. Well we calculated the measures surface area (SA) , thickness (THK), volume (VOL) in each participant (in surf folder) of our groups and evaluated the differences between them using Monte Carlo. Now we wanted ju

Re: [Freesurfer] Gray matter volume image per group

It will be easier not to use make_average_subject. Just use mris_preproc as if you are doing a group analysis. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 The output of mris_preproc (lh.gender_age.thickness.00.mgh) can be compressed to an average with mri_concat lh

Re: [Freesurfer] fsgd file - glmfit error

External Email - Use Caution Here is my fsgd file. Thank you! On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve wrote: > Please send the fsgd file > > On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab > of Autism and Developmental Neuroscience wrote: > >

Re: [Freesurfer] fsgd file - glmfit error

Try putting 1 after GroupDescriptorFile, ie, GroupDescriptorFile 1 On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Here is my fsgd file. Thank you! On Mon, Jul 27, 2020 at 8:44 PM

[Freesurfer] Longitudinal pipeline question

External Email - Use Caution Hi, I am working with some longitudinal data that was originally run through troubleshooting/recon-all in freesurfer 5.3. A lot of time went into the edits, so I definitely do not want to replicate these in freesurfer 6. Do I need to run the postproces

[Freesurfer] Thalamic nuclei in FSL

External Email - Use Caution Hi Freesurfer experts, I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’

[Freesurfer] Freesurfer 7.1.0 VirtualBox password

External Email - Use CautionI see that other users have come across this problem also… I hope this has not been formally adressed somewhere already.I would like to request the login password for the ‘development’ user as i can not seem to find it in any of the documentation. Best re

Re: [Freesurfer] Freesurfer 7.1.0 VirtualBox password

External Email - Use Caution Hello Joseph, I will sent the password directly to your email shorty.. - R. On Jul 28, 2020, at 17:59, Joseph Mewse wrote:External Email - Use CautionI see that other users have come across this problem also…

Re: [Freesurfer] Error in Trac-All Pre-Processing step

Hi Jocelyn - Although we could not replicate your error here, the error message mentions MKL, which is the Intel math kernel library. In case this library was not installed properly on your system, you can try (re)installing it from here: https://software.intel.com/content/www/us/en/develop/arti

Re: [Freesurfer] Thalamic nuclei in FSL

Can you run it with --debug as the first option, capture the (large amount of) terminal output in a file, and send the file? On 7/28/2020 1:26 PM, Erin Moe wrote: > External Email - Use Caution > > Hi Freesurfer experts, > > I ran segmentThalamicNuclei on my dataset and would like to use

Re: [Freesurfer] Longitudinal pipeline question

By post processing and stats, do you mean mris_preproc, mri_surf2surf, and mri_glmfit? You can run v6 of those on data reconned with any version of FS On 7/28/2020 1:25 PM, Rachel Romeo wrote: External Email - Use Caution Hi, I am working with some longitudinal data that was origina

[Freesurfer] 7.1 require experts opts for hires?

External Email - Use Caution Hi there FS gurus- We have fairly standard 7T structural data (0.7mm iso) and are using the -hires flag for recon-all. Per the old-ish page "Recon with native submillimeter resolution" we've also been using a higher mris_inflate value in an expert opti

Re: [Freesurfer] 7.1 require experts opts for hires?

You should not need to increase the the number of iterations. Most of the problems with the hi-res stream was due to the extra vertices. The new stream decimates the mesh down to the number of vertices that would have been in a 1mm scan. On 7/28/2020 8:37 PM, Salvatore Torrisi wrote: