[Freesurfer] local Gyrification Index

External Email - Use Caution Hello FreeSurfer Team, I am trying to compute the local Gyrification index on my subjects with recon-all -s -localGI. Running this under FS 6.0 runs without errors, with FS 5.3. I get: mesh_outer = struct with fields: vertices: [68598x

[Freesurfer] TRACULA prep gets stuck in -prior 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline'

External Email - Use Caution Dear all, I am trying to understand what is going on in my subjects (same problem with 5 different ones). the outputs from the first steps of trac-all seems to work fine, so I am running: trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -no

Re: [Freesurfer] local Gyrification Index

Sorry, the person who used to support the gyrification software has left. You're kind of on your own unfortunately. On 10/11/2019 6:04 AM, LOSKE, PHILIPP (PGR) wrote: External Email - Use Caution Hello FreeSurfer Team, I am trying to compute the local Gyrification index on my subjects

[Freesurfer] using dof9 or dof12 in preproc-sess

Hello, I posted this earlier and wasn't able to get a response. I am using freesurfer version 6 and I am having an issue with changing the degrees of freedom when I run preproc-sess. I made some registrations that are 9 and 12 dof instead of the default 6 using bbregister, however when I try t

Re: [Freesurfer] Freesurfer using dof9 with preproc-sess

This is a bug. I think I have fixed it. Can you download these files https://gate.nmr.mgh.harvard.edu/safelinks/greve/preproc-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/rawfunc2surf-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/rawfunc2tal-sess Copy them to $FREESURFER_HOME/fsf

Re: [Freesurfer] using dof9 or dof12 in preproc-sess

just posted solution to the freesurfer list. Are you running your analysis local to the martinos center? On 10/11/2019 11:02 AM, Droppa, Kyle Salmon wrote: Hello, I posted this earlier and wasn't able to get a response. I am using freesurfer version 6 and I am having an issue with changing the

Re: [Freesurfer] Freesurfer using dof9 with preproc-sess

You will also need https://gate.nmr.mgh.harvard.edu/safelinks/greve/register-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkbrainmask-sess On 10/11/2019 11:12 AM, Douglas N. Greve wrote: This is a bug. I think I have fixed it. Can you download these files https://gate.nmr.mgh.harvard.e

Re: [Freesurfer] ERROR gtmseg

Can you upload one of your problematic subjects? Follow these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: us

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shoul

[Freesurfer] covariate with repeated anova

External Email - Use Caution Hello Experts, I would like to include covariates in the freesurfer repeated anova steps https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i tried including 3 covariates, mri_glmfit complained about "martix is ill-conditioned". How

Re: [Freesurfer] TRACULA prep gets stuck in -prior 'WARN: Could not find satisfactory control point fit - try 20784 Finding center streamline'

Hi Cecilia - this commnd tells it to do the preprocessing (-prep), but then not to do any of the steps of the preprocessing (-no...) trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks -notensor -noprior -no-isrunning So this command won't do anything. Have you run those st