Re: [Freesurfer] Using external software to perform brain extraction, multiple T1s

There was a post in 2015 from Richard Parker talking about using SPM brainmasks instead of the Freesurfer ones. I would like to do this but in some cases I have multiple T1s and I get the motioncor step to make a registered template. What steps do I need to perform to get a brainmask from one

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

Hi Kasper, short answer: yes. long answer 1. yes 2. yes (you need to create a table in cross sectional format (no fsid-base column) and the fsid needs to be the tp.long.base names for baseline visit. the path should point to where these *.long.* directories are located). 2. yes (fsaverage

[Freesurfer] Cross sectional analysis of a longitudinal data

Dear FreeSurfer experts, We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start

Re: [Freesurfer] selxavg3-sess question

Dear. Freesurfer experts. Hi. I'm pretty sure that this error is due to the different number of slices in different runs I ran preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_Retino -nosmmth -per-run -force Then I ran selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile I thought

Re: [Freesurfer] Patch for ribbon.mgz failure

Hi Doug, I copied the mri_segstats patch you provided to my freesurfer/bin location and reran the pipeline. However, I'm getting the same issue. Autorecon2 seems unable to create the ribbon.mgz file. Do you have any other suggestions for fixing this error? Also, can you explain what the

Re: [Freesurfer] System crash by extremely much generated output v6 beta-Repost

20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc. hth d On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) wrote: > Hi developers, > > Could you please help me out

[Freesurfer] System crash by extremely much generated output v6 beta-Repost

Hi developers, Could you please help me out on this problem. Should I upload the data? Cheers, Ed Begin forwarded message: From: Ed Gronenschild > Subject: System crash by extremely much generated output

[Freesurfer] Fsaverage

Dear FreeSurfer experts, In regard to fsaverage, we are wondering whether it is recommended to use the default fsaverage or if a new fsaverage should be created for the individual dataset. If there are no recommendations, what are the advantages and disadvantages? Best regards, Kasper Jessen MD,