[Freesurfer] OHBM Brainhack registration is open!

External Email - Use Caution Hey all, The OHBM Open Science Special Interest Group (OS-SIG) is very happy to announce: Registration is now open for the 2020 OHBM Brainhack (the hackathon organized by the OS-SIG) that will be held online, Jun

[Freesurfer] Permutation Simulation Question

External Email - Use Caution Hello FreeSurfer Experts, When we specify the number of spaces in running permutation simulation (i.e., 2spaces or 3spaces), does the program use a Bonferroni adjustment to correct? I’ve seen a couple references to Bonferroni correction in the wiki p

[Freesurfer] qcache error

Hi FreeSurfer team, I am trying to run qcache but it is exiting with errors because it is not able to find files in the fsaverage/surf directory. I looked in $FREESURFER_HOME/subjects/fsaverage and there is indeed not a surf folder. Should I use one of the other directories like fsaverage3? Th

Re: [Freesurfer] Group Analysis Covariates

ot;) are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read,

Re: [Freesurfer] Permutation Simulation Question

Yes, bonferroni On 5/22/2020 11:46 AM, Purcell, Juliann wrote: External Email - Use Caution Hello FreeSurfer Experts, When we specify the number of spaces in running permutation simulation (i.e., 2spaces or 3spaces), does the program use a Bonferroni adjustment to correct? I’ve see

Re: [Freesurfer] qcache error

It should be restored now, sorry for the problem On 5/22/2020 11:49 AM, Wang, Lily wrote: Hi FreeSurfer team, I am trying to run qcache but it is exiting with errors because it is not able to find files in the fsaverage/surf directory. I looked in $FREESURFER_HOME/subjects/fsaverage and there

[Freesurfer] missing files in he v6 fsaverage on the Martinos Center network

Sorry, I accidentally deleted some files from the v6 fsaverage located on the Martinos Center network. They have been restored, but it might have caused your recon-all process to fail if you had one running last night. Have a good weekend doug ___ F

Re: [Freesurfer] Group Analysis Covariates

(the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return

Re: [Freesurfer] Freesurfer 7.1 hires error

Hi Richard, the conclusion among us is that you have run out of memory. I'm not sure how much you will need, but with both hires and FLAIR, it will be a lot On 5/21/2020 9:35 AM, Jones, Richard wrote: External Email - Use Caution I ran freesurfer 7.1 with the following options:- -i

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I had the identical problem (failure at segmentation stage, as described below) in 4 subjects of my dataset. I have no possibility to run analyses on a linux machine… Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to

[Freesurfer] Are my slice-time corrected files being used in selxavg3-sess?

External Email - Use Caution Hi all, There was some ambiguity in communication from a previous MR technician regarding the slice ordering in our BOLD data. preproc-sess was applied to our data: preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder up -f

Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

Hi Antonin, Thanks for the report. We’ll look into this. Best, Ruopeng > On May 22, 2020, at 2:42 PM, Antonín Škoch wrote: > > External Email - Use Caution > > > Dear experts, > > I want to use freeview for viewing Gordon surface labels on inflated surface > with custom col

[Freesurfer] freeview is RAM greedy in version 7.1.0

External Email - Use Caution Dear experts, I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191

Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

External Email - Use Caution Please also let us know the version of the OS you are comparing running both the 6.0.0 and 7.1.0 release on. - R. On May 22, 2020, at 14:49, Ruopeng Wang wrote:Hi Antonin,Thanks for the report. We’ll look into this.Best,R