[Freesurfer] mac gcc builds

Notice to all mac FS developers, GCC builds on macOS have become increasingly difficult to maintain, mostly due to brew issues and gcc-version incompatibles with dependencies. Clang is now the "official" mac compiler for freesurfer. The external prebuilt packages (at https://surfer.nmr.mgh.harv

Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

External Email - Use Caution Hi Bram, Thanks very much for the detailed explanation. I understand that I have to edit the wm first, and only work on the brain.finalsurfs if wm edit does not help. I tried the command you suggested (recon-all -s -white -smooth2 -inflate2 -curvHK -

[Freesurfer] Cortical thickness values on a vertex base level

External Email - Use Caution Dear developers, For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain. Is it possible that, in addition to the significance

Re: [Freesurfer] nuisance factors

can you send your command line, terminal output, and the fsgd file? On 10/30/19 4:23 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Thank you very much! That makes a lot of sense. > However, when I tried to run the analysis using that contrast (0.5 0.5 > -0.5 -0.5 0

[Freesurfer] nuisance factors

External Email - Use Caution Thank you very much! That makes a lot of sense. However, when I tried to run the analysis using that contrast (0.5 0.5 -0.5 -0.5 0), the following error appears: dimension mismatch between X and contrast Contrasts/age_sim.mtx X has 4 cols, C h

Re: [Freesurfer] Matrix is ill-conditioned or badly scaled

The problem is that some of your groups are very small, eg, groups 2 and 4 only have 3 subjects. The way you have it set up, there are four parameters (offset and 3 slopes) for each group. Thus, you are running out of DOFs for those two groups (and not so much better on some of the others). On

[Freesurfer] registration

External Email - Use Caution Instead of mri_cvs_register Which type of registration is more accurate or coparative to this. Best Regards Nader ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] Mapping coordinates from sphere file to ?h.white

I don't know what you mean by "expand this sphere to the fsaverage's white surface". I don't know what fsLR coords are. Please explain further On 10/28/2019 6:58 PM, Oscar Esteban wrote: External Email - Use Caution Dear experts, In the context of the BIDS transforms extension and the

Re: [Freesurfer] FSGD file formatting for Xhemi

I don't understand. What per hemisphere variable? On 10/25/2019 3:15 AM, Jose Graterol wrote: External Email - Use Caution Thanks for your answer. A follow up question: How should I then specify the variable's values per hemisphere while making the FSGD file if I want to add covariates w

Re: [Freesurfer] nuisance factors

You are almost there. In the first step, you would test for an interaction between age and diagnosis in the DODS model with: 0 0 0 0 1 1 -1 -1 If there is no interaction, then you can move to the DOSS model (which includes age) with contrast 0.5 0.5 -0.5 0.5 0 You need that last 0 to account fo

Re: [Freesurfer] question about qdec 'Generate Stats Data Tables'

Sorry, we are not supporint QDEC any more. Try using asegstats2table separately. You can cut and paste the printed asegstats2table command into the shell On 10/29/2019 10:05 AM, ?? wrote: External Email - Use Caution Hello, We had a problem when using QDEC for group analysis. After g

Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through some type of batch server? cheers Bruce On Wed, 30 Oct 2019, Emanuel Alvaredo wrote: External E

Re: [Freesurfer] recon-all -skullstrip issues

I mean to run recon-all from the beginning. It looks like you tried to run just the skull stripping, but it needs some files before that step On 10/28/2019 4:17 PM, Adam Rytina wrote: External Email - Use Caution Hello, what do you mean by the beginning? You mean to download the tutori

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

I'm not sure what you are asking. What do you mean you want to compare the correlation maps between the two groups? If you just want to look at them, then set up contrasts for each. On 10/28/2019 3:36 PM, Nillo, Ryan Michael R wrote: > External Email - Use Caution > > Thanks, Doug. One

Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

External Email - Use Caution Hello Developers! I am getting the same error in several patients (not all). The common error between all of them is this line Waiting for PID 2778 of (2778 2781) to complete... /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fau