[Freesurfer] mri_ca_label segfaults

Hi, I have an emergency here with recon-all -all on a VIP, which segfaults on mri_ca_label -align -nobigventricles ...I tried to run it from the command line and left out the -nobigventricles argument, since actually the subject has enlarged ventricles, but it didn't help. After running for ab

RE: [Freesurfer] mri_glmfit problem

Dear Doug, Thank you, this is very helpful! I had searched the web and the fs site extensively but did not find anything helpful on this problem before you rescued me. I have some follow up questions: 1. Can the DeMeanFlag be used in qdec (qdec was segfaulting when doing similar analyses and

Re: [Freesurfer] isxconcat-sess question

I've just added something to do this. Add -talxfm fsl-tal.xfm to the cmd line. Live on next dev update. doug Bill Monaco wrote: Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default

[Freesurfer] Re: How to analyze fMRI data with mixed design?

If you are using the 4-column par file, then just code them as separate, overlapping events, ie. If condition 1 is the block (lasting 10 sec) and condition 2 is the event (lasting 2 sec), then 0 1 10 1 ---> starts at t=0, lasts 10 sec 0 22 1 > starts att=0, lasts 2 sec 5 2

[Freesurfer] more de-meaning

Hi Chistophe, I'm not surprised by your results as it is very likely that DIQ and F1 have non-zero means. If you were to demean them, then the no-variable analysis would be the same as the with-variable analysis. I actually just sent an email to the Freesurfer list on this topic of demeaning

Re: [Freesurfer] mri_glmfit problem

The problem is that there is a strong correlation in the two continuous variables due to their large non-zero means. The knee-jerk reaction is to simply demean the variables which is sometimes the right thing to do and sometimes not. In this case, I think it is ok because you are using DOSS.

[Freesurfer] isxconcat-sess question

Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default is mri/transforms/talairach.xfm, but I want it to use one I had outputted from a previous processing step - mri/transforms/fsl-ta1.xf

[Freesurfer] How to analyze fMRI data with mixed design?

Dear, Dr. Greve: I hope I don't bother you too much. But I'm wondering about how to analyze mixed blocked/event related design with FSFAST. In our experiment, we have two blocked conditions and three event-related conditions in every block. We are not sure how to write the parfiles and construct t