[Freesurfer] Checking optseq efficiency of a custom par file.

Dear Freesurfer list, Using the optseq2 program, is it possible to calculate the efficiency of a custom par file? I have an fMRI task that will be split into three blocks. I want to calculate the overall efficiency of my overall design byconcatenating the best par file from optimizing each

[Freesurfer] Using the cluster to speed up tractography

Hi Freesurfer experts, I am trying to use the clusters to run BedpostX on a Connectome dataset. Although the job is running now, it is running slowly. It has only got though 18 slices over the last 10 hours: pbsubmit -n 8 -m bl744 -c "bedpostx

Re: [Freesurfer] Compiling dev version in ubuntu 15.10

Is is a warning or an error? Passing the --disable-Werror flag to the configure script will prevent the build from erroring out if it comes across a warning from the compiler. I havent testing on Ubuntu 15 but I will give it a shot early early next week. -Zeke > I'm preparing to migrate over to

Re: [Freesurfer] mri_convert with --like and -rt options

Hi Bruce,Thank you for response. This is the output message:$ mri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gzmri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from

[Freesurfer] R: Re: R: import FS-FAST results in FSL

I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --template? It should be in Tailairach space? Where can I find the template that I should added? Thanks, Stefano

[Freesurfer] mri_convert segmentation fault after tracula update on Linux/glibc-2.20 (Gentoo)

Dear List, I am facing a similar problem as described by Knut Bjuland: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg39745.html I could not find a public reply in the mailing list archives. Therefore I would like to know whether it would be safe to either downgrade

[Freesurfer] mri_convert with --like and -rt options

Dear all, I wish to know whether mri_convert provide a nifty way to reslice and crop a NIFTI image with labels (positive integers) with “—like” and “-rt” options. It seems like “—like” option overrides “-rt” option, thus the result from such a command: > mri_convert -rt nearest —like

Re: [Freesurfer] FreeSurfer and OpenMP

It is -openmp 8 Delete the less than and greater than characters around the 8 > On 16 Oct 2015, at 3:25 PM, Linda BOUMGHAR wrote: > > I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : > recon-all -all -i >

Re: [Freesurfer] mri_convert with --like and -rt options

Dear freesurfer developers, Following the previous e-mail, it seems like a variable handling bug. From the mri_convert.c, lines from 2588 to 2606 appear to be the part that handles “out_like” option. the variable “resample_type_val” in line 2605 should contain the user-specified value, but it

[Freesurfer] SOLVED - mri_convert segmentation fault after tracula update on Linux/glibc-2.20 (Gentoo)

Dear all, in reply to myself as a documentation for others: I tried a recent development version of mri_convert. Instead of crashing, this version instructed me to get a new license file for systems running GNU glibc version greater 2.15. The new license file (.license, not license.txt)

Re: [Freesurfer] pial surface encircling the optical chiasm

Dear experts, I am sending the example subject named chiasma_question.tar.gz to your FTP server. The issue with encircling chiasma is located in slices ~134-140. According to Aparc.a2009s+aseg the tissue is marked as optical chiasm, but also part of it is labeled as left cerebral white

Re: [Freesurfer] FreeSurfer and OpenMP

Hi Linda did you actually include the angle brackets? If so, try without them. And don't you want 4 there instead of 8 (if you have 4 processors)? On Fri, 16 Oct 2015, Linda BOUMGHAR wrote: > I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : > recon-all -all -i >

Re: [Freesurfer] mri_convert with --like and -rt options

Hi Seung-Goo I would have that that your command line would work as is. Can you send us the full screen output? cheers Bruce On Fri, 16 Oct 2015, Seung-Goo KIM wrote: Dear all, I wish to know whether mri_convert provide a nifty way to reslice and crop a NIFTI image with labels (positive

Re: [Freesurfer] Recon-all variations and 3T flag

Hi Kaspar, It doesn't matter where you place the flags in your command line, as long as all of them are there. Also, -s and -subjid are equivalent, so the first two commands would be the same (although the path to your input data is different after the -i flag, and your subject name is

[Freesurfer] recon-all stripped brains

Dear experts, I want to run recon-all on a stripped brains ( T1 images after applying bet tool). Do I need to add any flags to the command recon -all -all subjid       Bests, John   ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo Yes, too many locations at which the estimation algorithm didn't converge is problematic. That might mean that having two random effects is not appropriate for your data. You should try to run the command with just a single random effect for the intercept term: lhstats =