Re: [Freesurfer] too much white matter

Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: "ckuehn" An: "Freesurfer support list" Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, yes, it is an mp2rag

Re: [Freesurfer] correction for field dishomogeneity

Hi Clelia, I think the reviewer might refer to the -3T flag of recon-all which enables 3T-specific NU intensity correction parameters and usage of a special atlas for Talairach alignment. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im

Re: [Freesurfer] too much white matter

glad to hear it Bruce On Mon, 6 Jul 2015, Clara Kühn wrote: Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: "ckuehn" An: "Freesurfer support list" Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Free

[Freesurfer] feat statistics on surface

Hi Freesurfer experts, I am still trying to resolve the problem detailed below. It seems my version of reg-feat2anat is not working properly since it does not created the anat2exf.register.dat file needed to view fmri data analysed with FSL on the subjects native surface in FS. Doug posted a

Re: [Freesurfer] TRACULA analyses in glmfit

Hi Pedro - The point-wise stats from tracula are a 1D sequence of values, so they cannot be analyzed with functions that work on 2D data on the surface or 3D data in the volume. At present, you'd have to do a seperate analysis for every point along the tract. It's on my list to implement a mo

[Freesurfer] couple TRACULA questions

Hi Anastasia, We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA.  Is a paper on the longitudinal aspect of TRACULA in the works? If we have multiple dMRI runs/series per imaging session, do we need to merge/concatenate thos

Re: [Freesurfer] couple TRACULA questions

Hi Michael - Thanks for finding longitudinal tracula attractive! :) The paper is under review. There's an ISMRM abstract that I can send you. About the cluster customization: bedpostx_mgh and fsl_sub_mgh are supersets of bedpostx and fsl_sub, so they have all the original functionality of th

Re: [Freesurfer] couple TRACULA questions

Forgot to reply re: merging. You have to merge them yourselves, sorry. On Mon, 6 Jul 2015, Harms, Michael wrote: Hi Anastasia, We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA.  Is a paper on the longitudinal aspect of TRACULA i

Re: [Freesurfer] longitudinal analysis

Hi Yawu, no, that would be the simple average. Temporal average is the linear fit (within each subject) evaluated at the mid time. So if you had 10 time points at the same day and 1 a year later, it would look like a .5 years time point. This is used to compute symmetrized percent change, repr

[Freesurfer] Recon-all terminated abruptly

Hello Freesurfer expert Recon abruptly terminated with error message from the recon-all. log: #@# Skull Stripping Mon Jul 6 13:16:25 EDT 2015 /autofs/cluster/scratch/monday/jungmi/anat_subjects/r0401AG/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas

Re: [Freesurfer] Recon-all terminated abruptly

it sounds like you ran out of memory. Were other things running on the machine at the same time? How much ram does it have? On Mon, 6 Jul 2015, Park, Jung Mi wrote: > Hello Freesurfer expert > > Recon abruptly terminated with error message > > from the recon-all. log: > > #@# Skull Stripping Mon

[Freesurfer] Data visualization

Hi FreeSurfers, I have a question regarding data visualization: Instead of presenting population average cortical thickness overlay of the right hemisphere on the right and of the left hemisphere on the left, I’d like to show thickness data from epileptogenic hemisphere on one side (let’s say l

[Freesurfer] convert FS volume in scanner space

Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates.

Re: [Freesurfer] TRACULA analyses in glmfit

Hi Anastasia, Thanks for the clarification. I am happy to hear that you are working on that! As the byvoxel data includes MNI coordinates, I though it could be possible to assemble them to MNI 3D space. Thanks again! Pedro Rosa. On Monday, July 6, 2015 at 12:19 PM, Anastasia Yendiki wrote: >

Re: [Freesurfer] convert FS volume in scanner space

Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the "reslice like" and "resample type" flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: > Dear FreeSurfers, >

Re: [Freesurfer] isxconcat-sess

Hi Surfers and Doug, I was trying to average two scan sessions of the same subject and isxconcat-sess under dev-env failed again. This time I get this message: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.

[Freesurfer] (no subject)

Hello Freesurfers I meet a problem in calculate Lgi I run fs in vituralBOX, matlab is installed. At the begining everything seems fine .but error come in "make_outer_surface". The details are in below. = xubuntu-VirtualBox:~> recon-all -s test001 -loc

Re: [Freesurfer] (no subject)

On the surface it seems like you moved the FS directory from one pathway to another. If you place FS back into your applications folder, it may work. Also, if you have Matlab 2014b or 2015a installed, it won’t work. You need 2012b-2014a for the process to run. Hope this helps in any way. Noah

Re: [Freesurfer] (no subject)

THX for your response. I have never move fs files. but i had a MATLAB 2011b, because of the virtual machine`s 32 bit. May this do harm? Or I don't configure the mat lab rightly? here is the startup.m in ~/fsuser % FreeSurfer -% fshome = getenv('FREESURF