[Freesurfer] -legacy flag in version 5.1

Hi everyone, Just a quick question: I noticed that the -legacy option of recon-all was removed in version 5.1. Is there any way to keep the manual edits and all the processing from previous versions while reprocessing with 5.1? Thank you very much, Marie __

Re: [Freesurfer] Corrections with brainmask volume

Hi Antonella those look good to me. Note that you can't tell defects from a single slice. You need to scroll back and forth and look in different orientations. That said, the surfaces look pretty accurate cheers Bruce On Wed, 13 Jul 2011, Antonella Kis wrote: Good morning Bruce,   I am  c

[Freesurfer] reg-feat2anat: correct anat2exf.register.dat only or also func2std?

Dear experts, I am using reg-feat2anat to register my functional data from FSL to anatomical and starndard space in Freesurfer. For some subjects the registration is bad. I can easily fix anat2exf.register.dat. However, as specified in reg-feat2anat ‹help, I know that the registration failed as

Re: [Freesurfer] tracula - fix bad bbregister's

Hi Greg, You can do the following to skip eddy current correction and intra subject registration: trac-all -inter -masks -tensor -prior -c /path/to/configurationfile/config_file If you want to get tracula based files for the bbregister you've run with manual fixes, can you please let me know the

[Freesurfer] error messages in running mri_convert

Hi, I used to be able to run command "mri_convert" in the matlab environment through "system" command. Now I received the error messages as below: mri_convert: error while loading shared libraries: requires glibc 2.5 or later dynamic linker Any suggestions ? Is it related to the new update of fr

Re: [Freesurfer] Corrections with white matter

Hi Antonella, what format are the attachments in? They don't have an extension Bruce On Wed, 13 Jul 2011, Antonella Kis wrote:  Hi Bruce, Sorry to bother you again. I am doing my corrections for the white matter and I have few slides where I am not sure what should I do. On the slice no. 8

Re: [Freesurfer] Corrections with white matter

Hi Bruce, Thanks again for helping so much. But how about the example in the tutorial * FsTutorial/WhiteMatterEdits.I was following the example in how to fill the cutting into for yellow line. There is mentioned only to open the brainmask and wm.mgz and switching/checking between t

Re: [Freesurfer] Corrections with white matter

yes, the brainmask would be fine. The wm.mgz is to diagnose what went wrong, but the brainmask tells you whether it is right or not On Wed, 13 Jul 2011, Antonella Kis wrote:  Hi Bruce, Thanks again for helping so much. But how about the example in the tutorial * FsTutorial/WhiteMatterEdits

[Freesurfer] longitudinal base creation error

Hi all, I'm trying to analyze longitudinal data with for a subject with six time points. However, when I try to create a within-subject template using all six time points, I get the following error message on TP 3: Resolution: 0 Iteration(single-prec): 1MRIalloc(256, 256, 256): could not alloca

Re: [Freesurfer] longitudinal base creation error

Hi Jessica, you need more memory. What FS version do you use, I think more recent versions of mri_robust_template are a little less memory hungry. 6 time points are not that many. I registered 15 on my machine recently (I have 32 gig, but usually only a fraction of that is free). Martin On Wed