[Freesurfer] slice thickness

2008-01-26 Thread Brian C. Schweinsburg, Ph.D.
I have an older dataset with .938 x .938 x 2mm resolution but good contrast and SNR. In previous posts, I have seen recommendations to not exceed 1.5 mm thickness for z-plane. I was wondering if this resolution was equally problematic for volume (aseg) labeling, similar to the surface path. Thanks

Re: [Freesurfer] slice thickness

2008-01-26 Thread Bruce Fischl
Hi Brian, no, the aseg should be fine. The truth is that the surfaces will probably work as well, but the thickness estimates probably won't be terribly good. It should be ok for functional overlay and inter-subject averaging though. cheers, Bruce On Sat, 26 Jan 2008, Brian C. Schweinsburg

Re: [Freesurfer] slice thickness

2008-01-26 Thread Brian C. Schweinsburg, Ph.D.
Thanks Bruce. I'll give it a try then. Brian On 1/26/08 10:15 AM, "Bruce Fischl" <[EMAIL PROTECTED]> wrote: > Hi Brian, > > no, the aseg should be fine. The truth is that the surfaces will probably > work as well, but the thickness estimates probably won't be terribly > good. It should be ok fo

[Freesurfer] recon-all error, COR-.info...

2008-01-26 Thread Cameron Ellis
Hi, I keep getting an error when I submit jobs to seychelles that a COR-.info file cannot be found. Do you know why this would be? I pasted the full command and error log below. Thanks! Cameron recon-all -i /space/grouch/4/users/ponce/ponce_002d2/3danat/003 -i /space/grouch/4/users/ponce/ponce_

Re: [Freesurfer] recon-all error, COR-.info...

2008-01-26 Thread Bruce Fischl
what is in space/grouch/4/users/ponce/ponce_002d2/3danat/003? If they are dicoms try giving it one slice in the right series instead of the whole directory On Sat, 26 Jan 2008, Cameron Ellis wrote: Hi, I keep getting an error when I submit jobs to seychelles that a COR-.info file cannot be fou

Re: [Freesurfer] Labelling Results on Tksurfer

2008-01-26 Thread Bruce Fischl
Hi Christine, what subject are you overlaying the results on? If it's fsaverage (our average subject) then it should have ?h.aparc.annot files in the label subdirectory that you can load file->label->import annotation. cheers, Bruce On Fri, 25 Jan 2008 [EMAIL PROTECTED] wrote: Hi I am us