[Freesurfer] registering a segmentation from one time-point to another

2010-08-11 Thread Mehul Sampat
Hi Folks, I have two MR scans per subject. Lesions (white matter hypo-intensities) have been manually outlined for the first time-point. I would like to create a lesion mask for the 2nd time-point. But instead of starting from scratch, I would like to use the lesion-mask from the 1st time-point a

[Freesurfer] Curvature of the Corpus Callosum in Schizophrenia

2010-08-11 Thread Alan Francis
Hi All: Does a lower score on the curvature of the CC (as done by FreeSurfer) imply that the Corpus Callosum is more curved or is it the other way around? If I am not making any sense in my previous statement, a simpler question would be : What do the scores on the curvature index mean for the sh

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18

2010-08-11 Thread Bruce Fischl
Hi Jeff, we autoamtically segment the cc from an anatomical, which would probably be a more accurate measure. cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote: > Sure. Right now I would like to extract the corpus callosum, as defined > by DTI. After some image arithmetic and

[Freesurfer] 4PM FSFAST Users Group Meetings

2010-08-11 Thread Douglas N Greve
This is another reminder of the meeting today. NOTE 4PM! The slides are in the same location http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt mtg will go from 4-530 doug > > > Douglas N Greve wrote: > > To clarify, the material covered should be about the same in all the > > meetings, so n

Re: [Freesurfer] LGN and Heschl's gyrus in freesurfer

2010-08-11 Thread Bruce Fischl
Hi Ri, 1) No, sorry. 2) Yes, mri_ms_fitparms generates the parameter maps if you give it at least two FLASH acquisitions with different flip angles. cheers Bruce On Wed, 11 Aug 2010 rida...@mail.med.upenn.edu wrote: > Hello All, > > I have two questions - > > 1) Is there an LGN label or ROI i

[Freesurfer] using matlab loops for MRIwrite

2010-08-11 Thread corinna bauer
Is there a way to use a loop with MRIwrite such that each subject's output has a different name? Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

[Freesurfer] LGN and Heschl's gyrus in freesurfer

2010-08-11 Thread ridatta
Hello All, I have two questions - 1) Is there an LGN label or ROI in freesurfer ? 2) Is this implemented in freesurfer ? Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: a possible marker for primary cortex and hemispheric differences. Sigalovsky IS, Fisch

[Freesurfer] autorecon2

2010-08-11 Thread Mareen Kussatz
Hi to all, after correcting white matter problems, we saved the wm as aux volume and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there w