[Freesurfer] RE: question about qdec analysis

2008-05-04 Thread Teddy Youn
Hi again, I had another question for the listserv about the uses of qdec. After finishing a set of subjects (12 controls and 6 subjects), our group wanted to see if we could use qdec to report the number of voxels that are different (e.g. measuring volume, thickness, etc.) between one group t

[Freesurfer] Fwd: segmentation fault error, mri_ca_register

2008-03-31 Thread Teddy Youn
i incompletely copied the error message from recon-all.log: gca peak Unknown = 0.94091 ( 0) gca peak Left_Inf_Lat_Vent = 0.14709 (39) gca peak CSF = 0.14344 (47) gca peak Left_Accumbens_area = 0.20088 (67) gca peak Left_undetermined = 0.98433 (34) gca peak Left_vessel = 0.32698 (60) gca peak Left_

[Freesurfer] segmentation fault error, mri_ca_register

2008-03-31 Thread Teddy Youn
Hi all, I have a scan of a patient that I've tried troubleshooting via the listserv and fswiki, but with no success. Generally, during mri_ca_register, I end up with a segmentation fault of the following: - gca peak Unknown = 0.94091 ( 0) gca peak Left_Inf_Lat_Vent = 0.14709 (3

[Freesurfer] Re: problems with retaining wm edits using -autorecon2-cp flag

2008-03-05 Thread Teddy Youn
Hi all, another quick question. I don't know if anyone else has encountered this problem, but after making pial, wm and cp edits our group don't seem to retain all our edits. The OtherUsefulFlags wikipage suggests that FS should retain all the edits from a flag that is more upstream in the au

[Freesurfer] question about generating wmparc.stats

2008-03-03 Thread Teddy Youn
Hi again, I had a quick question about generating wmparc.stats. I have tried to run recon3 with the -wmparc flag and have encountered an error where ?h.smoothwm is not being read even though my /surf folder has the files. Below is the output of what occurs in my xterm. We have v4.0.2 of FS o

[Freesurfer] RE: annotation binary files into ascii format

2008-02-28 Thread Teddy Youn
annotation files? Thanks very much, -Teddy Youn Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 [EMAIL PROTECTED] (401)-714-2847 --- Begin Message ---

[Freesurfer] Talairach transformations in tkregister2 and WM editing for aseg.stats

2008-02-01 Thread Teddy Youn
Hi, Our group is currently trying to use FS on a cohort of DAI/TBI patients and have encountered several problems. We recognize the limitations with using FS on brains that may have severe deformation; however, we wanted to get some feedback: 1) When loading the talairach transformation on tk