[Freesurfer] (un)successfully extracted surfaces from FBIRN traveling subjects?

2012-11-03 Thread Forrest Sheng Bao
Hi, Has anyone (un)successfully extracted surfaces from FBIRN traveling subjects? I just tried on the first 5 subjects of FBIRN traveling subjects Phase I. To every subject, the surfaces extracted from data sampled at Iowa (scans 1 and 2), Duke (scans 1 and 2) and UCI (scan 1) do not look well. S

[Freesurfer] label value 0 in annot file

2011-07-31 Thread Forrest Sheng Bao
hi, I noticed an interesting thing today. I used read_annotation function in matlab to load an .annot file, i.e., [Vertexes,Label,Colortable]=read_annotation(AnnotFile); But some labels in Labels were 0's. They did not appear in the 5th column of Colortable.table. And 0 was the only label that i

[Freesurfer] mri_convert generates different mgz from nii and nii.gz

2011-08-15 Thread Forrest Sheng Bao
hi there, i noticed a strange problem tonight. I had a .nii.gz file. I used mri_convert to convert it into a .mgz file. I also used gzip to unzip the .nii.gz file and then used mri_convert again to get another .mgz file. But the two .mgz files have different md5 sums. Does anyone know what caused

Re: [Freesurfer] mri_convert generates different mgz from nii and nii.gz

2011-08-16 Thread Forrest Sheng Bao
line gunzip and the libraries > > cheers > Bruce > > On Mon, 15 Aug 2011, Forrest Sheng Bao wrote: > > hi there, >> >> i noticed a strange problem tonight. I had a .nii.gz file. I used >> mri_convert to convert it into a .mgz file. I also used gzip to unzip

[Freesurfer] files in surf and label subfolders in a subject's folder

2011-10-31 Thread Forrest Sheng Bao
hi, I wonder whether there is a document describing files in surf and label subfolders in a subject's folder. I wanna know what kind of information is stored in each of those files. Cheers, Forrest ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] different vertexes and faces on pial and inflated surface of the same hemisphere

2011-04-03 Thread Forrest Sheng Bao
hi all, I encountered a strange problem today. I used recon-all -all to get surfaces of a subject. I have no problem with his/her left hemisphere. But for the right hemisphere, the numbers of vertexes and faces of pial surface are different from those of the inflated surface. I checked the heade