[Freesurfer] mri_convert with IMA files

2005-04-06 Thread mperry
Hi, I am trying to use mri_convert to convert Siemens .IMA files to COR files. I have tried a few different ways and none seem to be working. Here is what I've tried and the error messages. Do you have any advice? >mri_convert -it siemens <$SUBJECTS_DIR/subjid/mri/orig> mri_convert -it siemen

[Freesurfer] .bhdr file questions

2005-04-06 Thread Nicole Aucoin
Hello, I'm trying to orient bfloat and bshort volumes in 3D Slicer, and to do that, need to calculate the corners of the volumes to calculate an RAS to IJK transform matrix. The .bhdr files that I have contain the top left, top right and bottom right corners, which I'm using as is with the assumpt

[Freesurfer] parcellation

2005-04-06 Thread Wan Park
Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks