Re: [Freesurfer] tkmedit crashes/freezes

2006-08-29 Thread Bruce Fischl
were these processed any differently? The .xdebug_tkmedit should be in pwd wherever you ran it from. Bruce On Tue, 29 Aug 2006, Derin Cobia wrote: Kevin- Yeah, either way. In my infinite wisdom I thought that scrolling slower would help, but not so. Nick- I'm unable to locate a

Re: [Freesurfer] Regarding missing DICOM fields

2006-08-29 Thread Niels Bergsland
Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial

Re: [Freesurfer] tkmedit crashes/freezes

2006-08-29 Thread Derin Cobia
Sorry, visual artifacts- yes (still there), crashing/freezing- no (but I've been trying hard). It's only been about an hour since the update, I'll keep you posted. So, should I worry about the artifacts affecting output? If I scroll through the slices long enough, they eventually all disappear.

Re: [Freesurfer] preprocessing question

2006-08-29 Thread Frederick Klauschen
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the

Re: [Freesurfer] preprocessing question

2006-08-29 Thread Bruce Fischl
Hi Frederick, mri_info will give you the various transformations back to native (i.e. scanner) RAS coords. cheers, Bruce On Tue, 29 Aug 2006, Frederick Klauschen wrote: Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I

Re: [Freesurfer] Regarding missing DICOM fields

2006-08-29 Thread Doug Greve
No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like: mri_probedicom --i slice1.dcm --o slice1.dat slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then

Re: [Freesurfer] Regarding missing DICOM fields

2006-08-29 Thread Niels Bergsland
Thanks for the help Doug! I will let you know how it goes. Niels On 8/29/06, Doug Greve [EMAIL PROTECTED] wrote: No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like: mri_probedicom --i slice1.dcm --o slice1.dat