I've been playing around with reconstruction at higher resolutions and have been getting some unusual behavior so I decided to do some testing on bert.
I convert bert to 0.7mm isotropic and 366 slices with:
mri_convert -cs 0.7 ~/subjects/bert/mri/orig ~/subjects/bert0.7/mri/orig
Then I fired up recon-all. Bert's surface came out beautifully without doing any manual editing. There are 276,245 nodes in the surface instead of 137,497 when reconstructed at 1.0mm. The inflated surface also looks a bit more convoluted at 0.7mm than at 1.0mm.
However when I tried to recon bert at 0.5, mri_watershed gave some interesting errors:
Skull Stripping Thu Sep 1 19:07:40 EDT 2005 /misc/radium0/adamt/subjects/bert0.5/mri mri_watershed T1 brain
************************************************************ The input file is T1 The output file is brain If this is incorrect, please exit quickly the program (Ctl-C)
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=252 y=303 z=228 r=259 first estimation of the main basin volume: 73641890 voxels Error w=White Matter =Intensity too high (>240)...valid input ? warning: non-standard value for imnr1 (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for x (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for y (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for thick (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for psiz (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.inf o ERROR: mri_watershed exited with non-zero status
Why would resampling to 0.5mm affect white matter intensity?
Thanks, -Adam
--- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370
I installed Freesurfer on a G5 Tiger Mac, but mri_convert and mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a Siemens Trio 3T) as DICOM files. Has anyone else encountered this?
Other programs can read the DICOM files just fine.
keith
Keith,
Can you tell me the command line use to attempt the conversion?
It should be possible to convert DICOMS from a Siemens Trio 3T.
Try this command-line, assuming the filename of the first slice of the structural run is called 958000-2-1.dcm:
mri_convert -it dicom -ot mgz 958000-2-1.dcm 002.mgz
This should produce a file called 002.mgz, which should be placed in the <subjid>/mri/orig directory. If you have additional runs, be sure to name them in the same manner (###.mgz, with preceding zeroes).
Nick
On Tue, 2005-09-27 at 13:42 -0400, Keith Schneider wrote:
I installed Freesurfer on a G5 Tiger Mac, but mri_convert and mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a Siemens Trio 3T) as DICOM files. Has anyone else encountered this?
Other programs can read the DICOM files just fine.
keith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Keith Schneider -
Nick Schmansky -
Thomas, Adam (NIH/NIMH)