Hi,
Ran into an odd problem with some of our scans. After processing the dicoms with recon-all autorecon2, we open the brain.mgz and T1.mgz images in tkmedit. The brain.mgz image tends to have terrible contrast.
The problem seems to be the 'colorscale' for the image. The max values are around 185 (as compared to 244-254 for images acquired using a different scan protocol). Resetting the max to 254 fixes the problem.
I am wondering if this indicates something went wrong in the automatic generation of the brain image?
How would you go about forcing tkmedit to have the max value be 254 at startup (so the lab tech doesn't have to manually reset this each time she loads the image)? Include a tcl script on the command-line with "SetVolumeMinMax 0 254" in it? Tkmedit reads the min and max values for the volumes when it loads them, correct?
Note we only see this problem on some scans, not all. Also, we have scans from several projects/magnets/protocols. It is only one magnet/protocol where we see the problem.
Thanks!
details: FreeSurfer v3.0.3 on FC4. The scans in question are from a Siemens machine with the following specs (output of mri_convert): Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel SonataVision Date and time StudyDate 20060429 StudyTime 093246.125000 SeriesTime 110508.984000 AcqTime 105807.800018 Acquisition parameters PulseSeq *tfl3d1_ns Protocol unknown PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.93 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.4460 179.1284 108.3390 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 160 Vc 0.0209 -0.9998 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9998 -0.0209 0.0000 VolCenter -1.8558 49.4811 -19.6610 TransferSyntaxUID 1.2.840.10008.1.2.1
-------------------------------------- I'm only in it for the glory.
Glenn Lawyer < +352 661 967 244 < Instituttgruppe for psykiatri < Postboks 1130 Blindern < 0318 Oslo <
< http://folk.uio.no/davidgl >
<><><><><><><><><><><:)
Hi Glenn,
I think it just depends on whether things like the orbital fat got stripped by the skull stripping. Nothing really to do with the intrinsic tissue contrast. Kevin: maybe you can put something in to allow the user to specify the max?
Bruce On Mon, 27 Nov 2006, Glenn Lawyer wrote:
Hi,
Ran into an odd problem with some of our scans. After processing the dicoms with recon-all autorecon2, we open the brain.mgz and T1.mgz images in tkmedit. The brain.mgz image tends to have terrible contrast.
The problem seems to be the 'colorscale' for the image. The max values are around 185 (as compared to 244-254 for images acquired using a different scan protocol). Resetting the max to 254 fixes the problem.
I am wondering if this indicates something went wrong in the automatic generation of the brain image?
How would you go about forcing tkmedit to have the max value be 254 at startup (so the lab tech doesn't have to manually reset this each time she loads the image)? Include a tcl script on the command-line with "SetVolumeMinMax 0 254" in it? Tkmedit reads the min and max values for the volumes when it loads them, correct?
Note we only see this problem on some scans, not all. Also, we have scans from several projects/magnets/protocols. It is only one magnet/protocol where we see the problem.
Thanks!
details: FreeSurfer v3.0.3 on FC4. The scans in question are from a Siemens machine with the following specs (output of mri_convert): Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel SonataVision Date and time StudyDate 20060429 StudyTime 093246.125000 SeriesTime 110508.984000 AcqTime 105807.800018 Acquisition parameters PulseSeq *tfl3d1_ns Protocol unknown PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.93 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.4460 179.1284 108.3390 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 160 Vc 0.0209 -0.9998 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9998 -0.0209 0.0000 VolCenter -1.8558 49.4811 -19.6610 TransferSyntaxUID 1.2.840.10008.1.2.1
I'm only in it for the glory.
Glenn Lawyer < +352 661 967 244 < Instituttgruppe for psykiatri < Postboks 1130 Blindern < 0318 Oslo <
< http://folk.uio.no/davidgl >
<><><><><><><><><><><:)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can use the -mm-main option:
-mm-main <min> <max> : color scale min and max for main volume -mm-aux <min> <max> : color scale min and max for aux volume
e.g.
$ tkmedit bert T1.mgz -mm-main 0 255
On Mon, Nov 27, 2006 at 07:35:18AM -0500, Bruce Fischl wrote:
Hi Glenn,
I think it just depends on whether things like the orbital fat got stripped by the skull stripping. Nothing really to do with the intrinsic tissue contrast. Kevin: maybe you can put something in to allow the user to specify the max?
Bruce On Mon, 27 Nov 2006, Glenn Lawyer wrote:
Hi,
Ran into an odd problem with some of our scans. After processing the dicoms with recon-all autorecon2, we open the brain.mgz and T1.mgz images in tkmedit. The brain.mgz image tends to have terrible contrast.
The problem seems to be the 'colorscale' for the image. The max values are around 185 (as compared to 244-254 for images acquired using a different scan protocol). Resetting the max to 254 fixes the problem.
I am wondering if this indicates something went wrong in the automatic generation of the brain image?
How would you go about forcing tkmedit to have the max value be 254 at startup (so the lab tech doesn't have to manually reset this each time she loads the image)? Include a tcl script on the command-line with "SetVolumeMinMax 0 254" in it? Tkmedit reads the min and max values for the volumes when it loads them, correct?
Note we only see this problem on some scans, not all. Also, we have scans from several projects/magnets/protocols. It is only one magnet/protocol where we see the problem.
Thanks!
details: FreeSurfer v3.0.3 on FC4. The scans in question are from a Siemens machine with the following specs (output of mri_convert): Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel SonataVision Date and time StudyDate 20060429 StudyTime 093246.125000 SeriesTime 110508.984000 AcqTime 105807.800018 Acquisition parameters PulseSeq *tfl3d1_ns Protocol unknown PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.93 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.4460 179.1284 108.3390 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 160 Vc 0.0209 -0.9998 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9998 -0.0209 0.0000 VolCenter -1.8558 49.4811 -19.6610 TransferSyntaxUID 1.2.840.10008.1.2.1
I'm only in it for the glory.
Glenn Lawyer < +352 661 967 244 < Instituttgruppe for psykiatri < Postboks 1130 Blindern < 0318 Oslo <
< http://folk.uio.no/davidgl >
<><><><><><><><><><><:)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Glenn Lawyer -
Kevin Teich