Our group are using PET images to study dopamine receptors with AFNI. The receptors are highly concentrated in striatum; we usually see strong signals (values) in the entire region of striatum. In the first step of our analyses, we convert dicom files to AFNI files. However, I noticed that sometime there appear a few voxels with extremely low values in this hot region (striatum). These extreme values produce a lot of troubles in the downstream analyses. This problem happens in a quite number of subjects in our study.
In the attached picture, the voxel at crosshair has a value of 63, which is extremely lower than the surrounding voxels with values about 30000. The voxels with extremely low values are those black dots within the white region of striatum in the picture. I have also converted my dicom files in SPM and got a value of 65597 in the same voxel (I understand the coordinates are different in RAI and LPI spaces). But I have got similar values in most of the other voxels in the striatum comparing AFNI to SPM.
I suspect that it may be related to the format of data storage in computer. During conversion, I have to run “ step(a) *a + step(-a)*(a+65536)” to convert negative values.
Do you have any idea of what is going on? Any suggestion is appreciated.
Best,
Juen

Use this command to convert dicom to AFNI file:
Dimon -infile-patter '*.dcm' -dicom-org -GERT_Reco -Quit
3dcalc -a filename “ step(a) *a + step(-a)*(a+65536)” -datum float

I have just tried to convert dicom to nii in spm and then to afni. The problem is gone if I do this way. But I don't know too much about spm and can n't handle data files in batches in SPM.

Another thing I don’t understand is that the dicom headers says Bits stored = unsigned, length = 2, value=16. Does it mean the max value = 2^16=65536. If it is true, how come does SPM give a voxel value of 65597 which is greater than the max value. Is it related to “length =2”? But this 65597 does make sense to me.

information on data type from dicom header
(Group,Element) TAG Description VR VM Length Value
(0028,0100) Bits Allocated US 1 2 16
(0028,0101) Bits Stored US 1 2 16
(0028,0102) High Bit US 1 2 15
operation system and hardware:
Red Hat Enterprise Linux Server 6.6
Kernel Linux 2.6.32-504.el6.x86_64
Processor: Intel Xeon CPU X5482@3.2GHz



Edited 3 time(s). Last edit at 01/18/2022 12:09PM by Juen.