Concatenating DWI data

AFNI Message Board
1

I have a question about DTI analysis acquired on the 3T.

In this I have 2 sessions of DTI ( DTI-1, DTI-2) for each subject.
I am using AFNI FATCAT TORTOISE pipeline. To get DTI volume and b-vec files from dicom files, '‘fat_proc_convert_dcm_dwis’ is performed with DTI-1 and DTI-2 separately. Output will be 2 sets of DTI data, each of which have dwi.nii.gz, dwi_bval.dat, dwi_cmd.txt, dwi_cvec.dat, dwi_matA.dat, dwi_matT.dat and dwi_rvec.dat. Now I need to concatenate the data to run the analysis, which means every files from two sets should be converted to just one set.

Is there any way to do this?

Thanks

Jung

2

Hi-

Let’s say you have a directory called TOP_DIR, and inside of it are the separate directories of your dicoms to be glued togehter. Then something like:


fat_proc_convert_dcm_dwis -indir "./TOP_DIR/*" -prefix OUTPUT

should produce just one DWI output?

–pt

3

In the TOP_DIR, I have two directories (DTI-1 and DTI-2), each directories has DWI dicom files.

I ran fat_proc_convert_dcm_dwis -indir “./TOP_DIR/DTI-1” -prefix ./TOP_DIR/DTI-1/DWI/dwi1 and
fat_proc_convert_dcm_dwis -indir “./TOP_DIR/DTI-2” -prefix ./TOP_DIR/DTI-1/DWI/dwi2

I obtained
in the ./TOP_DIR/DTI-1/DWI/, dwi1.nii.gz, dwi1_bval.dat, dwi1_cmd.txt, dwi1_cvec.dat, dwi1_matA.dat, dwi1_matT.dat and dwi1_rvec.dat
in the ./TOP_DIR/DTI-2/DWI/, dwi2.nii.gz, dwi2_bval.dat, dwi2_cmd.txt, dwi2_cvec.dat, dwi2_matA.dat, dwi2_matT.dat and dwi2_rvec.dat

now I would like to concatenate two results above into one result, for example,

in the ./TOP_DIR/DTI-con/DWI/, dwi_con.nii.gz, dwi_con_bval.dat, dwi_con_cmd.txt, dwi_con_cvec.dat, dwi_con_matA.dat, dwi_con_matT.dat and dwi_con_rvec.dat

I am still not sure if 1) I need to concatenate them at the DICOM level and do fat_proc_convert_dcm_dwis, or
2) fat_proc_convert_dcm_dwis first and concatenate them ( I mentioned above)?

Also which command or which method can perform this?

Jung

4

Did you try the command I suggested in my post?:


fat_proc_convert_dcm_dwis -indir "./TOP_DIR/*" -prefix OUTPUT

What does that produce for you?

–pt

5

Yes, this command worked well for concatenating data.

Thanks