Hi, Rick,

Thanks so much for your prompt feedback.

Sorry, those are the dcm files (DICOM). They can be either functional or anatomical dcm files. for instance, in my folder" anatomical", there are many dcm files: image00005.dcm,image00006.dcm,image00007.dcm,image00008.dcm,image00009.dcm,image00010.dcm,....image00150.dcm,

I just tried using the command below,and got outputs: dimon.files.run.010; GERT_Reco_dicom_010;OutBrick_run_010.nii

Dimon -dicom_org -gert_create_dataset -gert_write_as_nifti -infile_pattern 'anatomical/*.dcm'

Several questions: What is the file "GERT_Reco_dicom_002" for? I got some warnings:

*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center : 2.0819 -9.08766 45.4386
Slice-based Center: 3.58128 -7.88988 44.5345


Significant outliers detected in these sub-bricks:
0 1 2 4 45 46 52

How should I handle this, or just ignore this? I have not tried "3dToutcount -save outnam dataset | 1dplot -stdin" in the past. Any good pointers?

I am noted that "if images are wrong, try using '-assume_dicom_mosaic'", how should I use this?

Thanks so much,
J



Edited 1 time(s). Last edit at 12/06/2016 04:44PM by Juan.