Dear Afni experts
I'm trying to generate AFNI BRIKS from EPI data which were acquired on a 3T Siemens Trio system. I used Dimon off-line within the directory that has the scans:
Dimon -infile_prefix image -dicom_org -GERT_Reco -quit
280 volumes were detected
The output of output of ./GERT_Reco_dicom
to3d: AFNI version=AFNI_2007_05_29_1644 (Aug 10 2007) [32-bit]
++ Authored by: RW Cox
++ Counting images: total=5600 2D slices
** Number of slices on command line = 5600
** Number of slices needed for -time: = 280
** Something is wrong with your command line!
Only when I changed the to3d command line of GERT_Reco_dicom
from
to3d -prefix ${OutPrefix}_run_015 \
-time:zt 1 280 2.0sec alt+z \
-@ < dimon.files.run.015
to
to3d -prefix ${OutPrefix}_run_015 \
-time:zt 20 280 2.0sec alt+z \
-@ < dimon.files.run.015
it worked.
I don´t understand the output of the unchanged script and I don´t know whether the dataset I created with the changed script are right now. Can anybody tell me why that happend and what to do so that the GERT_Reco_script works correctly?
Another question:
If I just do (instead of using Dimon before)
to3d -prefix to3d -time:zt 20 280 2.0sec alt+z *.IMA
Is the created dataset ok although the files were not ordered before?
I´m sorry for these questions. I really don´t want to bother you too much but I´m new to AFNI and processing of fMRI data.
I would really appreciate any help!!
Thank you in advance!
Beate