AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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August 13, 2007 11:47AM
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

Subject Author Posted

ima to AFNI dataset

Beate August 13, 2007 11:47AM

Re: ima to AFNI dataset

Daniel Glen August 15, 2007 11:23AM

Re: ima to AFNI dataset

Beate August 30, 2007 01:33PM