About the ACPC alignment (align_acpc)

51 views
Skip to first unread message

Xiaoxiao Bai

unread,
Oct 23, 2023, 6:27:47 PM10/23/23
to DSI Studio

Hi Frank,

 I have a question about the "align_acpc" parameter for data reconstructed by QSIPREP. It seems that the processed data in QSIPREP is already aligned with the ACPC orientation. To verify this, I ran two identical reconstruction commands, with the only difference being the value of "align_acpc" set to 1 for the first command and 0 for the second command:

1. singularity exec dsistudio_latest.sif dsi_studio --action=rec --source=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz --method=4 --param0=1.25 --thread_count=8 --align_acpc=1 --dti_no_high_b=0 --check_btable=1 --record_odf=1 --output=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz.ap1.icbm152_adult.fib.gz >> log_rec_ap1.txt

 2. singularity exec dsistudio_latest.sif dsi_studio --action=rec --source=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz --method=4 --param0=1.25 --thread_count=8 --align_acpc=0 --dti_no_high_b=0 --check_btable=1 --record_odf=1 --output=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz.ap0.icbm152_adult.fib.gz >> log_rec_ap0.txt

 For the first command (align_acpc=1), the results of fiber tracking from both the GUI and CLI are the same.

 However, for the second command (align_acpc=0), the results of fiber tracking from the GUI and CLI differ.

Here is the fiber tracking command,

singularity exec dsistudio_latest.sif dsi_studio --action=trk --source=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz.ap1.icbm152_adult.fib.gz --track_id=Frontal_Aslant_Tract_L --seed_count=1000000 --fa_threshold=0 --min_length=30 --max_length=200 --turning_angle=0 --step_size=0 --tolerance=24 --output=sub-01_ses-pre_acq-singleband_dir-AP_run-1_space-T1w_desc-preproc_dwi.src.gz.ap1.icbm152_adult.fib.gz.FATL.tt.gz --export=stat >> log_trk_ap1.txt

Thanks,

Xiaoxiao

Frank Yeh

unread,
Oct 23, 2023, 6:53:58 PM10/23/23
to baix...@gmail.com, DSI Studio
The log output from GUI and CLI may give a hint about why their
results are different.
There are many possible causes that interact with the image orientation.
Best regards,
Frank
> --
> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/65537ff1-796b-4a9a-993b-9c0430578957n%40googlegroups.com.

Bai, Xiaoxiao

unread,
Oct 23, 2023, 7:23:36 PM10/23/23
to Frank Yeh, baixx013, DSI Studio
For qsiprep data, should I set up the align_acpc =0 for the CLI?

Thanks a lot.

Best

Xiaoxiao
From: Frank Yeh <fran...@gmail.com>
Sent: Monday, October 23, 2023 6:53 PM
To: baixx013 <baix...@gmail.com>
Cc: DSI Studio <dsi-s...@googlegroups.com>
Subject: Re: [dsi-studio] About the ACPC alignment (align_acpc)
 
[You don't often get email from fran...@gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]

Frank Yeh

unread,
Oct 23, 2023, 7:33:03 PM10/23/23
to Bai, Xiaoxiao, baixx013, DSI Studio
I would say yes.
Frank

Bai, Xiaoxiao

unread,
Oct 23, 2023, 7:33:51 PM10/23/23
to Frank Yeh, baixx013, DSI Studio
Thanks, Frank.

Have a good evening!

Xiaoxiao
From: Frank Yeh <fran...@gmail.com>
Sent: Monday, October 23, 2023 7:32 PM
To: Bai, Xiaoxiao <xiaoxi...@psu.edu>
Cc: baixx013 <baix...@gmail.com>; DSI Studio <dsi-s...@googlegroups.com>
Reply all
Reply to author
Forward
0 new messages