Head motion output in DPARSFA

Submitted by leemon on

YAN Chao-Gan

Sun, 11/03/2013 - 01:50

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Hi Meng,
Did you change the SPM version during the test?

I just tested with SPM8 r4667, DPARSF and SPM gave the same results in rp*.txt.

Or, you tested for multiple session data? Have you confirmed the input data are the same?

Best,

Chao-Gan


On Sat, Nov 2, 2013 at 4:40 PM, The R-fMRI Network <rfmri.org@gmail.com> wrote:
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]

By 李猛 (leemon)

Hey, everyone.

I have noticed the rp_*txt created by DPARSFA is quite different form the
standard procedure in both of spm8 and spm12. Has anyone met same problem
before?

All the best
Meng


Online version of this post: http://www.rfmri.org/content/head-motion-output-dparsfa


ktillisch

Sun, 11/03/2013 - 22:30

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Yes, I have found this to be the case. I'd be interested to know the answer as well. Kirsten Tillisch, M.D. Associate Professor Oppenheimer Family Center for Neurobiology of Stress Division of Digestive Diseases David Geffen School of Medicine at UCLA 310 206-6279(Clinical Office) 310 206-0192 (Research Office) From: The R-fMRI Network > Reply-To: The R-fMRI Network > Date: Saturday, November 2, 2013 1:40 PM To: "rfmri.org@rnet.co" > Subject: [RFMRI] Head motion output in DPARSFA [To post a comment, please reply to rfmri.org@gmail.com ABOVE this line] By 李猛 (leemon) Hey, everyone. I have noticed the rp_*txt created by DPARSFA is quite different form the standard procedure in both of spm8 and spm12. Has anyone met same problem before? All the best Meng Online version of this post: http://www.rfmri.org/content/head-motion-output-dparsfa Mail comment ID: http://www.rfmri.org/mailcomment/redirect/%3C31.1702.0.1383424801.eaf62168b4f141f85c5c37119adc5560%40www.rfmri.org%3E ________________________________

YAN Chao-Gan

Mon, 11/04/2013 - 03:50

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Just did a test.

 

Condition 1 and condition 2 is exactly the same.

Condition 3 (maybe this is the way you tested with SPM8 GUI?) has a tiny difference. I am not totally sure where this difference come from. But I am guessing:

1. If realign right follows slice timing by DPARSFA, there will be 3 files in FunImgA folder: a*.nii; a*.mat; ra*.mat. Even for a*.nii, the time of creation and the time of modification is different.

2. The realign step (call SPM) in DPARSFA may already changed some information in a*.nii, and stored something in ra*.mat. Thus, if using SPM8 GUI to perform realign again for this folder, there may be some unintended effect, which will cause this subtle difference.

Could you post a snapshot and details for how you tested the differences?

Best,

Chao-Gan

 

Hi, Chao-Gan

More findings on this issue (DPARSFA (Release=V2.2PRE_120905), SPM8 (4290))

Condition 1: dcm2nii+Slice timing + Realign,  Simens data,

Both of DPARSFA and SPM create the  same RealignParameters.

Condition 2: dcm2nii + Slice timing + Realign,  GE data,

The translations of in RealignParameters are different between DPARSFA and SPM. In this case,  the origin of converted  NIFTI files are different between DPARSFA and SPM8. It could be the reason. Could you help me figure it out? Thanks in advance.

 

Cheers

Meng

 

Simens data GE data

 

 

Hi Meng,

Thanks a lot for your report! Seems dcm2nii (DPARSFA based on it) and SPM output NIfTI files differently for GE data.

The realignment procedure in SPM is highly depend on the origin of the image, thus you will get different realign parameters. However, I guess the "voxel specific head motion" should be the same for the two sets (images and realign parameters). And I think this will not affect the results too much.

Best,

Chao-Gan

Hey, everyone. I have noticed the rp_*txt created by DPARSFA is quite different form the standard procedure in both of spm8 and spm12. Has anyone met same problem before? All the best Meng