rat fMRI, realign | The R-fMRI Network

Submitted by YukiSakai on Mon, 11/30/2015 - 08:56

Dear DPARSFA experts,

Thank you very much for the powerful tool. I think this toolbox could be applied to rat fMRI data and I have several questions.

*If we realign rat fMRI data (X10 space), the output rp~.txt can be simply interpreted as in unit 'mm' and 'degree' in X10 space? Or do we have to change original spm realign function to get the absolute value of motion paramters?

*When we want to couduct the scrubbing in rat fMRI data, how was framewise displacement calculated in DPARSF? Since the method of Power et al. supposed the mean distance from the cerebral cortex to the center of the head as 50mm in order to convert from degrees to mm, we have to change this parameter in my understanding.

Best,

Yuki

Re: [RFMRI] rat fMRI, realign

*******************************************************************************************

Yuki Sakai, M.D., Ph.D.

- Researcher, ATR Brain Information Communication Research Lab. Group.
- Research Assistant Professor, Department of Psychiatry,

　Graduate School of Medical Science, Kyoto Prefectural University of Medicine.

Address: 2-2-2 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0288, Japan
TEL +81-774-95-1250 FAX +81-774-95-1236
E-mail: yuki1209@koto.kpu-m.ac.jp
*******************************************************************************************

2015-11-30 17:56 GMT+09:00 The R-fMRI Network <rfmri.org@gmail.com>:

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By YukiSakai (YukiSakai)
Dear DPARSFA experts,

Thank you very much for the powerful tool. I think this toolbox could be applied to rat fMRI data and I have several questions.

*If we realign rat fMRI data (X10 space), the output rp~.txt can be simply interpreted as in unit 'mm' and 'degree' in X10 space? Or do we have to change original spm realign function to get the absolute value of motion paramters?

*When we want to couduct the scrubbing in rat fMRI data, how was framewise displacement calculated in DPARSF? Since the method of Power et al. supposed the mean distance from the cerebral cortex to the center of the head as 50mm in order to convert from degrees to mm, we have to change this parameter in my understanding.

Best,

Yuki

Online version of this post: http://rfmri.org/content/rat-fmri-realign

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Hi Yuki,

As the calculation is performed in X10 space, you can divide the translation mms by 10, while keep the degrees.

For calculating FD, if 5mm is a good number for rat, then you can divide the reported FD by 10.

By the way, you haven't anesthetized the rats for scanning?

Best,

Chao-Gan

Re: [RFMRI] rat fMRI, realign

Dear Dr. Chao-Gan,

Thank you very much for your kind and quick reply.

I understand. I'll change the parameter in DPARSFA_run considering the size of animal's brain.

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