Group connectometry analysis for mice brain

[wangn...@gmail.com]

Hi Frank,

I know DSI Studio is mainly designed for human brain dMRI analysis, however, it also gives great results  for mice brain dMRI analysis.

I'm working on the group connectometry analysis for mice brain (two groups, control vs disease). After I get all the individual .src files and try to create a connectometry database, I found DSI studio registered all the images to MNI atlas (correct me if I'm wrong), which may not suitable for rodent brain. I'm wondering whether I can choose my own altas, and can still go through the group connectometry analysis.

Thanks,

Nian

[Fang-Cheng Yeh]

Hi Nian,

It is doable but not yet supported in DSI Studio. We would need to
modify QSDR to work on an animal template and create a connectometry
database.

Do you have a mice FA template?

Best regards,
Frank

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[wangn...@gmail.com]

Hi Frank,

Yes, we do have an animal template. I'll send to you tomorrow. 

Thanks,

Nian

[Fang-Cheng Yeh]

Please also send me two sample SRC.gz files so that I can test whether
QSDR work on your dataset.

Best regards,
Frank

[wangn...@gmail.com]

Hi Frank,

Please check dropbox for the two sample SRC.gz files and the FA template (Reg_N.........fa.nii.gz).

If you need any info or related files, please let me know.

Thanks,

Nian 

[Fang-Cheng Yeh]

Hi Nian,

Thanks for sending me the data. I will do my best to make QSDR
work on this animal data (would take one or two weeks)

Best,
Frank

[wangn...@gmail.com]

Hi Frank,

Thank you so much! Let me know if you need further info about the data.

Thanks,

Nian

[pochry...@gmail.com]

Hello,

I would like know if you arrive to adapt QSDR to rodents study?

Cheers,

Chrystelle

[Fang-Cheng Yeh]

Yes, there is a dropdown list in the QSDR reconstruction for
specifying a relevant template for spatial normalization.

Best regards,
Frank

[wangn...@gmail.com]

Hi Frank,

The "Group connectometry analysis" works pretty well with our rodent data using Mac version.  Recently, we acquired higher spatial and angular resolution diffusion MRI dataset (16 objects) and want to do the similar process and have a few issues.

1) We only have 64 Gb RAM in our mac machine, which failed to run "Create a Connectometry Database", then cannot go through to "Group connectometry analysis". I know the mac version can support rodent data analysis (the length threshold are defined by voxel instead of mm).

2) We tried to use the latest DSIstudio Windows Version to process our data (since we have ~700 Gb RAM in our windows computer). It looks like the "Group connectometry analysis" is optimized for human studies, not for rodents since the length unit is still "mm" (correct me if I'm wrong), and we failed to get reasonable results. 

Is it any way we can go through the analysis with DSI studio Windows version which can support the Rodent data?

Or if you have any other suggestions, please let me know.

Thanks for all your help,

Nian 

[Fang-Cheng Yeh]

Hi Nian,

    

    Sorry for my delayed reply.

1) We only have 64 Gb RAM in our mac machine, which failed to run "Create a Connectometry Database", then cannot go through to "Group connectometry analysis". I know the mac version can support rodent data analysis (the length threshold are defined by voxel instead of mm).

You can create the connectometry db in Windows version and analyze it using Mac. Hope this helps resolve this problem.

 

2) We tried to use the latest DSIstudio Windows Version to process our data (since we have ~700 Gb RAM in our windows computer). It looks like the "Group connectometry analysis" is optimized for human studies, not for rodents since the length unit is still "mm" (correct me if I'm wrong), and we failed to get reasonable results. 

Is it any way we can go through the analysis with DSI studio Windows version which can support the Rodent data?

Or if you have any other suggestions, please let me know.

The length unit in group connectometry is using voxel distance, but the maximum length allowed here is only 200 voxels in the current version.

I can relex this limitation and see if this help resolve the issue.

Best,

Frank

[Fang-Cheng Yeh]

Hi Nian,

    I updated DSI Studio (Windows version). If it still does not work for you, please let me know. I can take a look at the data to fix the problem.

Best,

Frank

[Nian Wang]

Hi Frank,

Thanks for the updates. I'll let you know how it goes. 

Thanks again,

Nian

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