FA analysis

[ALBERTO BENELLI]

Dear Frank,
this software is amazing and I would like to know how to use its full potential. I am going to run a study to observe changes in White Matter, in particular about FA before and after a treatment. Where can I find useful guidance on how to choose the parameters, what settings to go to in order to perform the analyses and get results? I apologise for these general questions, but I am new in this research field.

Thank you again for your availability and congratulations again for your software.

Alberto

[Frank Yeh]

You can try region-based analysis and also tract-based analysis first following http://dsi-studio.labsolver.org/Manual/how-to-analyze-diffusion-data and see how it goes.

Best regards,

Frank

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[Alberto Benelli]

Thank you so much for these precious informations.

When I try to upload a Nifti file, converted by MRIConvert, the software shows me an issue: “ not a 4D NIFTI FILE”, how can I resolve the problem?

Thanks 

Alberto

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[Frank Yeh]

You may try dcm2nii to convert the files.

Best,

Frank

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[Alberto Benelli]

dcm2nii create many files but on DSI Studio I can open only “DICOM_ep2d_diff_mddw_2.3mm_1_media_20210611154045_13” file.

Having only this file is enough to perform a DTI analysis?

Thanks

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[Frank Yeh]

Please refer to this documents in details: http://dsi-studio.labsolver.org/Manual/Parse-DICOM#TOC-Read-DICOM-Files

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[Alberto Benelli]

I’ve another question about b-value window. What does b-value stand for? 

Thank you again

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[Frank Yeh]

You can find details on diffusion MRI textbooks.

Just google "diffusion mri textbook" and find one

Frank

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[Alberto Benelli]

I should work with nifty file having MNI coordinates but when I try to upload the nifti file, coregisterd before using coregister function on SPM to obtain a file with MNI coordinates, it figures this issue “not a 4D nifti file”. What should I do? Is there another way to upload a MNI file?

Thanks

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[Frank Yeh]

I would suggest you follow the documentation at the DSI Studio website, starting from Step t1.

If you run into "not a 4D nifti file”, then likely the data you have is not DWI. Then you will need to talk to the MR physicist who acquired the data.

Frank

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[Alberto Benelli]

Hi,

I have another question: if I click on the same target track of the the same subject, the “Fiber Tracking" show me always different tracks numbers and I don’t know why. Can you help me?

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[Frank Yeh]

It is expected because of the randomized parameters for parameter saturation.

The track count does not have meaning.

https://www.sciencedirect.com/science/article/pii/S1053811912007306?casa_token=IBEGB8bmtC0AAAAA:HpTH_A4tU2CirRi7MtvWQgIbjTG0bwiYIPBRzLdS92iMqr_V7DTYpmlRzvgyffDPEmGMtV3GgA

You may

Frank

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[Alberto Benelli]

I want to upload all MNI coordinates of the Arcuate_Fasciculus_L into a neuronavigator system, how can I extract them?

[Frank Yeh]

http://dsi-studio.labsolver.org/Manual/export-track-information-for-dbs-focused-ultrasound-or-surgical-navigation

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[ALBERTO BENELLI]

Hi,

I followed the instructions to download images for the neuronavigation, but I cannot upload the T1 in IMA format (an extension of DICOM format for Siemens RM). Can you help me?

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[Frank Yeh]

I am sorry only DICOM format is supported: http://dsi-studio.labsolver.org/Manual/export-track-information-for-dbs-focused-ultrasound-or-surgical-navigation

Best regards,

Frank

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[Alberto Benelli]

Hi Frank,

Thanks again for your support.

How can I investigate the fiber trackers between two or more ROIs? In particular, between subcortical and cortical areas. Which could be the format of the output file with these specific info.? Maybe always .nii? 

I have a second request to you, what could be the FA value associated to a demyelination disease? 

Thank you,

Alberto

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[Frank Yeh]

How can I investigate the fiber trackers between two or more ROIs? In particular, between subcortical and cortical areas.

You can assign these ROIs before fiber tracking: http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Region-of-interest-ROI-region-of-avoidance-ROA-

 

Which could be the format of the output file with these specific info.? Maybe always .nii? 

This depends on how you would like to use the results. 

DSI Studio supports track-based formats (*.trk *.tck *.tt) or voxel-based formats (*.nii)

 

I have a second request to you, what could be the FA value associated to a demyelination disease? 

Hope this helps:

http://dsi-studio.labsolver.org/course/apparent-diffusion-coefficient-and-the-tensor-model#TOC-3.-Biological-interpretation-of-diffusivity-based-measurements

Best regards,

Frank

 

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[Alberto Benelli]

Thank you for these precious info.

Which is the command to visualize the QA, FA, MD, RD VA values?

Thanks again

Alberto

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[Frank Yeh]

The dropdown list on the top of the 3D window can switch between different metrics.

Frank

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[Alberto Benelli]

Hi,

with connecometry analysis option I can run only regression analysis. Which command should I use to run analysis in order to show the common tracks activation between 7 healthy subjects, having their own T1?

How can I observe FA differences between PRE and POST farmacological treatment, on MS patients?

Thanks,

Alberto

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[Frank Yeh]

On Mon, Oct 18, 2021 at 3:16 AM Alberto Benelli <alberto...@stud.unifi.it> wrote:

Hi,

with connecometry analysis option I can run only regression analysis. Which command should I use to run analysis in order to show the common tracks activation between 7 healthy subjects, having their own T1?

I am listing this feature on my to-do list and will let you know once available.

 

How can I observe FA differences between PRE and POST farmacological treatment, on MS patients?

http://dsi-studio.labsolver.org/Manual/diffusion-mri-connectometry#TOC-Scatter-plots

Hope this helps.

Best regards,

Frank

 

[Alberto Benelli]

Hi Frank,

Thank you for the support; I hope that this new function could be implemented soon.

I don’t have clear how obtain the scatterplot and how this should help me to show any differences between pre and post condition. Can you help me?

Alberto

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[Frank Yeh]

I don’t have clear how obtain the scatterplot and how this should help me to show any differences between pre and post condition. Can you help me?

Have you opened the db file in Step T3 and load the connectometry result tt.gz file?

 

Alberto

On 18 Oct 2021, at 19:57, Frank Yeh <fran...@gmail.com> wrote:

On Mon, Oct 18, 2021 at 3:16 AM Alberto Benelli <alberto...@stud.unifi.it> wrote:

Hi,

with connecometry analysis option I can run only regression analysis. Which command should I use to run analysis in order to show the common tracks activation between 7 healthy subjects, having their own T1?

I am listing this feature on my to-do list and will let you know once available.

 

How can I observe FA differences between PRE and POST farmacological treatment, on MS patients?

http://dsi-studio.labsolver.org/Manual/diffusion-mri-connectometry#TOC-Scatter-plots

Hope this helps.

Best regards,

Frank

 

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[Alberto Benelli]

Yes I did it. I don’t be able to find the command to opens the scatterplot. Where can I open it? “TRACTS”—>”STATISTICS” and then?

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[Frank Yeh]

You will need to plot the scatter plot using Excel, MATLAB, or python.

Frank

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[Alberto Benelli]

Hi frank,

How can I  perform TBSS analysis? 

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[Frank Yeh]

TBSS is only available on FSL.

I am sorry DSI Studio doesn't have it.

Frank

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[Alberto Benelli]

Ok, thanks.

Can you espose me all the differences between these two software? 

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[Frank Yeh]

Sorry, there are just too many differences. They are just two different software.

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[Alberto Benelli]

Hi,

I want to check which fiber tracks are involved in L-Hippocampus area. Here, you can observe the L-hippocampus area taken from the atlas showed on the T1 subject. Using the option “fiber tracking" I don’t be able to show fiber tracks associated with this area. Actually, the bundles are behind the T1. How can you can help me to find the way to observed them directly on the T1 subject space, in order to save in NIFTI file?

Thanks 

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[Alberto Benelli]

How can I save all the end points on the cerebral cortex, as NIFTI file and txt file? 

On 25 Nov 2021, at 10:06, Alberto Benelli <albertob...@gmail.com> wrote:

Hi,

I want to check which fiber tracks are involved in L-Hippocampus area. Here, you can observe the L-hippocampus area taken from the atlas showed on the T1 subject. Using the option “fiber tracking" I don’t be able to show fiber tracks associated with this area. Actually, the bundles are behind the T1. How can you can help me to find the way to observed them directly on the T1 subject space, in order to save in NIFTI file?

Thanks 

<Screenshot 2021-11-25 at 09.55.36.png>

<Screenshot 2021-11-25 at 10.05.10.png>

[Frank Yeh]

You may try [Options][Restore Rendering Setting] to see if it helps to
show the tracts.
Frank

On Thu, Nov 25, 2021 at 4:06 AM Alberto Benelli
<albertob...@gmail.com> wrote:
>
> Hi,
> I want to check which fiber tracks are involved in L-Hippocampus area. Here, you can observe the L-hippocampus area taken from the atlas showed on the T1 subject. Using the option “fiber tracking" I don’t be able to show fiber tracks associated with this area. Actually, the bundles are behind the T1. How can you can help me to find the way to observed them directly on the T1 subject space, in order to save in NIFTI file?
> Thanks
>
>

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/2C4EEA01-33DE-4904-954D-61D8AFB7DF07%40gmail.com.

[Frank Yeh]

[Tracts][Endpoints to ROI]
Then save the regions

On Thu, Nov 25, 2021 at 6:57 AM Alberto Benelli
<albertob...@gmail.com> wrote:
>
> How can I save all the end points on the cerebral cortex, as NIFTI file and txt file?
>
>

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/F0145A31-C5D2-41B8-8BDE-A1BA44AD95BC%40gmail.com.

[Alberto Benelli]

Thank you. How can I save it on MNI coordinates?

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtKhatP3VF-3LYE3Yg-D5xz9tCon7toCWkqakWEowb2KDA%40mail.gmail.com.

[Frank Yeh]

Repeat the process, but with QSDR-reconstructed FIB file.
(e.g. [Step T2b(1)][QSDR])

On Fri, Nov 26, 2021 at 1:16 PM Alberto Benelli

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[Alberto Benelli]

Hi,
What can I do to visualize all the tracks between two or more area, before selected?
How can I set up the FA threshold?

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJSkS%3D%3DBkLZNFWFTDXd%3DS407c4xE20dWKs_tMi7XvCDwA%40mail.gmail.com.

[Frank Yeh]

What can I do to visualize all the tracks between two or more area, before selected?

You may need to use "ROI" to specify those regions: http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Region-of-interest-ROI-region-of-avoidance-ROA-

 

How can I set up the FA threshold?

You may use the default setting.

Some instructions here:  http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Anisotropy-threshold

Best regards,

Frank

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[Alberto Benelli]

Thank you.

Is there a DSI_STUDIO course in order to learn how using this amazing tool?

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[Frank Yeh]

Sorry currently we only have some videos at https://www.youtube.com/c/FrankYeh/videos

Most instructions are in the online document: http://dsi-studio.labsolver.org/Manual

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[Alberto Benelli]

Ok, no problem. Is it possible to have a call with you to answer some mine questions?

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[Frank Yeh]

Currently, due to limited resources, we only provide free online assistance through this discussion forum.

Best regards,

Frank

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[Alberto Benelli]

Ok. Where can I find all the suggestions in order to change visualization parameters? 

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[Frank Yeh]

You may check out the visualization section at http://dsi-studio.labsolver.org/Manual

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[Alberto Benelli]

Hi,

from [slices] option I should insert the T1 subject. In my case I don’t have this option to select. How can I check it?

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[Frank Yeh]

[Insert other images]

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[Alberto Benelli]

Hi Franck,

thanks again for your replies. To run my project study I should knowing which are the fasciculus arcuate coordinates of each subject (10 sbjs). Can I run a group connectometry analysis to find where overlap these areas, showing the common tracks and coordinates?

Best regards

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[Frank Yeh]

To know where the arcuate fasciculus is located, you can use automatic fiber tracking to map them.

Connectometry analysis is a statistical method that examines the significance of correlational tractography. It is used for different purposes.

Frank

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[Alberto Benelli]

Ok, thanks to let me know how does it work. If I want to observe differences pre post treatment for each of subject, which option should I select?

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[Frank Yeh]

Differential tractography: http://dsi-studio.labsolver.org/Manual/differential-tractography

Frank

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[Alberto Benelli]

Hi,

How can I "highlight" the bundles between two brain regions? Do I need to perform which kind of analysis? a seed to seed, ROI to ROI, seed to end / terminative?

Thank you 

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[Frank Yeh]

One quick approach is to add these two regions in Step T3a and specify their type from '...' to 'ROI' before running fiber tracking.

There are also other settings in the documentation: http://dsi-studio.labsolver.org/Manual/Fiber-Tracking

Frank

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[Alberto Benelli]

I tried it but doesn’t work well. I want to run a seed to seed analysis, showing only the bundles between these brain regions. Using “fiber tracking” option only “seed” denomination is useful to show tracks between 2 regions. How is it possible?

 

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[Frank Yeh]

Set two regions as ROI and set [Terminate if] = 10000 Tracts

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[Alberto Benelli]

Ok, thanks.

If I want to run analysis with more than two brain areas, which kind of area I need to choose? Seed and not ROI?

On 31 Dec 2021, at 15:53, Frank Yeh <fran...@gmail.com> wrote:

Set two regions as ROI and set [Terminate if] = 10000 Tracts

On Fri, Dec 31, 2021 at 9:34 AM Alberto Benelli <albertob...@gmail.com> wrote:

I tried it but doesn’t work well. I want to run a seed to seed analysis, showing only the bundles between these brain regions. Using “fiber tracking” option only “seed” denomination is useful to show tracks between 2 regions. How is it possible?

<PastedGraphic-1.png> 

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[Frank Yeh]

You may check out this documentation for details: http://dsi-studio.labsolver.org/doc/gui_t3_roi_tracking.html

There are recommended approaches.

Frank

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