ALPS

Алина Лясковик

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Jul 22, 2023, 9:56:38 PM7/22/23

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Hello!

I'm afraid I'm having trouble calculating the ALPS index and I really hope you can help me with this. After generating the GQI of the raw DTI data, I opened step 3 (Fiber Tracking and Visualization) and then placed the 2 ROIs in the projection and association regions. So what are my next steps? I'm really confused.
The attached screenshot shows my last action in DSI studio, I don’t understand what to do next

Thank you very much in advance!

Alina Lyaskovik, Radiologist,

PhD Student, Department of Radiation Diagnostics, Scientific Center of Neurology, Moscow

Алина Лясковик

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Jul 22, 2023, 10:11:44 PM7/22/23

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So after calculating statistics of these two ROIs I received this table:

Name com proj ass

voxel counts 216 224 195

volume (mm^3) 1728 1792 1560

center x 56 42.7857 61.3077

center y 47.1111 42.9375 47.7333

center z 42 42 43

bounding box x 57 44 62

bounding box y 49 44 49

bounding box z 42 42 43

bounding box x 55 42 60

bounding box y 46 42 46

bounding box z 42 42 43

qa 0.204689 0.415012 0.247799

dti_fa 0.398522 0.795297 0.55138

md 0.704848 0.808754 0.670298

ad 0.968708 1.7849 1.08811

rd 0.572918 0.320683 0.461391

iso 0.41775 0.353485 0.328037

rdi 0.374344 0.343024 0.315649

nrdi02L 0.284551 0.260361 0.240608

nrdi04L 0.0550983 0.0502507 0.0468759

nrdi06L 0 0 0

qa_max 0.270724 0.458436 0.278171

dti_fa_max 0.555618 0.87202 0.628202

md_max 0.834308 0.927298 0.786031

ad_max 1.15974 2.03226 1.16832

rd_max 0.71351 0.432315 0.624049

iso_max 0.47972 0.379606 0.360133

rdi_max 0.405155 0.355783 0.329243

nrdi02L_max 0.302702 0.268841 0.251372

nrdi04L_max 0.0572373 0.0532115 0.0491353

nrdi06L_max 0 0 0

qa_min 0.124615 0.339466 0.178352

dti_fa_min 0.154974 0.720495 0.42602

md_min 0.574121 0.681383 0.538279

ad_min 0.882606 1.55584 0.92158

rd_min 0.419879 0.213155 0.338149

iso_min 0.385733 0.334086 0.309886

rdi_min 0.344171 0.330772 0.308284

nrdi02L_min 0.26383 0.252166 0.237009

nrdi04L_min 0.0512369 0.0477756 0.0446866

nrdi06L_min 0 0 0 Name com proj ass

voxel counts 216 224 195

volume (mm^3) 1728 1792 1560

center x 56 42.7857 61.3077

center y 47.1111 42.9375 47.7333

center z 42 42 43

bounding box x 57 44 62

bounding box y 49 44 49

bounding box z 42 42 43

bounding box x 55 42 60

bounding box y 46 42 46

bounding box z 42 42 43

qa 0.204689 0.415012 0.247799

dti_fa 0.398522 0.795297 0.55138

md 0.704848 0.808754 0.670298

ad 0.968708 1.7849 1.08811

rd 0.572918 0.320683 0.461391

iso 0.41775 0.353485 0.328037

rdi 0.374344 0.343024 0.315649

nrdi02L 0.284551 0.260361 0.240608

nrdi04L 0.0550983 0.0502507 0.0468759

nrdi06L 0 0 0

qa_max 0.270724 0.458436 0.278171

dti_fa_max 0.555618 0.87202 0.628202

md_max 0.834308 0.927298 0.786031

ad_max 1.15974 2.03226 1.16832

rd_max 0.71351 0.432315 0.624049

iso_max 0.47972 0.379606 0.360133

rdi_max 0.405155 0.355783 0.329243

nrdi02L_max 0.302702 0.268841 0.251372

nrdi04L_max 0.0572373 0.0532115 0.0491353

nrdi06L_max 0 0 0

qa_min 0.124615 0.339466 0.178352

dti_fa_min 0.154974 0.720495 0.42602

md_min 0.574121 0.681383 0.538279

ad_min 0.882606 1.55584 0.92158

rd_min 0.419879 0.213155 0.338149

iso_min 0.385733 0.334086 0.309886

rdi_min 0.344171 0.330772 0.308284

nrdi02L_min 0.26383 0.252166 0.237009

nrdi04L_min 0.0512369 0.0477756 0.0446866

nrdi06L_min 0 0 0

Which of these numbers referes to Dxx, Dyy and Dzz? Or to dx0, dy0 and dz0?

воскресенье, 23 июля 2023 г. в 04:56:38 UTC+3, Алина Лясковик:

Frank Yeh

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Jul 22, 2023, 11:23:06 PM7/22/23

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At step T2 advance option

Specify "all" in the output and reconstruct the fib file again to get all metrics.

Best Regards

Frank

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jay Xu

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Aug 8, 2023, 8:09:20 AM8/8/23

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I followed the steps you mentioned, so here the txx, tyy, and tzz refer to the components of the diffusion tensor along the x, y, and z directions, respectively? 截屏2023-08-08 20.08.54.png

Frank Yeh

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Aug 8, 2023, 8:54:47 AM8/8/23

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No, they are the tensor elements.

Frank

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bill

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Aug 8, 2023, 8:34:27 PM8/8/23

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How would you go about calculating the Dxx, Dyy, and Dzz values used in the DTI ALPS equation using the txx, tyy, and tzz values outputted for an ROI?

Frank Yeh

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Aug 8, 2023, 9:05:38 PM8/8/23

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You may google DTI ALPS to find how it is calculated.

Leonardo Pertici

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Oct 1, 2023, 12:59:27 PM10/1/23

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Have you figured out how to do it? i have the same question

Leonardo Pertici

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Oct 1, 2023, 1:03:22 PM10/1/23

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I know the ALPS formula, but how can I extract the diffusivity in the direction of the x-axis (Dxx), y-axis (Dyy) and z-axis (Dzz) of a ROI?

Thanks

Frank Yeh

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Oct 3, 2023, 3:06:08 PM10/3/23

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At [Step T2b(2)][Advanced Options][Other output metrics], set it to all.

Then use [Step T3][Region][Statistics] to get the txx,tyy,tzz.

Leonardo Pertici

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Oct 4, 2023, 8:36:21 AM10/4/23

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But can we replace in the ALPS formula Dxx, Dyy and Dzz with txx, tyy and tzz?

Thanks

Frank Yeh

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Oct 4, 2023, 9:05:10 AM10/4/23

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Yes

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bahar hh

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Jan 21, 2024, 11:42:20 AM1/21/24

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In the ALPS formula, there are two Dxx values (Dxxproj, Dxxassoci). However, in the mentioned pathway (At [Step T2b(2)][Advanced Options][Other output metrics], set it to all. Then use [Step T3][Region][Statistics] to get the txx,tyy,tzz.), for a single ROI, we have only one Dxx. Which one of these (Dxxproj, Dxxassoci) is this Dxx, and how can we obtain the second Dxx?

bahar hh

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Jan 21, 2024, 11:42:25 AM1/21/24

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Hello, I encountered a problem in calculating ALPS. I would appreciate it if you could guide me.

Frank Yeh

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Jan 27, 2024, 2:26:35 AM1/27/24

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You may check out the ALPS paper to see how to calculate those metrics from tensor diffusivities.

Best regards

Frank

Hello, I encountered a problem in calculating ALPS. I would appreciate it if you could guide me.
In the ALPS formula, there are two Dxx values (Dxxproj, Dxxassoci). However, in the mentioned pathway (At [Step T2b(2)][Advanced Options][Other output metrics], set it to all. Then use [Step T3][Region][Statistics] to get the txx,tyy,tzz.), for a single ROI, we have only one Dxx. Which one of these (Dxxproj, Dxxassoci) is this Dxx, and how can we obtain the second Dxx?

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鹿小果

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Aug 18, 2024, 12:42:26 PM8/18/24

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In the context of the ALPS formula where Dxxproj and Dxxassoc are mentioned, these terms represent diffusivities related to different types of fiber connections within the brain. Given this, the diffusivity values like txx, tyy, and tzz should be calculated after defining the ROI in DSI Studio or a similar tool.

Yasin Celal Gunes

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Oct 23, 2024, 8:13:48 AM10/23/24

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Dear Alina,

I have some problems with you. I am confused about how to calculate and which metrics to use.

Did you find any solution to this matter?

Best wishes,

Yasin

23 Temmuz 2023 Pazar tarihinde saat 04:56:38 UTC+3 itibarıyla Алина Лясковик şunları yazdı:

Frank Yeh

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Oct 23, 2024, 2:40:05 PM10/23/24

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Googling the ALPS lead to this good materials about calculating it

https://www.researchgate.net/figure/Calculation-of-the-DTI-ALPS-index-A-Place-the-region-of-interests-in-the-areas-with_fig1_359349372

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Selina Selina

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Nov 24, 2025, 9:52:30 AM (5 days ago) Nov 24

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Hello! I encountered some problems and really hope you can help me. First, I couldn't find "all" in the advanced options in T2b; second, how would you go about calculating the Dxx, Dyy, and Dzz values used in the DTI ALPS equation using the txx, tyy, and tzz values outputted for an ROI?

Frank Yeh

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Nov 24, 2025, 2:11:21 PM (5 days ago) Nov 24

to selina537...@gmail.com, DSI Studio

Could you update DSI Studio and check the 'tensor' to get txx,tyy,tzz?
That is the dxx,dyy,dzz you are looking for.

On Mon, Nov 24, 2025 at 9:52 AM Selina Selina
<selina537...@gmail.com> wrote:
>
> Hello! I encountered some problems and really hope you can help me. First, I couldn't find "all" in the advanced options in T2b; second, how would you go about calculating the Dxx, Dyy, and Dzz values used in the DTI ALPS equation using the txx, tyy, and tzz values outputted for an ROI?
>
> On Thursday, October 24, 2024 at 2:40:05 AM UTC+8 Frank Yeh wrote:
>>
>> Googling the ALPS lead to this good materials about calculating it
>>
>> https://www.researchgate.net/figure/Calculation-of-the-DTI-ALPS-index-A-Place-the-region-of-interests-in-the-areas-with_fig1_359349372
>>
>> On Wed, Oct 23, 2024 at 8:13 AM Yasin Celal Gunes <gunesya...@gmail.com> wrote:
>>>
>>> Dear Alina,
>>>
>>> I have some problems with you. I am confused about how to calculate and which metrics to use.
>>>
>>> Did you find any solution to this matter?
>>>
>>> Best wishes,
>>> Yasin
>>>
>>> 23 Temmuz 2023 Pazar tarihinde saat 04:56:38 UTC+3 itibarıyla Алина Лясковик şunları yazdı:
>>>>
>>>> Hello!
>>>>
>>>> I'm afraid I'm having trouble calculating the ALPS index and I really hope you can help me with this. After generating the GQI of the raw DTI data, I opened step 3 (Fiber Tracking and Visualization) and then placed the 2 ROIs in the projection and association regions. So what are my next steps? I'm really confused.
>>>> The attached screenshot shows my last action in DSI studio, I don’t understand what to do next

>>>> Thank you very much in advance!
>>>>
>>>> Alina Lyaskovik, Radiologist,
>>>> PhD Student, Department of Radiation Diagnostics, Scientific Center of Neurology, Moscow
>>>
>>> --
>>>
>>> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
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>
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Selina Selina

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Nov 26, 2025, 2:01:43 AM (3 days ago) Nov 26

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Hello! Frank,I’m sorry to bother you. I want to know how I can ensure that all ROIs are the same size when I draw them.

Frank Yeh

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Nov 28, 2025, 3:41:45 AM (yesterday) Nov 28

to selina537...@gmail.com, DSI Studio

You may check out the region statistics to see if the volume is the same.

Best regards

Frank

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