"other_images" from CLI reconstruction not available in T3

[Daniel Brennan]

Hi team,

Having some trouble accessing data from images warped using QSDR reconstruction. I am using "--other_images:t2w:FA.nii.gz,t2w:MD.nii.gz" to warp FA/MD maps calculated outside DSI studio with the same DWI image processed with DSI studio. I am able to view the images as a "slice" in step T3, however they all have the same name (t2w).

Can these warped images be renamed? Especially for "exporting" the warped images from the *.fib.gz file.

I am hoping to get the "along tract" data from these images (for a given track e.g. L corticospinal), but "tract profile" does not seem able to load them individually: all "t2w"-named files give the same graph.

Finally, is there an easy way, given a track/track file, to extract the "along-tract" profile from the CLI, or in a batch-way? Specifically of these images that have been warped with the DSI data.

Thank you very much,

Daniel

[Frank Yeh]

Rename t2w to any other name should work.

> Finally, is there an easy way, given a track/track file, to extract the "along-tract" profile from the CLI, or in a batch-way? Specifically of these images that have been warped with the DSI data.

You may check out https://dsi-studio.labsolver.org/doc/cli_ana.html
Frank

>
>
>
> Thank you very much,
> Daniel
>

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[Daniel Brennan]

Thank you, this worked! I swear I tried it before.

How would we go about exporting data "along tracts" for external MNI images such as Jacobian? Or associating them with the *.fib.gz file? I see:

"--export=report:dti_fa:0:1" 

but what if the data file is not named in the *fib.gz (as "dti_fa" is here)? 

thanks again for a great tool and excellent support. Apologies if this is a 2nd message, I believe I replied incorrectly before.

Daniel

[Frank Yeh]

>
> How would we go about exporting data "along tracts" for external MNI images such as Jacobian? Or associating them with the *.fib.gz file? I see:
>
> "--export=report:dti_fa:0:1"
>

Just replace dti_fa with the metrics you would like to analyze.

A list of metrics can be produced in the FIB file: (see the list at
the bottom of https://dsi-studio.labsolver.org/doc/gui_t2.html)

You may need to specify it [Step T2b(2)]

> but what if the data file is not named in the *fib.gz (as "dti_fa" is here)?

Then it has to be a NIFTI file that can be registered with the QA/ISO
map in FIB.

--other_slices=some_metrics.nii.gz --export=report:some_metrics:0:1

>
> thanks again for a great tool and excellent support. Apologies if this is a 2nd message, I believe I replied incorrectly before.
>

No problem at all,
Frank

> On Thursday, August 31, 2023 at 12:28:44 PM UTC-4 Frank Yeh wrote:
>>
>> Rename t2w to any other name should work.
>>
>>
>> > Finally, is there an easy way, given a track/track file, to extract the "along-tract" profile from the CLI, or in a batch-way? Specifically of these images that have been warped with the DSI data.
>>
>> You may check out https://dsi-studio.labsolver.org/doc/cli_ana.html
>> Frank
>>
>> >
>> >
>> >
>> > Thank you very much,
>> > Daniel
>> >
>> > --
>> > You received this message because you are subscribed to the Google Groups "DSI Studio" group.
>> > To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
>> > To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/e20919ba-adc1-4c26-b4dc-99cb208c71cfn%40googlegroups.com.
>
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[Daniel Brennan]

One more question about QSDR warping - 

GUI instructions mention that you can warp T1-space lesion masks along with T1 image by attaching T1 and then T1 lesion. does this warp T1 to DWI image, then apply QSDR warping? Can this be accomplished on the command line, along with attaching t2w space images? 

Thank you

[Frank Yeh]

Yes, see CLI examples here: https://dsi-studio.labsolver.org/doc/cli_t2.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/69ec5a7d-31ce-47d2-85e4-9502a0ecc9f2n%40googlegroups.com.

[Daniel Brennan]

Thank you, I used:

"--other_image=FERNET_FA:FERNET_fw_tensor_FA.nii.gz,FERNET_VF:FERNET_fw_volume_fraction.nii.gz,t1w:s1.nii,jac:Template2Subject_Jacobian.nii.gz"

This was printed during reconstruction:

additional processing steps
│ │ │ │ align_acpc=0
│ │ │ └─0 ms
│ │ │ other_image=FERNET_FA:FERNET_fw_tensor_FA.nii.gz,FERNET_VF:FERNET_fw_volume_fraction.nii.gz,t1w:s1.nii,jac:Template2Subject_Jacobian.nii.gz
│ │ │ FERNET_FA:FERNET_fw_tensor_FA.nii.gz
add FERNET_fw_tensor_FA.nii.gz as FERNET_FA treated as DWI space images.
│ │ │ FERNET_VF:FERNET_fw_volume_fraction.nii.gz
add FERNET_fw_volume_fraction.nii.gz as FERNET_VF using previous registration.
│ │ │ t1w:s1.nii
add s1.nii as t1w and register image with DWI.
│ │ │ translocation: -4.58453 9.99005 4.00283
│ │ │ rotation: -0.0095 0.00233792 0.00118895
│ │ │ scaling: 1 1 1
│ │ │ shear: 0 0 0
│ │ │ 2.18749 0.00260081 -0.00514343 -31.0806
│ │ │ -0.00264928 2.1874 -0.0208996 16.2067
│ │ │ 0.00508926 0.020787 2.19989 19.9408
│ │ │ jac:Template2Subject_Jacobian.nii.gz
add Template2Subject_Jacobian.nii.gz as jac using previous registration.
│ │ ├─initializing
│ │ │ └─2 ms
│ │ ├─reconstructing
│ │ │ └─5.08 s
│ │ ├─initializing
│ │ │ │ width ratio (subject/template):(112/157) 0.713376
│ │ │ │ translocation: 3.45742 5.05857 1.78178
│ │ │ │ rotation: 0.168711 0.0571433 0.0283267
│ │ │ │ scaling: 0.984891 0.981156 0.980479
│ │ │ │ shear: 0.0111124 0.0212188 0.123893
│ │ │ │ 0.44981 0.0160628 -0.0155181 21.836
│ │ │ │ -0.00483436 0.432873 0.129844 9.04802
│ │ │ │ 0.0272014 -0.074093 0.438628 4.04058
│ │ │ │ linear r:0.771649
│ │ │ │ R2:0.762081
│ │ │ │ output dimension: (71,85,61)
│ │ │ │ output resolution:2.2
│ │ │ │ output dimension:(71,85,61)
│ │ │ └─1.0338 m

This means "jac"/"Template2Subject_Jacobian" will be warped along with t1w image, correct? They look mostly aligned, but want to confirm.

Thank you

[Frank Yeh]

Yes

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