Group connectometry without cerebellum

[Pedro Henrique Rodrigues da Silva]

Hello!

I would like to know if it is possible to perform group connectometry excluding the cerebellum (it was partially cut during acquisition). If so, what would be the specific procedures?

Kind regards

[Frank Yeh]

There is a check box in the advanced option to exclude the cerebellum.
Best regards,
Frank

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[Pedro Henrique Rodrigues da Silva]

Thank you very much. I have another question.

I received a DKI dataset, consisting of two DICOM folders: one with only 3 volumes (b0s) and another with 102 volumes (with 12 b0s distributed throughout the volumes), bvec and bval. However, despite the indication of AP and PA, respectively, in the file names, when I view the files, I get opposite information.

As you can see in the figure, the first row contains, for the same patient, the sagittal and axial T1-weighted images, followed by the same images (row two) for one of the DICOM folders (in this case, the one with 3 b0 volumes, supposedly AP) and, finally, by the same images (row three) for the other DICOM folder (with 102 volumes, bvec, bval and, supposedly, PA).

However, when checking the images, we see that, for the second row, the eyes are elongated forward, the nose is compressed, the scalp in the occipital region is expanded, and the cerebellum is slightly elongated, which actually corresponds to a PA acquisition. In the third line, we see the opposite patterns: the eyes flattened towards the brain, the nose expanded forward, the cerebellum compressed, and the scalp in the occipital region “thinner,” which would correspond to AP (contrary to what the name saved in the file suggests).

These characteristics were observed in the acquisitions of other patients. Therefore, I believe the names AP and PA were switched in the description. What do you think? Could you guide me?

Kind regards,

Pedro

[Pedro Henrique]

Hello, Frank! Thank you very much. 

I have another question. I received a DKI dataset, consisting of two DICOM folders: one with only 3 volumes (b0s) and another with 102 volumes (with 12 b0s distributed throughout the volumes), bvec and bval. However, despite the indication of AP and PA, respectively, in the file names, when I view the files, I get opposite information.

As you can see in the figure, the first row contains, for the same patient, the sagittal and axial T1-weighted images, followed by the same images (row two) for one of the DICOM folders (in this case, the one with 3 b0 volumes, supposedly AP) and, finally, by the same images (row three) for the other DICOM folder (with 102 volumes, bvec, bval and, supposedly, PA).

However, when checking the images, we see that, for the second row, the eyes are elongated forward, the nose is compressed, the scalp in the occipital region is expanded, and the cerebellum is slightly elongated, which actually corresponds to a PA acquisition. In the third line, we see the opposite patterns: the eyes flattened towards the brain, the nose expanded forward, the cerebellum compressed, and the scalp in the occipital region “thinner,” which would correspond to AP (contrary to what the name saved in the file suggests).

These characteristics were observed in the acquisitions of other patients. Therefore, I believe the names AP and PA were switched in the description. What do you think? Could you guide me?

Kind regards,

Pedro

Em terça-feira, 17 de fevereiro de 2026 às 09:42:58 UTC-3, Frank Yeh escreveu:

[Frank Yeh]

Hi Pedro,

Users may provide sequence names, but the signals themselves won’t lie.

What you are describing (eye elongation, frontal compression,
occipital expansion, etc.) is exactly how one can visually infer
phase-encoding direction from susceptibility distortion. If the
distortion pattern is opposite to what the file name suggests, then it
is very likely that the AP/PA labels were swapped during export or
naming.

The good news is that as long as the echo times are the same, it does
not matter much which folder is labeled AP or PA in the name. DSI
Studio determines the distortion direction from the data and header
information, not just the file name, and it will correctly identify
which volume corresponds to AP and which to PA during preprocessing.

So your visual inspection is valid, and the naming may indeed be
reversed—but this should not cause a problem as long as the
acquisition parameters are consistent.

Best regards,
Frank

On Mon, Feb 23, 2026 at 8:10 AM Pedro Henrique <pedrojo...@gmail.com> wrote:
>
> Hello, Frank! Thank you very much.
>
> I have another question. I received a DKI dataset, consisting of two DICOM folders: one with only 3 volumes (b0s) and another with 102 volumes (with 12 b0s distributed throughout the volumes), bvec and bval. However, despite the indication of AP and PA, respectively, in the file names, when I view the files, I get opposite information.
>
> As you can see in the figure, the first row contains, for the same patient, the sagittal and axial T1-weighted images, followed by the same images (row two) for one of the DICOM folders (in this case, the one with 3 b0 volumes, supposedly AP) and, finally, by the same images (row three) for the other DICOM folder (with 102 volumes, bvec, bval and, supposedly, PA).
>

> However, when checking the images, we see that, for the second row, the eyes are elongated forward, the nose is compressed, the scalp in the occipital region is expanded, and the cerebellum is slightly elongated, which actually corresponds to a PA acquisition. In the third line, we see the opposite patterns: the eyes flattened towards the brain, the nose expanded forward, the cerebellum compressed, and the scalp in the occipital region “thinner,” which would correspond to AP (contrary to what the name saved in the file suggests).
>
> These characteristics were observed in the acquisitions of other patients. Therefore, I believe the names AP and PA were switched in the description. What do you think? Could you guide me?
>
> Kind regards,
>
> Pedro
>
>
> Em terça-feira, 17 de fevereiro de 2026 às 09:42:58 UTC-3, Frank Yeh escreveu:
>>
>> There is a check box in the advanced option to exclude the cerebellum.
>> Best regards,
>> Frank
>>
>> On Sat, Feb 14, 2026 at 7:53 PM 'Pedro Henrique Rodrigues da Silva'
>> via DSI Studio <dsi-s...@googlegroups.com> wrote:
>> >
>> > Hello!
>> >
>> > I would like to know if it is possible to perform group connectometry excluding the cerebellum (it was partially cut during acquisition). If so, what would be the specific procedures?
>> >
>> > Kind regards
>> >
>> > --
>> > 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 visit https://groups.google.com/d/msgid/dsi-studio/dee13079-9976-4266-aced-83352013aa05n%40googlegroups.com.
>
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