# Signal loss after epi correction

**URL:** <https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723>\
**Category:** SlicerDMRI\
**Tags:** diffusion\
**Created:** [July 24, 2020, 3:41pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723 "2020-07-24T15:41:31Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![mali](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mali/32/65981_2.png) [@mali](https://discourse.slicer.org/u/mali)\
**Post date:** [July 24, 2020, 3:41pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/1 "2020-07-24T15:41:31Z")

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Dear Slicer community,

I hope you can help me with an issue I am struggling with. Iam currently working on DTI scans using Slicer and the PNL Pipeline. After applying epi correction (epi.sh) I am getting images that look a lot different and display much less glyphs in the DTI volume (see screenshots).

 ![Screenshot-pre-epi](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/a/fabee450b037eec83f85b94a90cd0e9757e6684b.jpeg)  
Have you experienced this and know what the problem could be?  
I really appreciate any advice! Thanks a lot in advance!

Best wishes,  
Marlene

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**Author:** ![tbillah](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tbillah/32/4139_2.png) [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Post date:** [July 24, 2020, 8:12pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/2 "2020-07-24T20:12:39Z")

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Hi @marlene,

Thanks for your question. PNL is a different entity from Slicer 🙂 Please report issues related to PNL pipeline [here](https://github.com/pnlbwh/pnlpipe/issues).

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**Author:** ![tbillah](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tbillah/32/4139_2.png) [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Post date:** [July 24, 2020, 8:15pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/3 "2020-07-24T20:15:06Z")

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That being said, we don’t support shell scripts (.sh extension) as part of our pipeline anymore. Please use [https://github.com/pnlbwh/pnlpipe/blob/py3-compatible/pnlscripts/epi.py](https://github.com/pnlbwh/pnlpipe/blob/py3-compatible/pnlscripts/epi.py) and report your observation back. Then we can try to answer your question.

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**Author:** ![zhangfanmark](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zhangfanmark/32/4451_2.png) [@zhangfanmark](https://discourse.slicer.org/u/zhangfanmark)\
**Post date:** [July 24, 2020, 9:39pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/4 "2020-07-24T21:39:32Z")

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Hi @mali It is hard to tell what is going wrong. As far as I know, the epi.sh code is computing a nonlinear registration between b0 and T1(or T2), then applying the transform to all gradient images. It could be something happening when do the transform interpolation. Your corrected DTI map seems to be very noisy. Anyway, I would suggest trying the code that Tashrif pointed out.

Regards,  
Fan

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**Author:** ![mali](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mali/32/65981_2.png) [@mali](https://discourse.slicer.org/u/mali)\
**Post date:** [July 25, 2020, 8:05pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/5 "2020-07-25T20:05:29Z")

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Thank you Fan, I will try to do so.  
Best wishes,  
Marlene

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**Author:** ![mali](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mali/32/65981_2.png) [@mali](https://discourse.slicer.org/u/mali)\
**Post date:** [July 25, 2020, 8:06pm UTC](https://discourse.slicer.org/t/signal-loss-after-epi-correction/12723/6 "2020-07-25T20:06:07Z")

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Thank you Tashrif,

I will try this and report back.

Best wishes,  
Marlene