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LabeoTech / Umit

universal mesoscale Imaging Toolbox
GNU General Public License v3.0
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genVSM #70

Closed C-A25 closed 1 year ago

C-A25 commented 1 year ago

No bug occured along the pipeline, but raw_VSM results without spatial filtering differ from ones obtained with another script. Elevation and azimuth maps were similar to ones previously acquired. Addind spatial filtering did not improve the VSM. image Similar results were obtained with two different acquisitions.

Steps to reproduce the behavior:

  1. run_ImagesClassification
  2. getEventsFromSingleChannel
  3. genRetinotopyMaps (nSweeps : 20 - ViewingDist : 12 - ScreenXsize : 59.9 - ScreenYsize : 33.7)
  4. genVSM (SpatialFilter_Sigma : 0 - CreateROIS : yes - standard option for all other parameters)

Expected behavior image Visual areas other than V1 can be easily discerned without spatial filtering.

BrunoOFSouza commented 1 year ago

Hi @C-A25 ,

Could you share the other script?

Thanks

C-A25 commented 1 year ago

I added them to the Google drive. The main script is RetinoAnalysis_main.mlx.

S-Belanger commented 1 year ago

There is clearly a spatial filter on the figure from your script. From the look of your figure, the filter was applied before the VSM generation.

A filter before VSM is usually used to smooth the signal and remove any local variations (that are generated from scratches or bone texture most of the time). The end result of such a filter will be a better segmentation of the -/+ 1 areas after VSM is computed.

A spatial filter after VSM is useful to clean the areas where the signal is low (so no activity at the stimulation frequency), phase will vary randomly between 0 and 2*pi. Then, by applying the spatial filter, these pixels should tend towards zero.

It is normal to apply a filter on the data when you generate a visual sign map. Both before and after. There is no way to get a good VSM without filtering.

BrunoOFSouza commented 1 year ago

Finally, the option for spatial filter of phase maps was available only in the master branch. It is now available in the Astrocyte branch as well ( commit 709a262b745f286e3ec4123b7129fb6c2f36f722).

By applying the filters in the phase maps, you should retrieve the same VSM.