Installing ISIS-conv on MAC

ISIS-conv is a very useful dicom to nii converter from Enrico Reimer. ISIS-conv gets along with a lot of challenging data sets that no other converter (that I know of) can handle so conveniently:

  • SMS-data, where individual slices have a non-constant inter-slice distances.
  • VASO data with non-constant TRs
  • Multi-echo, multi-coil, and Magnitude/Phase data.

There is a Mac-installation package of ISIS-conv. Unfortunately, however, with every IOS update, it has become more complicated to install it.

Since, I spend too much time figuring out how to install it after every update, I am collecting the necessary steps in this Blog post for future reference:

Continue reading “Installing ISIS-conv on MAC”

Anatomically informed spatial smoothing

In this blog post, I want to describe the application and working principle of a few spatial smoothing algorithms that are implemented in LAYNII.

  1. Confined smoothing along similar anatomical structures with LN_GRADSMOOTH
  2. Smoothing along the layers with LN_LAYERSMOOTH
  3. Smoothing within columns with LN_LAYERSMOOTH
  4. Smoothing across specific spatial dimensions only with LN_DIRECT_SMOOTH
  5. Smoothing long the time domain with LN_TEMPSMOOTH

Continue reading “Anatomically informed spatial smoothing”

Negative Voxels in VASO

In the last years, I and multiple other VASO users have encountered many occasions of voxels that show negative CBV change (positive VASO signal change) while the BOLD suggests that the activation should be positive. In this blog post, I want to list potential sources of this surprising effect.

Continue reading “Negative Voxels in VASO”

How send raw k-space data to any given server with Twix or with a modified ICE-chain

In this blog-post I want to describe a setup, how you can include an additional ICE functor in your reconstruction pipeline that sends raw Twix files from the Reconstruction computer to any given custom server.  Continue reading “How send raw k-space data to any given server with Twix or with a modified ICE-chain”