From 9e77aa03a7da5204f1547d194220a4eee5cef99f Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 16:54:02 -0700 Subject: [PATCH 1/7] Update README.md --- README.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/README.md b/README.md index 922ba01..fd4706a 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,6 @@ # An automated pipeline to create subject-specific headcases for fMRI scanning -

- -

- - + This repository contains an automated pipeline to create subject-specific headcases for fMRI scanning. Headcases reduce subject motion ([Power et al., 2019](https://pubmed.ncbi.nlm.nih.gov/30639840/)), increase subject's comfort, and facilitate consistent head positioning across multiple scanning sessions. The pipeline takes as an input a 3D model of the participant's head and generates STL files of the headcases for 3D printing. This pipeline has been tested only with a [Structure Sensor](https://structure.io/structure-sensor-pro), but we think other sensors may be used. From 9c62a87355235715e63133dd54abcf1ebe026448 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 16:58:25 -0700 Subject: [PATCH 2/7] Update README.md --- README.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index fd4706a..13b6114 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,18 @@ -# An automated pipeline to create subject-specific headcases for fMRI scanning +# An automated pipeline to create subject-specific headcases for fMRI -This repository contains an automated pipeline to create subject-specific headcases for fMRI scanning. Headcases reduce subject motion ([Power et al., 2019](https://pubmed.ncbi.nlm.nih.gov/30639840/)), increase subject's comfort, and facilitate consistent head positioning across multiple scanning sessions. +This repository contains an automated pipeline to create subject-specific headcases for fMRI. + +Headcases reduce subject motion (Power et al., 2019), increase subject's comfort, and facilitate consistent head positioning across multiple scanning sessions. The pipeline takes as an input a 3D model of the participant's head and generates STL files of the headcases for 3D printing. This pipeline has been tested only with a [Structure Sensor](https://structure.io/structure-sensor-pro), but we think other sensors may be used. -Headcases can be generated for the following head coils: -- Siemens 32 channel -- Siemens 64 channel -- Nova 32 channel +Headcases can be generated for the following head coils: Siemens 32ch, Siemens 64ch, and Nova 32ch. The pipeline is written in Python and uses [MeshLab](https://www.meshlab.net/) and [Blender](https://www.blender.org/). +

+ ## Usage From 26afa68992ad123326fc1dca1c585203e0384f4f Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 16:58:55 -0700 Subject: [PATCH 3/7] Update README.md --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 13b6114..6c88ffd 100644 --- a/README.md +++ b/README.md @@ -11,9 +11,6 @@ Headcases can be generated for the following head coils: Siemens 32ch, Siemens 6 The pipeline is written in Python and uses [MeshLab](https://www.meshlab.net/) and [Blender](https://www.blender.org/). -

- - ## Usage The basic [Structure Scanner iOS app](https://apps.apple.com/us/app/scanner-structure-sdk/id891169722) can be used to scan a 3D model of the participant's head. For recommendations on how to scan the participant's head, see [this document](docs/glab_headcase_pipeline.md). From the Scanner app, the 3D model file (`Model.zip`) will need to be sent to an email address. From d37056067e2f18de36a2021c3e5ed60cd6c9af5d Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 17:01:51 -0700 Subject: [PATCH 4/7] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 6c88ffd..7db75ef 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,7 @@ The pipeline takes as an input a 3D model of the participant's head and generate Headcases can be generated for the following head coils: Siemens 32ch, Siemens 64ch, and Nova 32ch. The pipeline is written in Python and uses [MeshLab](https://www.meshlab.net/) and [Blender](https://www.blender.org/). +
## Usage From 0a906121a15ed28c7769246db5e864b1c6f38c43 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 17:02:21 -0700 Subject: [PATCH 5/7] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7db75ef..99d3cce 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# An automated pipeline to create subject-specific headcases for fMRI +# An automated pipeline to create subject-specific headcases for fMRI scanning -This repository contains an automated pipeline to create subject-specific headcases for fMRI. +This repository contains an automated pipeline to create subject-specific headcases for fMRI scanning. Headcases reduce subject motion (Power et al., 2019), increase subject's comfort, and facilitate consistent head positioning across multiple scanning sessions. From 4bd3a09603ac1842fc183e8528c67e92828448a9 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 17:08:57 -0700 Subject: [PATCH 6/7] Update README.md --- README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/README.md b/README.md index 99d3cce..c9f1a44 100644 --- a/README.md +++ b/README.md @@ -69,3 +69,12 @@ The pipeline also requires - Blender 2.7.9 (**Do not use newer versions of Blender, or the pipeline won't work.**) - MeshLab 1.3.2 (**The pipeline has been tested only with this version.**) + +## Common problems + +- The participant's head is not aligned correctly inside the headcase (turned upside down, flipped front-back, etc.): this problem can be caused by a 3D model that covers too much of the participant's shoulders. The participant's head will need to be scanned again with a tighter bounding box only around the head. +- The participant reports that the headcase is too tight, especially on the cheeckbones: this is a known problem that can occur for some participants. We are currently working on a solution for this problem. + +## Getting help + +To get help or report problems, please open an issue on this github repository. From 411f65cfe82e61af025293ebbae36f6dd5372e29 Mon Sep 17 00:00:00 2001 From: Matteo Visconti di Oleggio Castello Date: Wed, 15 Jun 2022 17:09:27 -0700 Subject: [PATCH 7/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c9f1a44..9666417 100644 --- a/README.md +++ b/README.md @@ -77,4 +77,4 @@ The pipeline also requires ## Getting help -To get help or report problems, please open an issue on this github repository. +To get help or report problems, please open an [issue](https://github.com/gallantlab/headcase-pipeline/issues) on this github repository.