MRI数据格式转换——基于Nipype/FreeSurfer

1. 将数据转换为Nifti格式

a. 用MRICro的MRIConvert进行数据格式的转换

b. 用FreeSurfer’的 mri_convert函数，鉴于大多数的scanner格式默认为DICOM，这里我们介绍怎样将DICOM格式转换为Nifiti格式。

    首先需要确认文件夹的结构，假设dicom文件存放在一个名为raw_data的文件夹内，其结构类型如下：

raw_dicom
|-- sub001
|   |-- t1w_3d_MPRAGE
|   |   |-- 00001.dcm
|   |   |-- ...
|   |   |-- 00176.dcm
|   |-- fmri_run1_long
|   |   |-- 00001.dcm
|   |   |-- ...
|   |   |-- 00240.dcm
|   |-- fmri_run2_long
|       |-- ...
|-- sub0..
|-- sub010

批量进行格式转换的代码如下：

TUTORIAL_DIR=~/nipype_tutorial     # location of experiment folder
RAW_DIR=$TUTORIAL_DIR/raw_dicom    # location of raw data folder
T1_FOLDER=t1w_3d_MPRAGE            # dicom folder containing anatomical scan
FUNC_FOLDER1=fmri_run1_long        # dicom folder containing 1st     functional scan
FUNC_FOLDER2=fmri_run2_long        # dicom folder containing 2nd functional scan
DATA_DIR=$TUTORIAL_DIR/data        # location of output folder

for id in $(seq -w 1 10)
do
    mkdir -p $DATA_DIR/sub0$id
    mri_convert $RAW_DIR/sub0$id/$T1_FOLDER/00001.dcm    $DATA_DIR/sub0$id/struct.nii.gz
    mri_convert $RAW_DIR/sub0$id/$FUNC_FOLDER1/00001.dcm $DATA_DIR/sub0$id/run001.nii.gz
    mri_convert $RAW_DIR/sub0$id/$FUNC_FOLDER2/00001.dcm $DATA_DIR/sub0$id/run002.nii.gz
done

原文地址：miykael.github.io/nipype-beginner-s-guide/prepareData.html#make-the-dataset-ready-for-nipype