FSL -我可以将fsf文件(程序安装文件)中的路径设置为当前工作目录吗？

Question

我正在执行MRI分析，并编写了一个脚本，遍历每个主题的所有扫描，下一步是运行一个名为feat的命令，它可以在下面的编码块的末尾看到。

#! /bin/sh
path=~/rj82/james_folder/data_copy/
cd $path

# Loop through the MND and Control directories
for directory in * ; do
cd $path
cd $directory

# Loop through each subject in each directory
for subject in ??? ; do
cd $path/$directory/$subject

# Loop through each scan for each subject
for scan in MR?? ; do
cd $path/$directory/$subject/$scan

# Run feat on each scan
feat design.fsf

cd ..

done
done
done

您还将看到feat采用了一个design.fsf文件，该文件设置了feat的参数。为了制作这个文件，我使用了一个MRI扫描作为输入数据。

下面我附加了design.fsf代码中的区域，这些区域显示用于创建文件的文件的路径。

# 4D AVW data or FEAT directory (1)
set feat_files(1) "/projects/rj82/james_folder/data_copy/mnd/002/MR02/fmri/fmri_data"

# Add confound EVs text file
set fmri(confoundevs) 0

# Session's alternate reference image for analysis 1
set alt_ex_func(1) "/projects/rj82/james_folder/data_copy/mnd/002/MR02/fmri_ref/fmri_ref_brain"

# B0 unwarp input image for analysis 1
set unwarp_files(1) "/projects/rj82/james_folder/data_copy/mnd/002/MR02/fmaps/fmap_rads"

# B0 unwarp mag input image for analysis 1
set unwarp_files_mag(1) "/projects/rj82/james_folder/data_copy/mnd/002/MR02/fmaps/mag_e1_brain"

# Subject's structural image for analysis 1
set highres_files(1) "/projects/rj82/james_folder/data_copy/mnd/002/MR02/t1/t1_brain"

如果我运行的脚本(第一个编码块)的壮举将正确运行，但是，由于design.fsf文件中的路径仅指一次扫描，它将继续运行这一次扫描壮举。

由于每个主题中的子目录和文件具有相同的名称，我希望用脚本中的当前目录(第一个编码块)替换path "/projects/rj82/james_folder/data_copy/mnd/002/MR02，同时保留结束部分(例如fmri/fmri_data")，允许我遍历并运行每个主题的壮举。

我尝试过设置path=pwd并将上面的路径替换为无法工作的"$path/fmri/fmri_data"，以及完全删除"/projects/rj82/james_folder/data_copy/mnd/002/MR02部分，因为我希望它只使用当前目录，但这也不起作用。对于这两种情况，错误消息是相同的：

/bin/mkdir: cannot create directory ‘/fmri’: Permission denied
    while executing
"fsl:exec "/bin/mkdir -p $FD" -n"
    (procedure "firstLevelMaster" line 22)
    invoked from within
"firstLevelMaster $session"
    invoked from within
"if { $done_something == 0 } {

    if { ! $fmri(inmelodic) } {
       if { $fmri(level) == 1 } {
              for { set session 1 } { $session <= $fmri(mult..."
    (file "/usr/local/fsl/6.0.4/fsl/bin/feat" line 390)

Answer 1

我无法得到我想要实现的结果，所以我循环通过上面的内容，将我的design.fsf文件复制到每个目录中，然后用sed对它们进行编辑，以获得正确的路径。

#! /bin/sh
path=~/rj82/james_folder/data_copy/
cd $path

# Loop through the MND and Control directories
for directory in * ; do
cd $path
cd $directory

# Loop through each subject in each directory
for subject in ??? ; do
cd $path/$directory/$subject

# Loop through each scan for each subject
for scan in MR?? ; do
cd $path/$directory/$subject/$scan

# Copy template design.fsf into each scan folder
cp $path/../design.fsf design.fsf

# Change design.fsf file and replace the directory used 
# to create the template with the current directory
current=$directory/$subject/$scan
sed -i "s|mnd/002/MR02|$current|g" design.fsf

# Run feat using custome design.fsf file
feat design.fsf

cd ..

done
done
done