FSL - 我可以将 fsf 文件（程序设置文件）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，循环遍历每个对象的所有扫描，下一步是运行一个名为 feat 的命令，可以在下面的编码块末尾看到该命令。

#! /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 需要一个 design.fsf 文件，该文件设置了专长的参数。为了制作这个文件，我使用了一次 MRI 扫描作为输入数据。

下面我附上了design.fsf 代码中的区域，这些区域显示了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"

如果我运行脚本（第一个编码块）feat 将正确运行，但是由于design.fsf 文件中的路径仅指一次扫描，它只会在这一次扫描中连续运行feat。

由于每个主题中的子目录和文件具有相同的名称，我想将路径 "/projects/rj82/james_folder/data_copy/mnd/002/MR02 替换为脚本中的当前目录（第一个编码块），同时保留结尾部分（例如 fmri/fmri_data"）允许我循环遍历每个主题并运行壮举。

我尝试设置 path=pwd 并用 "$path/fmri/fmri_data" 替换上面的路径，这不起作用，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，但这也没有不行。两者的错误信息相同：

/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

我无法让我想要实现的目标发挥作用，因此我循环执行与上述相同的操作，将我的 design.fsf 文件复制到每个目录中，并使用 sed 对其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

Answer 2

我的脚本导航到每个单独的主题并进行扫描，因此我将设计文件更改为：set feat_files(1) "/fmri/fmri_data"

这是个好主意，但为了创建相对路径，您还必须删除前导 /;其中还提示错误消息cannot create directory ‘/fmri’。

在.fsf 文件中使用真正的相对路径，还应该可以通过调用feat /<i>path</i>/design.fsf 来使用公共design.fsf