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Set HOME to writable temp directory (for docker run --read-only).
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@gllmflndn
gllmflndn committed Sep 21, 2016
1 parent 7608778 commit 26e1124
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Showing 3 changed files with 57 additions and 48 deletions.
12 changes: 8 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -21,18 +21,22 @@ RUN mkdir /opt/mcr_install && \
# Configure environment
ENV MCR_VERSION v91
ENV LD_LIBRARY_PATH /opt/mcr/${MCR_VERSION}/runtime/glnxa64:/opt/mcr/${MCR_VERSION}/bin/glnxa64:/opt/mcr/${MCR_VERSION}/sys/os/glnxa64:/opt/mcr/${MCR_VERSION}/sys/opengl/lib/glnxa64
ENV MCR_INHIBIT_CTF_LOCK 1

# Install SPM Standalone
ENV SPM_VERSION 12
ENV SPM_REVISION r6876
ENV SPM_DIR /opt/spm${SPM_VERSION}
ENV SPM_EXEC ${SPM_DIR}/spm${SPM_VERSION}
RUN wget -P /opt http://www.fil.ion.ucl.ac.uk/spm/download/restricted/bids/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip && \
unzip -q /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip -d /opt && \
rm -f /opt/spm${SPM_VERSION}_${SPM_REVISION}_Linux_${MATLAB_VERSION}.zip && \
/opt/spm${SPM_VERSION}/spm${SPM_VERSION} function exit
${SPM_EXEC} function exit

# Configure SPM BIDS App entry point
COPY spm_BIDS_App.m /opt/spm${SPM_VERSION}/

COPY run.sh spm_BIDS_App.m /opt/spm${SPM_VERSION}/
RUN chmod +x /opt/spm${SPM_VERSION}/run.sh
COPY version /version

ENTRYPOINT ["/opt/spm12/spm12","script","/opt/spm12/spm_BIDS_App.m"]
ENTRYPOINT ["/opt/spm12/run.sh"]
#ENTRYPOINT ["/opt/spm12/spm12","script","/opt/spm12/spm_BIDS_App.m"]
4 changes: 4 additions & 0 deletions run.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
#!/bin/bash

HOME=$(mktemp -d)
exec ${SPM_EXEC} script ${SPM_DIR}/spm_BIDS_App.m $@
89 changes: 45 additions & 44 deletions spm_BIDS_App.m
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,10 @@


%==========================================================================
%-OpenfMRI structure
%-BIDS App structure
%==========================================================================

OpenfMRI = struct(...
BIDS_App = struct(...
'dir','', ... % BIDS root directory
'outdir','', ... % output directory
'level','', ... % first or second level analysis [participant*,group*]
Expand All @@ -31,8 +31,9 @@
if numel(inputs) == 1
switch inputs{1}
case {'-v','--version'}
fprintf('%s BIDS App version %s\n',...
spm('version'), deblank(fileread('/version')));
fprintf('%s BIDS App, %s %s, version %s\n',...
spm('version'), upper(spm_check_version), version, ...
deblank(fileread('/version')));
case {'-h','--help'}
fprintf([...
'Usage: bids/spm BIDS_DIR OUTPUT_DIR LEVEL [OPTIONS]\n',...
Expand Down Expand Up @@ -62,9 +63,9 @@
error('Missing argument participant/group.');
end

OpenfMRI.dir = inputs{1};
OpenfMRI.outdir = inputs{2};
OpenfMRI.level = inputs{3};
BIDS_App.dir = inputs{1};
BIDS_App.outdir = inputs{2};
BIDS_App.level = inputs{3};

i = 4;
while i <= numel(inputs)
Expand All @@ -81,7 +82,7 @@
i = i + 1;
if i <= numel(inputs)
if inputs{i}(1) == '-', break; end
OpenfMRI.(arg){j} = inputs{i};
BIDS_App.(arg){j} = inputs{i};
j = j + 1;
else
break;
Expand All @@ -95,25 +96,25 @@

%- bids_dir
%--------------------------------------------------------------------------
if ~exist(OpenfMRI.dir,'dir')
error('BIDS directory does not exist.');
if ~exist(BIDS_App.dir,'dir')
error('BIDS directory "%s" does not exist.',BIDS_App.dir);
end

%- level [participant/group] & output_dir
%--------------------------------------------------------------------------
if ~isempty(strmatch('participant',OpenfMRI.level))
if ~exist(OpenfMRI.outdir,'dir')
sts = mkdir(OpenfMRI.outdir);
if ~isempty(strmatch('participant',BIDS_App.level))
if ~exist(BIDS_App.outdir,'dir')
sts = mkdir(BIDS_App.outdir);
if ~sts
error('BIDS output directory could not be created.');
end
end
elseif ~isempty(strmatch('group',OpenfMRI.level))
if ~exist(OpenfMRI.outdir,'dir')
error('BIDS output directory does not exist.');
elseif ~isempty(strmatch('group',BIDS_App.level))
if ~exist(BIDS_App.outdir,'dir')
error('BIDS output directory "%s" does not exist.',BIDS_App.outdir);
end
else
error('Unknown analysis level.');
error('Unknown analysis level "%s".',BIDS_App.level);
end

%==========================================================================
Expand All @@ -124,7 +125,7 @@
%--------------------------------------------------------------------------
[status, result] = system('bids-validator --version');
if ~status
[status, result] = system(['bids-validator "' OpenfMRI.dir '"']);
[status, result] = system(['bids-validator "' BIDS_App.dir '"']);
if status~=0
fprintf('%s\n',result);
exit(1);
Expand All @@ -133,16 +134,16 @@

%-Parse BIDS directory
%--------------------------------------------------------------------------
BIDS = spm_BIDS(OpenfMRI.dir);
BIDS = spm_BIDS(BIDS_App.dir);

%- --participant_label
%--------------------------------------------------------------------------
if isempty(OpenfMRI.participants)
OpenfMRI.participants = {BIDS.subjects.name};
if isempty(BIDS_App.participants)
BIDS_App.participants = {BIDS.subjects.name};
else
OpenfMRI.participants = cellfun(@(s) ['sub-' s], ...
OpenfMRI.participants, 'UniformOutput',false);
df = setdiff(OpenfMRI.participants,{BIDS.subjects.name});
BIDS_App.participants = cellfun(@(s) ['sub-' s], ...
BIDS_App.participants, 'UniformOutput',false);
df = setdiff(BIDS_App.participants,{BIDS.subjects.name});
if ~isempty(df)
error('Participant directory "%s" does not exist.',df{1});
end
Expand All @@ -160,26 +161,26 @@
%==========================================================================

atExit = '';
OpenfMRI.tmpdir = OpenfMRI.dir;
BIDS_App.tmpdir = BIDS_App.dir;

if ~isempty(strmatch('participant',OpenfMRI.level)) && ~isempty(OpenfMRI.participants)
if OpenfMRI.temp
if ~isempty(strmatch('participant',BIDS_App.level)) && ~isempty(BIDS_App.participants)
if BIDS_App.temp
%-Create temporary directory
%------------------------------------------------------------------
OpenfMRI.tmpdir = tempname(OpenfMRI.outdir);
sts = mkdir(OpenfMRI.tmpdir);
BIDS_App.tmpdir = tempname(BIDS_App.outdir);
sts = mkdir(BIDS_App.tmpdir);
if ~sts
error('Output temporary directory could not be created.');
end
%atExit = onCleanup(@() rmdir(OpenfMRI.tmpdir,'s'));

%-Copy participants' data
%------------------------------------------------------------------
for s=1:numel(OpenfMRI.participants)
for s=1:numel(BIDS_App.participants)
fprintf('Temporary directory: %s\n',...
fullfile(OpenfMRI.tmpdir,OpenfMRI.participants{s}));
sts = copyfile(fullfile(OpenfMRI.dir,OpenfMRI.participants{s}),...
fullfile(OpenfMRI.tmpdir,OpenfMRI.participants{s}));
fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}));
sts = copyfile(fullfile(BIDS_App.dir,BIDS_App.participants{s}),...
fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}));
if ~sts
error('Data could not be temporarily copied.');
end
Expand All @@ -188,9 +189,9 @@

%-Uncompress gzipped NIfTI files
%----------------------------------------------------------------------
for s=1:numel(OpenfMRI.participants)
for s=1:numel(BIDS_App.participants)
niigz = spm_select('FPListRec',...
fullfile(OpenfMRI.tmpdir,OpenfMRI.participants{s}),'^.*\.nii\.gz$');
fullfile(BIDS_App.tmpdir,BIDS_App.participants{s}),'^.*\.nii\.gz$');
if ~isempty(niigz)
niigz = cellstr(niigz);
for i=1:numel(niigz)
Expand All @@ -203,19 +204,19 @@
%-Gather from BIDS structure all relevant information for analysis
%----------------------------------------------------------------------
% structural and functional images for each subject/visit/run/task
for s=1:numel(OpenfMRI.participants)
idx = find(ismember({BIDS.subjects.name},OpenfMRI.participants{s}));
for s=1:numel(BIDS_App.participants)
idx = find(ismember({BIDS.subjects.name},BIDS_App.participants{s}));
% numel(idx) > 1 for multiple sessions/visits
end
BIDS = spm_changepath(BIDS,BIDS.dir,OpenfMRI.tmpdir);
BIDS = spm_changepath(BIDS,BIDS.dir,BIDS_App.tmpdir);
BIDS = spm_changepath(BIDS,'.nii.gz','.nii');
end

%==========================================================================
%-Analysis level: participant
%==========================================================================

if ~isempty(strmatch('participant',OpenfMRI.level))
if ~isempty(strmatch('participant',BIDS_App.level))

%-fMRI Preprocessing
%======================================================================
Expand All @@ -230,10 +231,10 @@
vox_func = [3 3 3];
FWHM = [12 12 12];

for s=1:numel(OpenfMRI.participants)
for s=1:numel(BIDS_App.participants)
clear matlabbatch f a

idx = find(ismember({BIDS.subjects.name},OpenfMRI.participants{s}));
idx = find(ismember({BIDS.subjects.name},BIDS_App.participants{s}));
for i=1:numel(BIDS.subjects(idx).func)
f{i,1} = fullfile(BIDS.subjects(idx).path,'func',BIDS.subjects(idx).func(i).filename);
end
Expand Down Expand Up @@ -270,7 +271,7 @@
matlabbatch{6}.spm.spatial.smooth.data = cellstr(spm_file(f,'prefix','w'));
matlabbatch{6}.spm.spatial.smooth.fwhm = FWHM;

spm_jobman('run',matlabbatch);
[~,prov] = spm_jobman('run',matlabbatch);
end

% make sure relevant files are stored in OpenfMRI.outdir
Expand All @@ -279,7 +280,7 @@
%-First Level fMRI
%======================================================================
fprintf('Nothing to do at fMRI first level yet.\n');
for s=1:numel(OpenfMRI.participants)
for s=1:numel(BIDS_App.participants)

end

Expand All @@ -291,7 +292,7 @@
%-Analysis level: group
%==========================================================================

if ~isempty(strmatch('group',OpenfMRI.level))
if ~isempty(strmatch('group',BIDS_App.level))
fprintf('Nothing to do at the group level yet.\n');
end

Expand Down

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