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Columbia slaser condition fix #126

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Columbia slaser condition fix #126

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43 changes: 19 additions & 24 deletions inputOutput/io_loadspec_twix.m
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Original file line number Diff line number Diff line change
Expand Up @@ -229,30 +229,25 @@
end

%In the Columbia University sLASER sequence, there is an extra dimension
%where the water unsuppressed data are stored:
%where the water unsuppressed data are stored (MM/M with NPhs>1). Dedicated
%water-only scans are 3D (Col,Cha,Ave) with NPhs=1.
if isColumbia_sLASER
if ndims(fids)==4
temp = fids(1,1,:,1);
nRefs=size(squeeze(temp(temp~=0)),1);
%Remove the last dimension from sqzDims:
sqzDims=sqzDims(1:3);
elseif ndims(fids)==3
temp = fids(1,:,1);
nRefs=size(squeeze(temp(temp~=0)),1);
%Remove the last dimension from sqzDims:
sqzDims=sqzDims(1:2);
end

if nRefs>0
wRefs=true;
end

if ndims(fids)==4
fids_w=fids(:,:,1:nRefs,1);
fids=fids(:,:,:,2);
elseif ndims(fids==3)
fids_w=fids(:,1:nRefs,1);
fids=fids(:,:,2);
hasPhsContrast = twix_obj.image.NPhs > 1 && ...
numel(sqzDims) >= 4 && strcmp(sqzDims{end}, 'Phs');

if hasPhsContrast && ndims(fids) >= 4
temp = squeeze(fids(1, 1, :, 1));
refIdx = find(temp ~= 0);
nRefs = numel(refIdx);
sqzDims = sqzDims(1:3);
if nRefs > 0
wRefs = true;
fids_w = fids(:, :, refIdx, 1);
end
fids = fids(:, :, :, 2);
elseif twix_obj.image.NPhs <= 1 && ndims(fids) == 3
wRefs = true;
fids_w = fids;
end
end

Expand Down Expand Up @@ -659,7 +654,7 @@
if out_w.dims.subSpecs==0
out_w.flags.isFourSteps=0;
else
out_w.flags.isFourSteps=(out_w.sz(out_wop_pl.dims.subSpecs)==4);
out_w.flags.isFourSteps=(out_w.sz(out_w.dims.subSpecs)==4);
end
else
%No water reference data found. Returning empty struct for out_w:
Expand Down