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The benefits of skull stripping in the normalization of clinical fMRI data.

Fischmeister FP, Höllinger I, Klinger N, Geissler A, Wurnig MC, Matt E, Rath J, Robinson SD, Trattnig S, Beisteiner R - Neuroimage Clin (2013)

Bottom Line: The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed.Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches.Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space - particularly when used in combination with the New Segment normalization technique.

View Article: PubMed Central - PubMed

Affiliation: Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria ; High Field MR Center, Medical University of Vienna, Austria.

ABSTRACT
Establishing a reliable correspondence between lesioned brains and a template is challenging using current normalization techniques. The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed. Here we provide a first investigation into whether clinical fMRI benefits from skull stripping, based on data from a presurgical language localization task. Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches. Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space - particularly when used in combination with the New Segment normalization technique.

No MeSH data available.


Examples for misaligned brains. Patients with a large (top and middle row, cases 4 and 3) or a small (bottom row, case 25) difference in DICE indices. Most of the patients showed the largest DICE difference between standard normalization without skull-stripping and New Segment with skull-stripping. MNI slices z: − 40 and z: + 15 are shown. The MNI template is outlined in red. Note the considerable mismatch within ventricular planes (+ 15) in the top row and the mismatch within basal planes (− 40) for case 3. Case 25 (bottom row) with similar DICE values for all 6 pipelines shows also similar brain alignments. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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f0025: Examples for misaligned brains. Patients with a large (top and middle row, cases 4 and 3) or a small (bottom row, case 25) difference in DICE indices. Most of the patients showed the largest DICE difference between standard normalization without skull-stripping and New Segment with skull-stripping. MNI slices z: − 40 and z: + 15 are shown. The MNI template is outlined in red. Note the considerable mismatch within ventricular planes (+ 15) in the top row and the mismatch within basal planes (− 40) for case 3. Case 25 (bottom row) with similar DICE values for all 6 pipelines shows also similar brain alignments. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: Finally, a visual inspection of all brains was performed by two of the authors (RB, FF) evaluating every patients' normalized brain from all 6 pipelines with a focus on the pipelines with the largest DICE difference (see Fig. 5). This was carried out to identify poor normalization and segmentation results and to ensure that DICE values (see below) corresponded to visible outcomes.


The benefits of skull stripping in the normalization of clinical fMRI data.

Fischmeister FP, Höllinger I, Klinger N, Geissler A, Wurnig MC, Matt E, Rath J, Robinson SD, Trattnig S, Beisteiner R - Neuroimage Clin (2013)

Examples for misaligned brains. Patients with a large (top and middle row, cases 4 and 3) or a small (bottom row, case 25) difference in DICE indices. Most of the patients showed the largest DICE difference between standard normalization without skull-stripping and New Segment with skull-stripping. MNI slices z: − 40 and z: + 15 are shown. The MNI template is outlined in red. Note the considerable mismatch within ventricular planes (+ 15) in the top row and the mismatch within basal planes (− 40) for case 3. Case 25 (bottom row) with similar DICE values for all 6 pipelines shows also similar brain alignments. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814956&req=5

f0025: Examples for misaligned brains. Patients with a large (top and middle row, cases 4 and 3) or a small (bottom row, case 25) difference in DICE indices. Most of the patients showed the largest DICE difference between standard normalization without skull-stripping and New Segment with skull-stripping. MNI slices z: − 40 and z: + 15 are shown. The MNI template is outlined in red. Note the considerable mismatch within ventricular planes (+ 15) in the top row and the mismatch within basal planes (− 40) for case 3. Case 25 (bottom row) with similar DICE values for all 6 pipelines shows also similar brain alignments. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: Finally, a visual inspection of all brains was performed by two of the authors (RB, FF) evaluating every patients' normalized brain from all 6 pipelines with a focus on the pipelines with the largest DICE difference (see Fig. 5). This was carried out to identify poor normalization and segmentation results and to ensure that DICE values (see below) corresponded to visible outcomes.

Bottom Line: The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed.Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches.Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space - particularly when used in combination with the New Segment normalization technique.

View Article: PubMed Central - PubMed

Affiliation: Study Group Clinical fMRI, Department of Neurology, Medical University of Vienna, Austria ; High Field MR Center, Medical University of Vienna, Austria.

ABSTRACT
Establishing a reliable correspondence between lesioned brains and a template is challenging using current normalization techniques. The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed. Here we provide a first investigation into whether clinical fMRI benefits from skull stripping, based on data from a presurgical language localization task. Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches. Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space - particularly when used in combination with the New Segment normalization technique.

No MeSH data available.