Dear FreeSurfer experts,
I computed distances on the cortex surface using mris_pmake on a data set acquired at a 3T scanner (using an MPRAGE sequence and protocol recommendations for FreeSurfer). The exact syntax of the distance computation was:
mris_pmake --subject SUBJECT_ID --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:66245,endVertex:59104 .
Subsequently, the euclidean distance was computed using the Talairach coordinates displayed by tksurfer if the startVertex and the stopVertex are selected:
distance_euc = sqrt[(startTal_x-stopTal_x)^2+(startTal_y-stopTal_y)^2+(startTal_z-stopTal_z)^2] .
As you all know from your Tutorials, the in-surface distance must be larger or equal to the euclidean distance. Surprisingly, in the majority of cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution how it can be corrected? I am using FreeSurfer 5.1 and did not encounter any other problems in data evaluation. Any help us highly appreciated!
Sincerely yours
pfannmoe
don't use the Talairach, as that will include scaling to fit the talairach template. Just use the RAS coordinates (scanner or otherwise)
cheers Bruce
On Fri, 10 Jan 2014, Jörg Pfannmöller wrote:
Dear FreeSurfer experts,
I computed distances on the cortex surface using mris_pmake on a data set acquired at a 3T scanner (using an MPRAGE sequence and protocol recommendations for FreeSurfer). The exact syntax of the distance computation was:
mris_pmake --subject SUBJECT_ID --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:66245,endVertex:59104 .
Subsequently, the euclidean distance was computed using the Talairach coordinates displayed by tksurfer if the startVertex and the stopVertex are selected:
distance_euc = sqrt[(startTal_x-stopTal_x)^2+(startTal_y-stopTal_y)^2+(startTal_z-stopTal_z)^2] .
As you all know from your Tutorials, the in-surface distance must be larger or equal to the euclidean distance. Surprisingly, in the majority of cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution how it can be corrected? I am using FreeSurfer 5.1 and did not encounter any other problems in data evaluation. Any help us highly appreciated!
Sincerely yours
pfannmoe
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Jörg Pfannmöller