On 3/12/13 10:12 AM, Christopher wrote:
Hi Doug,
Not really clear, I do agree. 1/ I would like to measure the area of the surface called lesionMask_surf.mgh obtained with mri_vol2surf.
You can use mri_segstats, something like mri_segstats --i $SUBJECTS_DIR/$subject/surf/lh.area --seg lesionMask_surf.mgh --id 1 --accumulate --sum sum.dat The output is sum.dat. The number you will want will be the "Mean" column (column 6). Ignore the other columns that say NVoxels and Volume_mm3.
2/ In addition, I have two methods (M1 and M2) to measure a resected volume. The binary volumes M1_vol and M2_vol are processed with mri_vol2surf to obtain M1_surf and M2_surf. I would like to measure the area common to M1_surf and M2_surf.
First create a new volume corresponding to the overlap between the two: fscalc M1_surf.mgh and M2_surf.mgh -o M1_and_M2_surf.mgh Then use the command above to get the area doug
Best,
Christopher
On 11.03.2013 18:12, Douglas Greve wrote:
Hi Christopher, I'm not sure I understand your question. What do you mean by "simple measurements"? doug
On 3/11/13 10:59 AM, Christopher wrote:
Thanks Doug. I can know visualize the resected area using freeview.
As the output of mri_vol2surf produces an overlay and not a surface, measurements of area or/and intersection with other outputs from mri_vol2surf are not possible using mris_* functions. What is the best strategy to follow to be able to do simple measurments on these mri_vol2surf outputs ? Transform to surface, but how ?
Thanks in advance,
Christopher
The output of mri_vol2surf is not a surface but an overlay on a surface. You will need to run something like:
freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
You'll need to set the threshold to 0.5 in order to see the mask. doug
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