On 08/15/2014 10:33 PM, Chung, Yoonho wrote: > Hi, > > I am running Hippocampal subfield processing stream and I think I got all the > appropriate "posterior_*.mgz files" I need to get the stats, but I am not > seeing "nonPartialVolumeStatsRight.txt" anywhere as described in the wiki > under $subjectsdir. What I am seeing is "volumeStats_left.txt" and > "volumeStats_right.txt" files under the "$subject/mri" directory and one of > the text files look like this. > ------------------------------------ > volumeInVoxels: > Left-Hippocampus: 2616.97 > left_presubiculum: 4050 > left_CA1: 2880.55 > left_CA2_3: 8120.59 > left_fimbria: 212.439 > left_subiculum: 5985.02 > left_CA4_DG: 4459.07 > left_hippocampal_fissure: 358.59 > ------------------------------------- > > If I look at the end of the "hippo-subfields.log" file, it is saying it is > skipping the partial volume segmentation (see below). > > --------------------------- > ... > Debug: Off > Observers: > none > Matrix: > -0.5 0 0 > 0 0 0.5 > 0 -0.5 0 > Offset: [41.7047, -40.8148, -4.10007] > Center: [0, 0, 0] > Translation: [41.7047, -40.8148, -4.10007] > Inverse: > -2 0 0 > 0 0 -2 > 0 2 0 > Singular: 0 > spacing: [0.5, 0.5, 0.5] > origin: [41.7047, -40.8148, -4.10007] > direction: -1 0 0 > 0 0 1 > 0 -1 0 > > done! > Skipping the partial volume segmentation part > ------------------------------------------- > > Can please someone tell me what I am missing? > Also, what do I need to do to extract the values to a spreadsheet? Should I > use asegstats2table? under '-help' it doesn't say which options it should be > used to get the subfields. > > Thank you so much for the help in advance. > > Cheers, > Yoon
Hi, i just checked, we have that last line in the log too, so that seems to be normal. Just to make sure, you need to run kvlQuantifyHippocampalSubfieldSegmentations.sh to collect the stats, which is the hippocampus equivalent of asegstats2table. (From what i remember that script is a bit fragile and fails if it encounters anything other than a properly structured subject in the subjects dir, so i used a bunch of symbolic links to make a clean version of the subjects dir, without the qdec folder and so on.) regards, Andreas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
