External Email - Use Caution Dear FreeSurfer Developers,
I think my earlier email may have gotten lost. I've run the longitudinal hippocampal subfield pipeline using the following command on freesurfer version 6.0: longHippoSubfieldsT1.sh PAWS001_base_FS I received no errors and everything seems to have run fine. But on computing the subfields using the following command: quantifyHippocampalSubfields.sh T1.long PAWS_longitudinalhipsubfields.txt I noticed that all of subfields have negative volume values. I checked the individual text files within each subject's timepoint and indeed the output is showing negative volumes. I have also tested the same subject and run the cross-sectional hippocampal subfield pipeline using the following command: recon-all -s PAWS001_TP1_FS -hippocampal-subfields-T1 I'm really not sure why the longitudinal pipeline is showing negative values. Could it be a Freesurfer version issue? Am I doing something wrong? It is especially mind-boggling since I receive no error and the command is running smoothly! Please help. I have attached the text files of the same subject run cross-sectionally and longitudinally. 1. A single subject processed cross sectionally - lh.hippoSfVolumes-T1.v10.txt 2. The same subject process longitudinally - lh.hippoSfVolumes-T1.long.v10.txt Thank you so much!! Best regards, Ashwati [cid:image9b8575.PNG@bec4f33e.43bdc947] nnitagl1
Hippocampal_tail 551.985069 subiculum 441.678796 CA1 591.859199 hippocampal-fissure 190.568978 presubiculum 328.661302 parasubiculum 67.240990 molecular_layer_HP 543.065108 GC-ML-DG 283.344508 CA3 196.425693 CA4 248.349199 fimbria 71.368868 HATA 53.075778 Whole_hippocampus 3377.054511
Hippocampal_tail -553.862541 subiculum -425.430347 CA1 -569.070082 hippocampal-fissure -198.189351 presubiculum -309.228543 parasubiculum -55.836071 molecular_layer_HP -545.204527 GC-ML-DG -299.984481 CA3 -193.846037 CA4 -268.890367 fimbria -69.624316 HATA -46.845866 Whole_hippocampus -3337.823178
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