External Email - Use Caution

Dear Eugenio and experts,

I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR])

16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command:

freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut

However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt).

Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files?

Thanks in advance, Sally.

---

Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University

________________________________ From: Sally Grace Sent: Tuesday, April 30, 2019 12:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area not visible in visual QC

Dear Eugenio and experts,

I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR])

16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command:

freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut

However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt).

Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files?

Thanks in advance, Sally.

---

Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University

________________________________ From: Sally Grace Sent: Thursday, April 18, 2019 2:16 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Valentina Lorenzetti Subject: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area not visible in visual QC

Dear Eugenio and experts,

I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR])

16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command:

freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut

However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt).

Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files?

Thanks in advance, Sally.

---

Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University