Thank you Ashwati. This is very weird. Can you please send me a copy of the text files with the volumes for:

1. A single subject processed cross sectionally 2. The same subject process longitudinally Cheers, /E

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Ashwati Vipin (NNI)" ashwati_vipin@nni.com.sg Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, July 3, 2020 at 04:40 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Hippocampal Subfields - negative subfield volume values

External Email - Use Caution Dear FreeSurfer Developers,

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 as shown below:

[Inline image OWAPstImg380689]

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 received the following output with volumes:

[Inline image OWAPstImg750361]

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.

Thank you so much!!

Best regards, Ashwati

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