External Email - Use Caution

Hi John,

I don’t know what went wrong. But can you run mri_info for the following images in your subject mri/ directory – rawavg.mgz, orig.mgz, nu.mgz, T1.mgz?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jacoby, John Sent: Tuesday, July 11, 2023 11:36 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Indices out of bounds error during mri_watershed

External Email - Use Caution Hi all, I am running into an error running recon-all and I can't figure out what's going on just from the error messages. I'm hoping someone here can help.

I'm using FreeSurfer 7.2 and this is the command I'm trying to run: recon-all -subjid HCA6429272_V1_MR -i /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz -all

build stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

operating system: ​cat /etc/centos-release Rocky Linux release 8.8 (Green Obsidian)

I've run about 1200 recons in the last few weeks from the same dataset using analogous commands for the other T1s, but this is the only one that failed. The T1 isn't great quality, but not terrible either (screenshot below). The error happens during the watershed step: "mri_watershed Error: indices out of bounds". I've attached the log and error file from the recon.

Thanks for any help you can provide.

Best, John

Screenshot of the input T1: [cid:image001.png@01D9B4BA.A01A3890]