External Email - Use Caution Hello Freesurfer team + users,
I am looking to run segmentHA_T1.sh following samseg + samseg2recon, and came across this previous thread where it seemed to workout: https://secure-web.cisco.com/1u2xTmmnCUaxQQuSTDRURAlZzdIaStC1AkxmbcmeQ18lFvUX9K2uWKI-A9qp3cwvFJhZJu1ad-7LSt56tL9oPMTw-bCPlMGmVIEYFftMBifsmhTjMWcghE3o_DFOdGEhjrLAsBmlkQm19bGZVYDvk4ouX75UTHnDp58PHyXBF1yc452zGuux3E4k7RPx70jKpZ3mAQhoGxmSaOrkCPcYfSephzdHjtyo4MC-tW_7-QK5lm11eP6o3Cv0SdOmMqeL-VB7gvriKIObxrWYzIrTkHbWuhTq85QMcEXUNuENKXXN2PZrxsa0GY57xIso6sBfpm3qg6NUpek5wY-O_3b0YFg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66074.html Given that I am writing in, I have not yet gotten this to run properly... Below is my samseg command: samseg --t1w ${subject}_${ses}_T1w.nii.gz --sd . --s ${subject}_${ses}_samseg --refmode t1w --threads 16 --parallel >From the log file, samseg seems to run correctly, but once it reaches the >samseg2recon steps, I receive the following error: ln -sf orig.mgz rawavg.mgz ERROR: ln -sf orig.mgz rawavg.mgz ERROR: samseg2recon --s ${subject}_${ses}_samseg --tmpdir ${SUBJECTS_DIR}/${subject}_${ses}_samseg/mri/samseg/tmp.pyBLVF/tmp.mergeseg --cleanup If I then (re)run samseg2recon on the samseg directory (see cmd below) , I can execute the failed lines, and this script completes without error. samseg2recon --s ${subject}_${ses}_samseg However, when I then try to run: segmentHA_T1.sh ${subject}_${ses}_samseg, I receive the following error: Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? As the error message correctly states, within that subject's dir, I do not have an mri/norm.mgz or mri/wmparc.mgz. I do have an mri/samseg/transforms/samseg.talairach.xfm, but it is not in the scripts expected location/naming convention. If it is helpful to know: i. Running recon-all then segmentHA_T1.sh completes without error... ii. Copy over the mri dir from the recon-all to the samseg subject dir, then running segmentHA_T1.sh also completes without error... iii. I am running Ubuntu 20.04.4, freesurfer-linux-ubunu18x86_64_-7.2.0-20210721 Any idea what may be going wrong with samseg/samseg2recon? I am happy to use the workaround listed above, but I suspect there may be a more efficient way, and or unintended implications when mixing and matching recon-all and samseg...? Thank you for your help and insight! All the best, Jacob
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