Currently, you'll have to run recon-all to the end in order to run the hippo subfield seg
On 5/30/2022 5:55 AM, Jacob Levenstein wrote:
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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: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66074.html 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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