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/1u2xTmmnCUaxQQuSTDRURAlZzdIaStC1AkxmbcmeQ18lFvU...
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
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:
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: *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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Good evening Doug,
Thank you for the clarification.
All the best, Jacob ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Wednesday, June 1, 2022 8:22 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] samseg2recon error / missing files
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:
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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PE3_w3uU6HPkJup9NEwPKSMajN_T2sI-BuQE_CkuRXtvYB...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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1jNDEjh_jAgUsPHfeuM3OeE_dv9IShmkUj6rCWdS-M-aJMy...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Jacob Levenstein