External Email - Use Caution
Dear sir/madam,
When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning:
[cid:c2cf64e3-2dc8-4cea-a89b-0bbff6f0119b]
This the mri_info --orientation output:
raw T1-weighted image: [cid:2d90ae0c-c61f-473c-b0f5-37211a901743]
orig.mgz: [cid:6e8edb77-9aa2-4b11-8c61-34cfd759fde2]
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
[cid:dfd9e777-ad5e-46a3-8096-1968257e6ca9] [cid:4f4f38b4-3353-4afc-ab02-af4effb80a67] [cid:909b14ff-eea8-4312-af13-fe370ed77c17] [cid:a6b00c8d-6e6d-441d-b672-6f634302cf63] [cid:52d8b847-f6b4-45b6-bb9e-fd1e954f66e6] [cid:bc692c0b-8622-447d-832b-7cad3e44c4e2] [cid:bb6248c0-55e3-405a-883d-07a3ef218b2f] [cid:6f190870-8379-4583-adaf-c8e019738b2a]
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear sir/madam,
When running /fslregister /as part of our data (pre)processing steps, it consistently outputs the following warning:
This the mri_info --orientation output:
raw T1-weighted image:
orig.mgz:
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the bbregister command, not fslregister, as follows: bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" --dti --init-fsl
We use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "--init-fsl" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Tuesday, February 9, 2021 3:51 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear sir/madam,
When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning:
[cid:part1.CA36D320.8525613E@mgh.harvard.edu]
This the mri_info --orientation output:
raw T1-weighted image: [cid:part2.6C69F4D2.3DDF351B@mgh.harvard.edu]
orig.mgz: [cid:part3.172726D6.9558EE74@mgh.harvard.edu]
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
[cid:part4.6DD95C94.8DBD2D4F@mgh.harvard.edu] [cid:part5.16512999.E46A74F9@mgh.harvard.edu] [cid:part6.C2370B33.4A972A08@mgh.harvard.edu] [cid:part7.7968294B.38F2221E@mgh.harvard.edu] [cid:part8.C2BDD6A1.B3183D08@mgh.harvard.edu] [cid:part9.2308F35F.4E605796@mgh.harvard.edu] [cid:part10.B1E579CF.C75DDDD5@mgh.harvard.edu] [cid:part11.35FCDDCC.0B5CFA0C@mgh.harvard.edu]
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1HO_8ocVCrGSTLcsUB8LbkusQSEJF-mIf9GJTVDHopkXEPL...https://secure-web.cisco.com/1izqVpEntgAqTr2vO3f6K0ay6NT9g5ciTMQEnSjgYKX51fNfCMjvAPRB5K6zqSEwgyPlrq0VUrxzaRMXUMO4m9gNSysDkq8amddX4fhLSkQJk_rfB7Q1dqAk9P0dxzppByyblwWeZPG8wHEgCWkjVtFbzr9hGnnIeNNynuMaYtDk2OR7CikRCRMjss15K81Dm8O9FGxUUzyW8p2KWfrzsABQpFELwkT6AAxryvN-YpPCUlSuh6tnIHgjIGWMDvkMOEPJVy6IjgS1Hz5pY0evn8A/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cs.poortman%2540erasmusmc.nl%257Cd8a54c180bde45c32ece08d8cd0a3e9f%257C526638ba6af34b0fa532a1a511f4ac80%257C0%257C0%257C637484791181059675%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DEhIOcyJzEbUAwvdnNMaiY1cno9kri9ZnMm5hxbH%252Fgtg%253D%26reserved%3D0
Yes, when you use --init-fsl, it uses fslregister. If you exclude that flag, then you will get mri_coreg
On 2/10/2021 3:06 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the /bbregister /command, not /fslregister/, as follows:
bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \--dti --init-fslWe use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "/--init-fsl/" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Sent:* Tuesday, February 9, 2021 3:51 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail) It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear sir/madam,
When running /fslregister /as part of our data (pre)processing steps, it consistently outputs the following warning:
This the mri_info --orientation output:
raw T1-weighted image:
orig.mgz:
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1izqVpEntgAqTr2vO3f6K0ay6NT9g5ciTMQEnSjgYKX51fNfCMjvAPRB5K6zqSEwgyPlrq0VUrxzaRMXUMO4m9gNSysDkq8amddX4fhLSkQJk_rfB7Q1dqAk9P0dxzppByyblwWeZPG8wHEgCWkjVtFbzr9hGnnIeNNynuMaYtDk2OR7CikRCRMjss15K81Dm8O9FGxUUzyW8p2KWfrzsABQpFELwkT6AAxryvN-YpPCUlSuh6tnIHgjIGWMDvkMOEPJVy6IjgS1Hz5pY0evn8A/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cs.poortman%2540erasmusmc.nl%257Cd8a54c180bde45c32ece08d8cd0a3e9f%257C526638ba6af34b0fa532a1a511f4ac80%257C0%257C0%257C637484791181059675%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DEhIOcyJzEbUAwvdnNMaiY1cno9kri9ZnMm5hxbH%252Fgtg%253D%26reserved%3D0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Douglas,
Thank you for the clarification. Very helpful. Aside from the advantage of not needing FSL, what other benefit(s) does running bbregister without the --init-fsl flag have over running it wíth the --init-fsl flag?
Kind regards, Simon ________________________________ 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, February 10, 2021 4:05 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
Yes, when you use --init-fsl, it uses fslregister. If you exclude that flag, then you will get mri_coreg
On 2/10/2021 3:06 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the bbregister command, not fslregister, as follows: bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" --dti --init-fsl
We use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "--init-fsl" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Tuesday, February 9, 2021 3:51 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear sir/madam,
When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning:
[cid:part1.D514E0E7.F5236074@mgh.harvard.edu]
This the mri_info --orientation output:
raw T1-weighted image: [cid:part2.77F997A9.412CF1C7@mgh.harvard.edu]
orig.mgz: [cid:part3.62FA5BF1.20ED1A20@mgh.harvard.edu]
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
[cid:part4.F8B301DA.6ED180FF@mgh.harvard.edu] [cid:part5.B5879B88.33B06580@mgh.harvard.edu] [cid:part6.623E2F33.5C51F966@mgh.harvard.edu] [cid:part7.D82DF0DF.9C237E6B@mgh.harvard.edu] [cid:part8.CA3473BF.11142874@mgh.harvard.edu] [cid:part9.B82A2832.15747276@mgh.harvard.edu] [cid:part10.F69D3A25.C6F283E8@mgh.harvard.edu] [cid:part11.65E95DDC.D8757A63@mgh.harvard.edu]
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RU4cQtHAoak8eOG8W2tKBvXqwQ_ftFvdPofbDpXda5ruB0...https://secure-web.cisco.com/1mC7UBa6yJG-o-zo2makqEi3iKJXYrsLnir8qZY6qXbZqeSzsgf1QODeancFc9TTBrVa9a3JJqZ_ECPne9PGGbFnvIE7DiaOvp9ZQtkkPBBK1Lap6gKoSzxBY7v_3loupelgVBdPBv3wfl7x0XX1jZy9_Syr5dWAlmufloArK-jeDtCKBTVFc9BOAzEDe48rVZkoH20Y7U-2accJKuJrV40lZ40f5Zs8WQzpjHgbh5CJHAh7SyDKxxH_8xU52T1qYc4ajiL4vlZ99youaAGvmBQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1izqVpEntgAqTr2vO3f6K0ay6NT9g5ciTMQEnSjgYKX51fNfCMjvAPRB5K6zqSEwgyPlrq0VUrxzaRMXUMO4m9gNSysDkq8amddX4fhLSkQJk_rfB7Q1dqAk9P0dxzppByyblwWeZPG8wHEgCWkjVtFbzr9hGnnIeNNynuMaYtDk2OR7CikRCRMjss15K81Dm8O9FGxUUzyW8p2KWfrzsABQpFELwkT6AAxryvN-YpPCUlSuh6tnIHgjIGWMDvkMOEPJVy6IjgS1Hz5pY0evn8A%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cs.poortman%25252540erasmusmc.nl%2525257Cd8a54c180bde45c32ece08d8cd0a3e9f%2525257C526638ba6af34b0fa532a1a511f4ac80%2525257C0%2525257C0%2525257C637484791181059675%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DEhIOcyJzEbUAwvdnNMaiY1cno9kri9ZnMm5hxbH%2525252Fgtg%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cs.poortman%2540erasmusmc.nl%257Cee29ec48217a49bcf8b208d8cdd57694%257C526638ba6af34b0fa532a1a511f4ac80%257C0%257C0%257C637485664012697050%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DMaB8bA%252FGy1nWScaK%252BuSdysaHyDRe0Z0%252B1gPtIP5Vt5U%253D%26reserved%3D0
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The function it uses (mri_coreg) is more robust than fslregister. But in cases where they perform similarly, the final result will be nearly identical because they are just used to do initialization.
On 2/11/2021 3:39 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear Douglas,
Thank you for the clarification. Very helpful. Aside from the advantage of not needing FSL, what other benefit(s) does running /bbregister/ without the /--init-fsl/ flag have over running it wíth the /--init-fsl/ flag?
Kind regards, Simon
*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, February 10, 2021 4:05 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail) Yes, when you use --init-fsl, it uses fslregister. If you exclude that flag, then you will get mri_coreg
On 2/10/2021 3:06 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the /bbregister /command, not /fslregister/, as follows:
bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" \--dti --init-fslWe use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "/--init-fsl/" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU *Sent:* Tuesday, February 9, 2021 3:51 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail) It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear sir/madam,
When running /fslregister /as part of our data (pre)processing steps, it consistently outputs the following warning:
This the mri_info --orientation output:
raw T1-weighted image:
orig.mgz:
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
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Dear Douglas,
Thank you! You've been of great help once more. I will switch to bbregister without the --init-fsl flag!
Kind regards, Simon Poortman ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Thursday, February 11, 2021 4:31 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
The function it uses (mri_coreg) is more robust than fslregister. But in cases where they perform similarly, the final result will be nearly identical because they are just used to do initialization.
On 2/11/2021 3:39 AM, S.R. Poortman wrote:
External Email - Use Caution
Dear Douglas,
Thank you for the clarification. Very helpful. Aside from the advantage of not needing FSL, what other benefit(s) does running bbregister without the --init-fsl flag have over running it wíth the --init-fsl flag?
Kind regards, Simon ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Wednesday, February 10, 2021 4:05 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
Yes, when you use --init-fsl, it uses fslregister. If you exclude that flag, then you will get mri_coreg
On 2/10/2021 3:06 AM, S.R. Poortman wrote:
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Dear Douglas,
Thank you for your reply.
Apologies, we actually do run the bbregister command, not fslregister, as follows: bbregister --s "${FSDIR}" --mov "$dwiReferenceFile" --reg "$registrationMatrixFile" --dti --init-fsl
We use FreeSurfer version 7.1.1, and I'm just now reading in the release notes of version 6.0: "bbregister now uses the FS mri_coreg program by to initialize BBR. FSL or SPM/matlab are no longer needed. mri_coreg is based on spm_coreg and gives very similar results as to when spmregister is run."
Does that mean the "--init-fsl" option is completely redundant? And could the warning message have been caused by using that option?
Kind regards, Simon ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Tuesday, February 9, 2021 3:51 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fslregister - WARNING: possible left-right reversal (image-heavy e-mail)
It looks ok to me. Why are you using fslregister? it is kind of depricated. use mri_coreg or, even better, bbregister
On 2/5/2021 10:13 AM, S.R. Poortman wrote:
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Dear sir/madam,
When running fslregister as part of our data (pre)processing steps, it consistently outputs the following warning:
[cid:part6.96F2D9AD.45E00DFB@mgh.harvard.edu]
This the mri_info --orientation output:
raw T1-weighted image: [cid:part7.276B5AD3.C999F6E3@mgh.harvard.edu]
orig.mgz: [cid:part8.03BE8C93.A2C6B530@mgh.harvard.edu]
However, when I look at all the images, raw and processed, I see no discrepancies with respect to orientation. See the images below. For reference, encircled in red, is the vitamin pill we stuck to the right side of the participant's forehead. Apologies for the image-heavy e-mail. I want to be thorough in providing enough information.
[cid:part9.B783E016.40EA0F16@mgh.harvard.edu] [cid:part10.D3AFAC1B.28C9A46A@mgh.harvard.edu] [cid:part11.FBB1FF96.F12BBE25@mgh.harvard.edu] [cid:part12.14E395EA.51BE6C24@mgh.harvard.edu] [cid:part13.6F1329C8.9D94F872@mgh.harvard.edu] [cid:part14.D2439BAB.FF278D53@mgh.harvard.edu] [cid:part15.66820E3A.F45AE813@mgh.harvard.edu] [cid:part16.708B484F.28A237EC@mgh.harvard.edu]
Am I overlooking something, perhaps? Or does this warning also appear when nothing is wrong with the orientation(s) (the "possible" does seem to imply so)? Is there another way for me to make absolutely sure the orientations are correct and consistent?
Thank you for considering my questions.
Kind regards, Simon Poortman (Erasmus MC, Rotterdam)
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Douglas N. Greve -
S.R. Poortman