External Email - Use Caution
We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:
* In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. * However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: * In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. * When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. * Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:
mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ...
-- Christine Fennema-Notestine, Ph.D.
Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
External Email - Use Caution
We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:
- In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly.
- However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) /[instead of MNI N3 (i.e., nu_correct)]/, the effect of specifying the recon-all-3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: o In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not.We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. o When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. o Beloware the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:
_mri_nu_correct.mni.log:_
...
*/usr/local/freesurfer/bin/mri_nu_correct.mni*
*--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50*
nIters1
mri_nu_correct.mni 7.1.1
...
*AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz*
Using shrink factor: 4
...
--
Christine Fennema-Notestine, Ph.D.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for the confirmation, Doug, hope all is well with you. A few notes as follow-up below:
We haven’t used N4 for bias correction ourselves much nor explored it carefully, as we have been fairly happy with the N3/’zheng’ approach (using the recommendations from Zheng et al.) - we will compare them some time in the near future. For now, given the experience with FS7.1.1 default N4 corrections, we are going to stick with the MNI N3 zheng (stronger bias) call options we used before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4). We did rerun several of the recent 7.1.1 cases with our n3/zheng approach and it has improved the correction in our data, including no longer tlrc failures, improved signal falloff correction for better temporal lobe, improved hippocampal segmentations. Here are a couple of examples: [cid:image001.png@01D7E5E4.7768CCA0] - Above - aseg 7.1.1 default missed hpc on left, with n3/zheng captured hpc [cid:image002.png@01D7E5E4.7768CCA0] Above - aseg 7.1.1 default poorly separated hpc and amyg on left, better with n3/zheng on right
One naïve question, with respect to the n4 performance/parameters, my read from our mri_nu_correct.mni.log, it looked like there might be some parameters that were passed along to nu_correct for ANTS (in blue bold below) but perhaps were not actually implemented (in red bold below), but I am not experienced with the tool so wouldn’t know if my interpretation is correct. In the mri_nu_correct.mni.log, these parameters looked passed to nu_correct:
* /usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.1.1 …
* AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz …
Regardless, given these changes for v7.x with ANTSN4 that no longer calls any -3T option, it might be best if references to this flag are modified on the web, unless other options become available, to avoid confusion e.g., recon-all - - help still says: USING IMAGES FROM A 3T SCANNER The -3T flag enables two specific options in recon-all for images acquired with a 3T scanner: 3T-specific NU intensity correction parameters are used in the Non-Uniform normalization stage, and the Schwartz 3T atlas is used for Talairach alignment.
And the -3T option is still listed on https://secure-web.cisco.com/19bDyVsWA2VNmfjDVR4NdZRObv2oMAe1YgFh8RMURNxDtmn...
Many thanks for your time, Peace, Chris
-- Christine Fennema-Notestine, Ph.D.
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 Sent: Friday, November 19, 2021 7:58 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
External Email - Use Caution We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:
1. In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. 2. However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction:
* In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. * When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. * Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:
mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ...
-- Christine Fennema-Notestine, Ph.D.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/14SHpbFgM1Yspa1KNoJp5em7d8y4JomO2GDjPGY6IPGUUxD...https://secure-web.cisco.com/1iDii7PTjyE7hqHFAGRGEtH7wDeNykG82TpJx5_5DvQWY6nBoAdQf5TYh18p7-8Q6LPo2dmfjfrS0Ex1KK6wQWkrcQrQkKmZR_C_u4GSKtT1x2jvoZbgagtGAR2CFwf7u4fU7eZV9WJqMncCpmTanU99o8Oy2G94tKC3l62wvZPIGEwtUVRyJLsSTWw2crETL1lmjXU4pfAr5HWw6rAmF1dMKvq6kMPyjiShEZmWDq7RU8W7wNXHyET3ns9CPdGsABeL6lbgOrfwcssl5BuqxsvPabMko4yQFOo7PfAYIOmvBKRak9Rc_ziamOrO6O38WLXzBAKC5CtAZoV6iQoiVuw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21LLK065n_VXAQ%213glO-Pijub1d2M9d2JMIlztBfjL4AwXovJpK1Vcd9ONoxkRauTMtgsEBKDgj7eFr%24
External Email - Use Caution
Thanks for the confirmation, Doug, hope all is well with you. A few notes as follow-up below:
We haven't used N4 for bias correction ourselves much nor explored it carefully, as we have been fairly happy with the N3/'zheng' approach (using the recommendations from Zheng et al.) - we will compare them some time in the near future. For now, given the experience with FS7.1.1 default N4 corrections, we are going to stick with the MNI N3 zheng (stronger bias) call options we used before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4). We did rerun several of the recent 7.1.1 cases with our n3/zheng approach and it has improved the correction in our data, including no longer tlrc failures, improved signal falloff correction for better temporal lobe, improved hippocampal segmentations. Here are a couple of examples: [cid:image001.png@01D7E5E4.7768CCA0]- Above - aseg 7.1.1 default missed hpc on left, with n3/zheng captured hpc [cid:image002.png@01D7E5E4.7768CCA0] Above - aseg 7.1.1 default poorly separated hpc and amyg on left, better with n3/zheng on right
One naïve question, with respect to the n4 performance/parameters, my read from our mri_nu_correct.mni.log, it looked like there might be some parameters that were passed along to nu_correct for ANTS (in blue bold below) but perhaps were not actually implemented (in red bold below), but I am not experienced with the tool so wouldn't know if my interpretation is correct. In the mri_nu_correct.mni.log, these parameters looked passed to nu_correct:
· /usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.1.1 ...
· AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz ...
Regardless, given these changes for v7.x with ANTSN4 that no longer calls any -3T option, it might be best if references to this flag are modified on the web, unless other options become available, to avoid confusion e.g., recon-all - - help still says: USING IMAGES FROM A 3T SCANNER The -3T flag enables two specific options in recon-all for images acquired with a 3T scanner: 3T-specific NU intensity correction parameters are used in the Non-Uniform normalization stage, and the Schwartz 3T atlas is used for Talairach alignment.
And the -3T option is still listed on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ECa1DtOjHefbc_wYdoMdPDjDaMxnuF5bUIkBYBPHytTPSn...https://secure-web.cisco.com/1u5k6-3S4b13ISyowTS0JWpCFDcfmizJnrmEiSgy7w1IMBZP9qgGF0qHUGPRD5p6Dk7ZjAYc9VjzhAH3b9W5ms19tdsuzGqD3kZkYDGi2E3I4GD3bAQhg6R_odZyewhOXnayihJkgnABe8zCjt6DLFw9hgndR7PQypPnNZVUezrsErpDSpqtAAdN7DcxZTmnoP0mZ9o_W73F5hJlt1E5lVWJct0QQ39xSEq0s_TJWSFBsA2DpSKqEYQHjG8u-6tHTMKLwD8z-fFm2SyKO1wm2A8AU6tjWv8qSZIsIBBo98d6kwNJMhW_j30-Y-6acgtp2/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F19bDyVsWA2VNmfjDVR4NdZRObv2oMAe1YgFh8RMURNxDtmnRvsa8NHwVzKJGFycLCRWDLEt43ivmjXyCgYE7ytfazB2fcnaz2ChVhTTad9tvdS-yyDHfPesaHONuGsPwJ1UhFx6WzHOujAv3neqcF1RiTxQer3Ua0t-qZMl1EOt0dlKqiJGpEpmVaX-ZUAA5CkKBEHWF2UGcaXpfL5VCP4Ggwp5yg6gA_SAhQ5q-qG7kwEVQ75foJ9o3UAxhOH6Ge0miiY6fjJFOjxzQdHxsMsMqjvn65HR_EXltxgsgHtsisJV8vwzcuqzDHsD0jYGvzGS7Xqj3BUZe7n2i8tiSR0Q%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FOtherUsefulFlags__%3BJSUlJSU%21%21LLK065n_VXAQ%210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql5Eehpwt%24
Many thanks for your time, Peace, Chris
-- Christine Fennema-Notestine, Ph.D.
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 Sent: Friday, November 19, 2021 7:58 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
External Email - Use Caution We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:
1. In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly.
2. However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction:
1. In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script.
2. When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs.
3. Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:
mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ...
-- Christine Fennema-Notestine, Ph.D.
_______________________________________________
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/1MQDeCSvXz7MjJH1ckDjfx3LxqUSahVl2SUDpgcBk4nZfdQ...https://secure-web.cisco.com/14Z5l95jcm2UKLB0LNFbJQbOQZDoZKEOCKGk1QKMfjeVnqMs97vc6duhXt2jjosNa5c1ykSil4i3QtAPEmJmegjtu4u8ufzDbjp-hfarPfNjV11KiAD0EdILft8WMrPoGIt85SNaSahrBMxPdGHm04YTehEWO2N9YLKPGbTUUg6aTSRYy1XYw-rD6ulec2suNxRdqBUOCanc2Hyn5zA3u_bJJBAqu8XmmCs0fo4y1Ij3B3KcXAfMyLuLmntUOZCUYh7W9tQeIxWHQG7_MzzzvuLmNkOO8mlcenksPMrNTrmDX2RM8FKVZZiDFBYr9yCr7/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1iDii7PTjyE7hqHFAGRGEtH7wDeNykG82TpJx5_5DvQWY6nBoAdQf5TYh18p7-8Q6LPo2dmfjfrS0Ex1KK6wQWkrcQrQkKmZR_C_u4GSKtT1x2jvoZbgagtGAR2CFwf7u4fU7eZV9WJqMncCpmTanU99o8Oy2G94tKC3l62wvZPIGEwtUVRyJLsSTWw2crETL1lmjXU4pfAr5HWw6rAmF1dMKvq6kMPyjiShEZmWDq7RU8W7wNXHyET3ns9CPdGsABeL6lbgOrfwcssl5BuqxsvPabMko4yQFOo7PfAYIOmvBKRak9Rc_ziamOrO6O38WLXzBAKC5CtAZoV6iQoiVuw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21LLK065n_VXAQ%2A213glO-Pijub1d2M9d2JMIlztBfjL4AwXovJpK1Vcd9ONoxkRauTMtgsEBKDgj7eFr%2A24__%3BJSUlJSUlJSUlJSUlJSUl%21%21LLK065n_VXAQ%210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql-b5_a2h%24
Hi Chris, I saw that you posted this a 2nd time. Did you have a question to be answered or is this just a comment? doug
On 12/6/2021 12:06 PM, Notestine, Christine wrote:
External Email - Use Caution
Thanks for the confirmation, Doug, hope all is well with you. A few notes as follow-up below:
We haven’t used N4 for bias correction ourselves much nor explored it carefully, as we have been fairly happy with the N3/’zheng’ approach (using the recommendations from Zheng et al.) - we will compare them some time in the near future. For now, given the experience with FS7.1.1 default N4 corrections, we are going to stick with the MNI N3 zheng (stronger bias) call options we used before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4). We did rerun several of the recent 7.1.1 cases with our n3/zheng approach and it has improved the correction in our data, including no longer tlrc failures, improved signal falloff correction for better temporal lobe, improved hippocampal segmentations. Here are a couple of examples:
Above - aseg 7.1.1 default missed hpc on left, with n3/zheng captured hpc
Above - aseg 7.1.1 default poorly separated hpc and amyg on left, better with n3/zheng on right
One naïve question, with respect to then4 performance/parameters, my read from our _mri_nu_correct.mni.log_, it looked like there /might/ be some parameters that were passed along to nu_correct for ANTS (in blue bold below) but perhaps were not actually implemented (in red bold below), but I am not experienced with the tool so wouldn’t know if my interpretation is correct.In the _mri_nu_correct.mni.log_, these parameters looked passed to nu_correct_:_
·/usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --*ants-n4 --n 1 --proto-iters 1000 --distance 50*
nIters 1
mri_nu_correct.mni 7.1.1 …
·*AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz …*
Regardless, given these changes for v7.x with ANTSN4 that no longer calls any -3T option, it might be best if references to this flag are modified on the web, unless other options become available, to avoid confusione.g.,*recon-all - - help* still says:
USING IMAGES FROM A 3T SCANNER
The -3T flag enables two specific options in recon-all for images acquired with
a 3T scanner: 3T-specific NU intensity correction parameters are used in the
Non-Uniform normalization stage, and the Schwartz 3T atlas is used for
Talairach alignment.
*And the -3T option *is still listed on*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags https://secure-web.cisco.com/1qWJAa1w89BVjc_2u-k770IRxnYxWfhFv-4PiiCN0ELPBcgXFOevUsxihVa9q1MA-0VLPNvyYvjSRPC81FBPRROG-BCCrIQQ7bO2FQ5VRIx7WlYhEwZe7sURclpdH1sbCTNav7gBi_puZRzOI8WfOC3-A5_70kUR5Aw5ixUQ1hgJWdsxWov453-vpY_1_57KV2DBgIEyW-MT9jN1Khjg_uugq7mglKSj7r5dELisweIITVp0iY7zuZEUgBPH0vIz8MQsdqtuWEE-DTW3ghp7XkdkZt_bEuu58XwpNriLw3-L0re7D2JswMTB-WD_1y-hO/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F19bDyVsWA2VNmfjDVR4NdZRObv2oMAe1YgFh8RMURNxDtmnRvsa8NHwVzKJGFycLCRWDLEt43ivmjXyCgYE7ytfazB2fcnaz2ChVhTTad9tvdS-yyDHfPesaHONuGsPwJ1UhFx6WzHOujAv3neqcF1RiTxQer3Ua0t-qZMl1EOt0dlKqiJGpEpmVaX-ZUAA5CkKBEHWF2UGcaXpfL5VCP4Ggwp5yg6gA_SAhQ5q-qG7kwEVQ75foJ9o3UAxhOH6Ge0miiY6fjJFOjxzQdHxsMsMqjvn65HR_EXltxgsgHtsisJV8vwzcuqzDHsD0jYGvzGS7Xqj3BUZe7n2i8tiSR0Q%2Fhttps%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FOtherUsefulFlags__%3BJSUlJSU%21%21LLK065n_VXAQ%210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql5Eehpwt%24
Many thanks for your time,
Peace,
Chris
--
Christine Fennema-Notestine, Ph.D.
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, November 19, 2021 7:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
* External Email - Use Caution * We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks: 1.In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. 2.However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) /[instead of MNI N3 (i.e., nu_correct)]/, the effect of specifying the recon-all-3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: 1.In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not.We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. 2.When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. 3.Beloware the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs: _mri_nu_correct.mni.log:_ ... */usr/local/freesurfer/bin/mri_nu_correct.mni* *--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50* nIters 1 mri_nu_correct.mni 7.1.1 ... *AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz* Using shrink factor: 4 ... -- Christine Fennema-Notestine, Ph.D. _______________________________________________ Freesurfer mailing list 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/1JwW-pb4AjhzP9JiHfjhrTLesYQA9nfddqGQz_lsbroBm6gZ2k5VBAnBlY3btY5Jr3ORyDUi97nNQ6XDUkrkmzdM5cDqNNcecZwS-wo5nL45RYEsOi9-UfnFpDGcTDoUhBjgdeAxyCWW-pI2odfQ4ChjccoObNv06gcXFJHjWLT_-nxQkEh-tPbNl0XplSzW9POgtsJZOIFpcVF0G8M9RMM2x3DBswaNzGodyIfOInLmPW1JuH_R1eR5UaxHCYA7Sp5bS3dKHG4ZzIchlMFNnE1wpvaxO3JGYuoh3BCmi_8bBMdl15KACMWcGEkB5lpvw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1iDii7PTjyE7hqHFAGRGEtH7wDeNykG82TpJx5_5DvQWY6nBoAdQf5TYh18p7-8Q6LPo2dmfjfrS0Ex1KK6wQWkrcQrQkKmZR_C_u4GSKtT1x2jvoZbgagtGAR2CFwf7u4fU7eZV9WJqMncCpmTanU99o8Oy2G94tKC3l62wvZPIGEwtUVRyJLsSTWw2crETL1lmjXU4pfAr5HWw6rAmF1dMKvq6kMPyjiShEZmWDq7RU8W7wNXHyET3ns9CPdGsABeL6lbgOrfwcssl5BuqxsvPabMko4yQFOo7PfAYIOmvBKRak9Rc_ziamOrO6O38WLXzBAKC5CtAZoV6iQoiVuw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21LLK065n_VXAQ%2A213glO-Pijub1d2M9d2JMIlztBfjL4AwXovJpK1Vcd9ONoxkRauTMtgsEBKDgj7eFr%2A24__%3BJSUlJSUlJSUlJSUlJSUl%21%21LLK065n_VXAQ%210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql-b5_a2h%24>
External Email - Use Caution
Hi, Doug,
Thanks for checking, the two questions were:
-were there different parameters for the AntsN4 call that were not getting used, or did I misread that (second paragraph below)?
-and then just a request to note somewhere in the online/help files that the -3T flag is no longer an option, since it still looks as though they are in the links noted below
Many thanks, Chris
-- Christine Fennema-Notestine, Ph.D.
From: Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, December 10, 2021 3:40 PM To: Notestine, Christine fennema@health.ucsd.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: FW: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Chris, I saw that you posted this a 2nd time. Did you have a question to be answered or is this just a comment? doug
On 12/6/2021 12:06 PM, Notestine, Christine wrote:
External Email - Use Caution Thanks for the confirmation, Doug, hope all is well with you. A few notes as follow-up below:
We haven’t used N4 for bias correction ourselves much nor explored it carefully, as we have been fairly happy with the N3/’zheng’ approach (using the recommendations from Zheng et al.) - we will compare them some time in the near future. For now, given the experience with FS7.1.1 default N4 corrections, we are going to stick with the MNI N3 zheng (stronger bias) call options we used before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4). We did rerun several of the recent 7.1.1 cases with our n3/zheng approach and it has improved the correction in our data, including no longer tlrc failures, improved signal falloff correction for better temporal lobe, improved hippocampal segmentations. Here are a couple of examples: [cid:image001.png@01D7EE82.AE399F10]- Above - aseg 7.1.1 default missed hpc on left, with n3/zheng captured hpc [cid:image002.png@01D7EE82.AE399F10] Above - aseg 7.1.1 default poorly separated hpc and amyg on left, better with n3/zheng on right
One naïve question, with respect to the n4 performance/parameters, my read from our mri_nu_correct.mni.log, it looked like there might be some parameters that were passed along to nu_correct for ANTS (in blue bold below) but perhaps were not actually implemented (in red bold below), but I am not experienced with the tool so wouldn’t know if my interpretation is correct. In the mri_nu_correct.mni.log, these parameters looked passed to nu_correct:
1. /usr/local/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.1.1 …
2. AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz …
Regardless, given these changes for v7.x with ANTSN4 that no longer calls any -3T option, it might be best if references to this flag are modified on the web, unless other options become available, to avoid confusion e.g., recon-all - - help still says: USING IMAGES FROM A 3T SCANNER The -3T flag enables two specific options in recon-all for images acquired with a 3T scanner: 3T-specific NU intensity correction parameters are used in the Non-Uniform normalization stage, and the Schwartz 3T atlas is used for Talairach alignment.
And the -3T option is still listed on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JvN_sdYBzRh5mYOX_eKCh8leEgaeZBNXbbHaEHcJUfVgmt...https://secure-web.cisco.com/1X7i__TMBOHAIPGpbGcQyjL9Lt89OK41f4sb7002Zd69S8O-ryku89LmLR_2BDciiamvlbWS34Ms7ZE6eyCEi0qekI3fVAQTirQsg6_syQO1Uei-ww1i6FE-vzmtViL0VjuQujS8hzguq-DCv2vSg6t8_E7vT9pJRfmI7dHN460OC8sceV32OkENmux1UcDeMI5k1XBcMLRKN0O9G4qDGOWGV9zkp3Ko1hiajt4yVHFyjOhASbDccKU8y5pkMgc-rqGxscK7u3ro-dqxZcaqJ0vM-YN8JVcQWtFpzzjRu8IUOD9Ccs2pNUmxOcFQ03zCyeq_5cJSMnOTNHu47knpYFQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1qWJAa1w89BVjc_2u-k770IRxnYxWfhFv-4PiiCN0ELPBcgXFOevUsxihVa9q1MA-0VLPNvyYvjSRPC81FBPRROG-BCCrIQQ7bO2FQ5VRIx7WlYhEwZe7sURclpdH1sbCTNav7gBi_puZRzOI8WfOC3-A5_70kUR5Aw5ixUQ1hgJWdsxWov453-vpY_1_57KV2DBgIEyW-MT9jN1Khjg_uugq7mglKSj7r5dELisweIITVp0iY7zuZEUgBPH0vIz8MQsdqtuWEE-DTW3ghp7XkdkZt_bEuu58XwpNriLw3-L0re7D2JswMTB-WD_1y-hO%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F19bDyVsWA2VNmfjDVR4NdZRObv2oMAe1YgFh8RMURNxDtmnRvsa8NHwVzKJGFycLCRWDLEt43ivmjXyCgYE7ytfazB2fcnaz2ChVhTTad9tvdS-yyDHfPesaHONuGsPwJ1UhFx6WzHOujAv3neqcF1RiTxQer3Ua0t-qZMl1EOt0dlKqiJGpEpmVaX-ZUAA5CkKBEHWF2UGcaXpfL5VCP4Ggwp5yg6gA_SAhQ5q-qG7kwEVQ75foJ9o3UAxhOH6Ge0miiY6fjJFOjxzQdHxsMsMqjvn65HR_EXltxgsgHtsisJV8vwzcuqzDHsD0jYGvzGS7Xqj3BUZe7n2i8tiSR0Q%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2FOtherUsefulFlags__%2A3BJSUlJSU%2A21%2A21LLK065n_VXAQ%2A210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql5Eehpwt%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacEflFTMZ%24
Many thanks for your time, Peace, Chris
-- Christine Fennema-Notestine, Ph.D.
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 Sent: Friday, November 19, 2021 7:58 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
External Email - Use Caution We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks:
1. In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly.
2. However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) [instead of MNI N3 (i.e., nu_correct)], the effect of specifying the recon-all -3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction:
1. In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not. We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script.
2. When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs.
3. Below are the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs:
mri_nu_correct.mni.log: ... /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 ... AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz Using shrink factor: 4 ...
-- Christine Fennema-Notestine, Ph.D.
_______________________________________________
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/1J53TTlZCH4vaQ1mw6rKctm-5NwN02ntibnlMu-8lQw4zT_...https://secure-web.cisco.com/1JnoRDgGzzpL4k6oc6L2mC7mz-e-f94f-orLdwLZ6Y3Pw6ryJKxztg9JAsptY96AqzdLjsBrvuOVKxYZtFeJ5R1Z5RENXNEMtGy-uIYb-R0BJNF95fMnFQThI5_k8BSLzFqGrdTMU4qjfpBy_2vC-Cx-QJqlsJL4L8zynIxgAQQ9y4j2-fBJkece4InS-LQs64qK4Jb-FNBKO8Ld6ihAQZyXWmvz3x1cySPBzF9b6qJIUgWo7PRyblGCC-XYS_jMWCc5xU4rHmLcuZkVkKDhkvnXFOkVwhZF2KiiqbOtu9PFgzhaSvqHN7dYqpAHC8-L65PwrPQytOfpVAMq7JVYQQQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1JwW-pb4AjhzP9JiHfjhrTLesYQA9nfddqGQz_lsbroBm6gZ2k5VBAnBlY3btY5Jr3ORyDUi97nNQ6XDUkrkmzdM5cDqNNcecZwS-wo5nL45RYEsOi9-UfnFpDGcTDoUhBjgdeAxyCWW-pI2odfQ4ChjccoObNv06gcXFJHjWLT_-nxQkEh-tPbNl0XplSzW9POgtsJZOIFpcVF0G8M9RMM2x3DBswaNzGodyIfOInLmPW1JuH_R1eR5UaxHCYA7Sp5bS3dKHG4ZzIchlMFNnE1wpvaxO3JGYuoh3BCmi_8bBMdl15KACMWcGEkB5lpvw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1iDii7PTjyE7hqHFAGRGEtH7wDeNykG82TpJx5_5DvQWY6nBoAdQf5TYh18p7-8Q6LPo2dmfjfrS0Ex1KK6wQWkrcQrQkKmZR_C_u4GSKtT1x2jvoZbgagtGAR2CFwf7u4fU7eZV9WJqMncCpmTanU99o8Oy2G94tKC3l62wvZPIGEwtUVRyJLsSTWw2crETL1lmjXU4pfAr5HWw6rAmF1dMKvq6kMPyjiShEZmWDq7RU8W7wNXHyET3ns9CPdGsABeL6lbgOrfwcssl5BuqxsvPabMko4yQFOo7PfAYIOmvBKRak9Rc_ziamOrO6O38WLXzBAKC5CtAZoV6iQoiVuw%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fmail.nmr.mgh.harvard.edu%2A2A2Fmailman%2A2A2Flistinfo%2A2A2Ffreesurfer__%2A2A3B%2A2A21%2A2A21LLK065n_VXAQ%2A2A213glO-Pijub1d2M9d2JMIlztBfjL4AwXovJpK1Vcd9ONoxkRauTMtgsEBKDgj7eFr%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUl%2A21%2A21LLK065n_VXAQ%2A210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql-b5_a2h%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacJoiS0V_%24
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1hp-q0WZzjeZhybLCb1mt9mQUzzuUTcefKMUz62y_u7AbHYN...https://secure-web.cisco.com/1JlQlZAmvEoUKqqH0vbYkjvUtncg8yXY-StcrFzvx-b8flZslPzqrjsW-r0L8ALYTO9Zy9xl9PIg8QuL3yOXD2LL7nXlcnCdaUQzEQp46PNQD0DYgoz9OCZLRKkVBkcaUrUtXsYrc3g9CYu9RZLNohslwy9NDM8fodd0DAfDZwM24bGp36SudYshFOekIbYx4QrFa-A4U-AkomO31EAXFMA02OZbXxvkopmp65E5cTBIOKWFG4TGMUcUEa4ZKb3unSfVOB51Khqdbk1BRCt4WVYpvqxGeviXbNLv0DoNFwbvbCMQAHEFhDaFnNXunjOTO8AxpuErWaqpFVhIQMnhXQw/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacBToCL2c%24 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
On 12/11/2021 2:31 PM, Notestine, Christine wrote:
External Email - Use Caution
Hi, Doug,
Thanks for checking, the two questions were:
-were there different parameters for the AntsN4 call that were not getting used, or did I misread that (second paragraph below)?
No, they were not getting used.
-and then just a request to note somewhere in the online/help files that the -3T flag is no longer an option, since it still looks as though they are in the links noted below
Sorry, I'll try to add something. BTW, you can still use the original MNI n3 if you create an expert options file with the content mri_nu_correct.mni --no-ants-n4 In that case, all your usual options will work doug
Many thanks,
Chris
--
Christine Fennema-Notestine, Ph.D.
*From:*Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Friday, December 10, 2021 3:40 PM *To:* Notestine, Christine fennema@health.ucsd.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: FW: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working
Hi Chris, I saw that you posted this a 2nd time. Did you have a question to be answered or is this just a comment? doug
On 12/6/2021 12:06 PM, Notestine, Christine wrote:
* External Email - Use Caution * Thanks for the confirmation, Doug, hope all is well with you. A few notes as follow-up below: We haven’t used N4 for bias correction ourselves much nor explored it carefully, as we have been fairly happy with the N3/’zheng’ approach (using the recommendations from Zheng et al.) - we will compare them some time in the near future. For now, given the experience with FS7.1.1 default N4 corrections, we are going to stick with the MNI N3 zheng (stronger bias) call options we used before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4). We did rerun several of the recent 7.1.1 cases with our n3/zheng approach and it has improved the correction in our data, including no longer tlrc failures, improved signal falloff correction for better temporal lobe, improved hippocampal segmentations. Here are a couple of examples: - Above - aseg 7.1.1 default missed hpc on left, with n3/zheng captured hpc Above - aseg 7.1.1 default poorly separated hpc and amyg on left, better with n3/zheng on right One naïve question, with respect to then4 performance/parameters, my read from our _mri_nu_correct.mni.log_, it looked like there /might/ be some parameters that were passed along to nu_correct for ANTS (in blue bold below) but perhaps were not actually implemented (in red bold below), but I am not experienced with the tool so wouldn’t know if my interpretation is correct.In the _mri_nu_correct.mni.log_, these parameters looked passed to nu_correct_:_ 1./usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --*ants-n4 --n 1 --proto-iters 1000 --distance 50* nIters 1 mri_nu_correct.mni 7.1.1 … 2.*AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz …* Regardless, given these changes for v7.x with ANTSN4 that no longer calls any -3T option, it might be best if references to this flag are modified on the web, unless other options become available, to avoid confusione.g.,*recon-all - - help* still says: USING IMAGES FROM A 3T SCANNER The -3T flag enables two specific options in recon-all for images acquired with a 3T scanner: 3T-specific NU intensity correction parameters are used in the Non-Uniform normalization stage, and the Schwartz 3T atlas is used for Talairach alignment. *And the -3T option *is still listed on *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags <https://secure-web.cisco.com/1YPqIsOd6V69HkwAd5K-Nx-He-uSEqPEDaKlbScMcqIrXNuaNfGCU3_mb4LkrUuDeiqgLpDCjd8jqC62tQx4kWcQ6xQh2wdMbLy4Ra372g5gOauES1gUWkiyH3EXx3QuWv5-Xv5z_NrueqfP2XKYm-PMpx3xIp-fNFBdqt_lgH_f8lmuaR6R0UaQLcodz2LXU_yx7TKlcO2wWiFIDOXCsrLX3KIxXR_Eo7LazmSZDB4aNc9dX3Hr_ncbpl5rtJJgAnfDE5K6I4YeVesUCDsVxHP9Guf7tp9rF0H4hp4O5uJYIklO5nrGUW-rcAkprRkwa/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1qWJAa1w89BVjc_2u-k770IRxnYxWfhFv-4PiiCN0ELPBcgXFOevUsxihVa9q1MA-0VLPNvyYvjSRPC81FBPRROG-BCCrIQQ7bO2FQ5VRIx7WlYhEwZe7sURclpdH1sbCTNav7gBi_puZRzOI8WfOC3-A5_70kUR5Aw5ixUQ1hgJWdsxWov453-vpY_1_57KV2DBgIEyW-MT9jN1Khjg_uugq7mglKSj7r5dELisweIITVp0iY7zuZEUgBPH0vIz8MQsdqtuWEE-DTW3ghp7XkdkZt_bEuu58XwpNriLw3-L0re7D2JswMTB-WD_1y-hO%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F19bDyVsWA2VNmfjDVR4NdZRObv2oMAe1YgFh8RMURNxDtmnRvsa8NHwVzKJGFycLCRWDLEt43ivmjXyCgYE7ytfazB2fcnaz2ChVhTTad9tvdS-yyDHfPesaHONuGsPwJ1UhFx6WzHOujAv3neqcF1RiTxQer3Ua0t-qZMl1EOt0dlKqiJGpEpmVaX-ZUAA5CkKBEHWF2UGcaXpfL5VCP4Ggwp5yg6gA_SAhQ5q-qG7kwEVQ75foJ9o3UAxhOH6Ge0miiY6fjJFOjxzQdHxsMsMqjvn65HR_EXltxgsgHtsisJV8vwzcuqzDHsD0jYGvzGS7Xqj3BUZe7n2i8tiSR0Q%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2FOtherUsefulFlags__%2A3BJSUlJSU%2A21%2A21LLK065n_VXAQ%2A210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql5Eehpwt%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacEflFTMZ%24> Many thanks for your time, Peace, Chris -- Christine Fennema-Notestine, Ph.D. *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Friday, November 19, 2021 7:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug On 11/15/2021 12:52 PM, Notestine, Christine wrote: * External Email - Use Caution * We recently moved to FreeSurfer 7.1.1 running it on ~ 100 different types of cases using the -3T options, but after a case failure, we looked deeper into the v7.x changes related to bias correction, and it seems that using the -3T option did not produce a different bias corrected outcome than using the default for any cases (see description below). IF this is truly the case, our workaround would be to continue using the MNI N3 approach options we had before (e.g., an expert option file with the line: mri_nu_correct.mni --no-ants-n4), since that improved the correction in our data previously, but would like to make sure we are interpreting the v7 approach correctly. Thoughts on this appreciated, many thanks: 1.In earlier FreeSurfer versions, we used the options based on the Zheng paper with N3 as recommended for 3T data. So with our switch to v7.1.1 which is now using ANTs N4, we looked into the 3T options with the flags described on the wiki, and used those flags in our runs accordingly. 2.However, once we had this case failure (which had worked in a prior FS version run with the N3 3T flags), we dug into things and did some test runs. We found that in Freesurfer v7.1.1 when using ANTs N4 (i.e., AntsN4BiasFieldCorrectionFs) /[instead of MNI N3 (i.e., nu_correct)]/, the effect of specifying the recon-all-3T (or -nuintensitycor-3T) option did not change the outcome relative to the default bias correction: 1.In v7.1.1, it seems that when ANTs N4 is used for bias field correction, the same bias field correction is performed whether the -3T (or -nuintensitycor-3T) option is specified or not.We assessed this by creating nu.mgz difference images (between runs with and without the -3T option) and confirmed by reviewing logs and the mri_nu_correct.mni script. 2.When the ANTs N4 bias field correction is used with the -3T options, the parameters for stronger bias field correction (i.e., "--n 1 --proto-iters 1000 --distance 50") are passed to mri_nu_correct.mni, but then seem to be dropped by mri_nu_correct.mni and not included in the subsequent call to AntsN4BiasFieldCorrectionFs. 3.Beloware the relevant lines extracted from a mri_nu_correct.mni.log when stronger bias field correction was specified via the -3T (or -nuintensitycor-3T) option to recon-all but the parameters do not seem to be used by ANTs: _mri_nu_correct.mni.log:_ ... */usr/local/freesurfer/bin/mri_nu_correct.mni* *--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50* nIters 1 mri_nu_correct.mni 7.1.1 ... *AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.2116356/nu0.mgz* Using shrink factor: 4 ... -- Christine Fennema-Notestine, Ph.D. _______________________________________________ Freesurfer mailing list 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/1YKkejSNDK2YGiz72rcp9WAQhI2pOUqQOG8Qzd8KPhx_AneXudzsWVXvQihY8upR0HVEXdrwlP4xufxwcKSSR8acJ6mv2q1Bw8u1ofNy1KjU4d0Oir8fAYr0zt7EQm0GLOTC47OoJ02hrmYFYPnZ3tUBTUO05DI4hnilkqPrD87B7Nzr_zSTVWfM0bSKN8V1F12dpEaOZ9nBUID8ET5f_eL1xNYfew_27RrcyyemHEQ3s6CTRqvSF5wTGxYW3BdXevuTIhpGdZzuMQ_AKnjR5TjXIOBb_JgTztlro9r7O0S2WFDcLZFQiUdUcYcbfMDhv/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1JwW-pb4AjhzP9JiHfjhrTLesYQA9nfddqGQz_lsbroBm6gZ2k5VBAnBlY3btY5Jr3ORyDUi97nNQ6XDUkrkmzdM5cDqNNcecZwS-wo5nL45RYEsOi9-UfnFpDGcTDoUhBjgdeAxyCWW-pI2odfQ4ChjccoObNv06gcXFJHjWLT_-nxQkEh-tPbNl0XplSzW9POgtsJZOIFpcVF0G8M9RMM2x3DBswaNzGodyIfOInLmPW1JuH_R1eR5UaxHCYA7Sp5bS3dKHG4ZzIchlMFNnE1wpvaxO3JGYuoh3BCmi_8bBMdl15KACMWcGEkB5lpvw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1iDii7PTjyE7hqHFAGRGEtH7wDeNykG82TpJx5_5DvQWY6nBoAdQf5TYh18p7-8Q6LPo2dmfjfrS0Ex1KK6wQWkrcQrQkKmZR_C_u4GSKtT1x2jvoZbgagtGAR2CFwf7u4fU7eZV9WJqMncCpmTanU99o8Oy2G94tKC3l62wvZPIGEwtUVRyJLsSTWw2crETL1lmjXU4pfAr5HWw6rAmF1dMKvq6kMPyjiShEZmWDq7RU8W7wNXHyET3ns9CPdGsABeL6lbgOrfwcssl5BuqxsvPabMko4yQFOo7PfAYIOmvBKRak9Rc_ziamOrO6O38WLXzBAKC5CtAZoV6iQoiVuw%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fmail.nmr.mgh.harvard.edu%2A2A2Fmailman%2A2A2Flistinfo%2A2A2Ffreesurfer__%2A2A3B%2A2A21%2A2A21LLK065n_VXAQ%2A2A213glO-Pijub1d2M9d2JMIlztBfjL4AwXovJpK1Vcd9ONoxkRauTMtgsEBKDgj7eFr%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUl%2A21%2A21LLK065n_VXAQ%2A210aRoJKanFx3X_f0qmmYUgHbehfXQN_0y4Fpp1feVdGYt2zvVs1zMFlsql-b5_a2h%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacJoiS0V_%24>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1EsFNtDp61wZq_gEnEornsDb8_EabPvwD-2Dq4ypD8e0XqRdxkbHbUobzpQQ2jksOAFSVj56w9mJafVKYv44I-o7qD4DwxxaUaKe6HDlhH1yikPH9z4gxiI-XvUbGrdWIP9E4CNJirVWA7dHhiqIZwYFwZSHhlOzfx7wl96SHM49IA0NTMSNv3nSHYHQJcoL0FkNsJ8qUaebkjY1z8GUYIuBu8npLpWxW6IOF5fO7rd5yXz3BulBiA3H6qI9nSKHILgQ3nUhfiMb-OpNzXcYCAFeNuaXXvKmiVp2ocylinrejZF-Xnal8BsRuY632nXuH/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LLK065n_VXAQ%211Xl9HlqPOybUHqjDdXwB7JJ-2DPmL0qiKS-g4P6fw9vHnWMuh2eEugIacBToCL2c%24 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Notestine, Christine