External Email - Use Caution Sorry for the confusion, but as you may have realized I am dealing with quite an intricated mess. My main objective is to realize a 3D model of this brain, so that I need to extract the white matter and pial surfaces, as well as the other subcortical surfaces. As I am dealing with a bad white matter segmentation, I would like to check if the new wm surfaces are rebuilt correctly, though I have a serious problem with that due to this apparently unfixable offset error. Also, I was wondering if after fixing the wm.mgz file I should correct somehow the aseg.mgz file with my new segmentation.
The warning message I reported previously was, I think, the reason behind this issue. Thanks in advance, Tommaso Mariani Il Mar 25 Mar 2025, 14:39 Douglas N. Greve <dgr...@mgh.harvard.edu> ha scritto: > Sorry, I'm a little lost as to what problem we are trying to solve. In > your first post, you included some warnings, but I'm not sure if those > warnings are actual errors. Can you restate your problem? > > > On 3/17/2025 11:24 AM, Tommaso Mariani wrote: > > External Email - Use Caution > The error occurred just immediately after having loaded the surfaces in > freeview. There have been no modifications as the output is the one that is > given straight out of recon-all command. The issue is encountered both in > freesurfer 7.2.0 and 7.4.1 versions. > > For what concern the wm edits, I performed some volume edits hoping to fix > the hypo- and hyper-intensity problems, but it is more of a side question > with respect to the main problem, that is the misregistration of the > surfaces. > > As for the offset, I mean that the surfaces are not overlapping the volume > images, not the orig.mgz nor the wm.mgz ones, giving me the feeling that > there is a misregistration problem. > I tried to treat it as a tailarach.xfm error, so after following the > tutorial I performed the command > tkregisterfv --s ./subj01 --fstal > Though the recon-all launched after this did not produce anything > different from the beginning. > > I tried the command > mri_convert --conform ./subj01/mri/orig.mgz orig_fixed.mgz > And it gives me as output the message: > > input_transform(): error reading transform elem [1,1] > input_transform: error reading transform > error: error loading transform from <path_to_file>/talairach.xfm > > The xform info prints out this matrix: > x_r = -1.0000 y_r = 0.0000 z_r = 0.0000 c_r = 0.9241 > x_a = 0.0000 y_a = 0.0000 z_a = 1.0000 c_a = -5.7364 > x_s = 0.0000 y_s = -1.0000 z_s = -0.0000 c_s = -19.9210 > > If you need anything else please reach me out. > I am available also to schedule a brief call to find out what's going on, > as this issue is what keeps me apart from being able to use the brain model > for an important project. > > Thank you in advance, > Tommaso Mariani > > Il Lun 17 Mar 2025, 14:56 Douglas N. Greve <dgr...@mgh.harvard.edu> ha > scritto: > >> Did that error happen before you did anything to the volume? Can you give >> a list of commands you used to get to that point? What do you mean by >> offset? >> >> On 3/10/2025 4:23 AM, Tommaso Mariani wrote: >> >> External Email - Use Caution >> Hi everyone, >> I am experiencing a tricky situation in freesurfer. Due to hypo- and >> hyper-intensity problems I obtained a bad reconstruction and I've been >> working on it since. My first question is then: do I need to refresh the >> aseg file after the wm.mgz intensities modifications? >> >> However I also noticed that when I loaded the surface to verify the >> corrections they were all with a significant offset and this message was >> printed on the console: >> Warning: MatrixInverse failed. >> Did not find any volume info >> Warning: MatrixInverse failed. >> Did not find any volume info >> Warning: MatrixInverse failed. >> Did not find any volume info >> Warning: MatrixInverse failed. >> Did not find any volume info >> >> Together with that, I was also unable to obtain the final parcellization, >> possibly due to the absence of correlation between the volumes and surfaces. >> I already tried to manually adjust the offset and relaunch the >> reconstruction, as suggested in the Freesurfer documentation for tailarach >> errors, but it looks like it did nothing to it. >> >> If you need any file or info to examine the situation further, feel free >> to contact me, I would really appreciate your help. >> Thanks in advance, >> Tommaso Mariani >> >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1MF4VrRpcUL4tNPaYzZXJN_TaugHjriEpwuogrix64KA2RSbILH5jbyn4zZL6m9jVX2yrbI2rVWdqHBB3Fg5tlkDpTXF7enyCKZcg7v-MO1JJFU6AQDLYnYVK-zIWkFtUvawsNDck35NSFlhkv6RMLkjT_8gdO9paSMwGriUhJP6UuDymO6nluHxuujoMJz0SOT0qrezxpV5Z3bZHvyvfrf9sIRx5muBKEh9DISfS-Xm2CmMmGSVUElWqwdZEzp4lP4fn4MuyczfZcOmUbPWZrX2k7KMH-PoecPeDPn3dSXvgx65Y9ZJe7Hjqtnza8npuYAFgjMhP31ZUqWzfLKFSYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1qGUxMURp_i4a-2P85dBz7fWQoRYvCnTZtY_bLPDHGvvIvc1EZ2BIjoVkeTPEb6FR_uLZjaOD97F8oyJkjm_a4wsN7RliogjVOhrGNm-4PSDW9INpb-2EDiXo1mQa03Is3PqOwjhRPom4bHSZB2N1RhAoCrUq-Z2zcRBCtl_Pjg8bCF00JG7fHLT3fgPobLVUcIcoBl02pt3154ty8QcXBUKwbRfl_igChzO7y4s2aoWSXe1wtV7WdG7ejPM1fpNfMX89DnXk6aqfeJrKbCYGXXYhv5nnELAZbIwZjMxdnTcYhs4rF3NftUMgp4-5lQhC9G9ndq0bUhuyOALSyC-KeQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> 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/1MF4VrRpcUL4tNPaYzZXJN_TaugHjriEpwuogrix64KA2RSbILH5jbyn4zZL6m9jVX2yrbI2rVWdqHBB3Fg5tlkDpTXF7enyCKZcg7v-MO1JJFU6AQDLYnYVK-zIWkFtUvawsNDck35NSFlhkv6RMLkjT_8gdO9paSMwGriUhJP6UuDymO6nluHxuujoMJz0SOT0qrezxpV5Z3bZHvyvfrf9sIRx5muBKEh9DISfS-Xm2CmMmGSVUElWqwdZEzp4lP4fn4MuyczfZcOmUbPWZrX2k7KMH-PoecPeDPn3dSXvgx65Y9ZJe7Hjqtnza8npuYAFgjMhP31ZUqWzfLKFSYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1qGUxMURp_i4a-2P85dBz7fWQoRYvCnTZtY_bLPDHGvvIvc1EZ2BIjoVkeTPEb6FR_uLZjaOD97F8oyJkjm_a4wsN7RliogjVOhrGNm-4PSDW9INpb-2EDiXo1mQa03Is3PqOwjhRPom4bHSZB2N1RhAoCrUq-Z2zcRBCtl_Pjg8bCF00JG7fHLT3fgPobLVUcIcoBl02pt3154ty8QcXBUKwbRfl_igChzO7y4s2aoWSXe1wtV7WdG7ejPM1fpNfMX89DnXk6aqfeJrKbCYGXXYhv5nnELAZbIwZjMxdnTcYhs4rF3NftUMgp4-5lQhC9G9ndq0bUhuyOALSyC-KeQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> 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 *MailScanner has detected a possible >> fraud attempt from "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1hgRj9A22fsL9VztJqa0d9IZJbc5ccmHJWD0Sq7bvmTiqC6VMN76BsqsW255ODH3fSef4x_D4BS3BzPpM8MAPl-5Vb93pfGYbOoEzXVVxuGoZeIHAAfy7A8d7pwEbeleq4KEjZRaTxoDBUGDfNEu7loE2lXu5Iu_KWTXnTWXvJZ72puEZq01L69i1nDqX5cwFP_ZD24VafBx4KndasCPdGvdRWTmr502bj-Fg4aMI0R6SCHCNiUT2bUNRwkMeheJ7uCHZCuZQ0k15tL9IjZHkWdHo7lCc5kkvWDh26GS7t5lr2C-clXf12Vr04p6koEPqaHYS-QWqeysO3ZgE0bPChA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <https://secure-web.cisco.com/1H0DGfoWjqvWtfPHbOVzsUFsTrg89bxFuT18k2Q5AbrjgfhvkTyZnswJKggUvFS2NBKSZSqLMPeitKcFg3RImdyhVtRcK2BTCxXYulSNgvyndCVBn8FEwlOGKI1oiJzv0lDF95za3a-0SeOg9in0-O9uWMbBkTA8cPzzqbI-K5rEtKHGRknQMS9PoA3RCog1oOZ_sLgKQ8ZCI_0h0behiNqYJh8bPp44CikPqx95dE84yWjXOjVvbB_P_w9C1emEVGR_jLTXlJhFYXdEStBUCFXcDESpP6tyfBr9q_mALkD5a6EA7yZ1UDAwfCGnEgo0HRNM49k2nHo3i5HQf-krmxQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> <*MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1hgRj9A22fsL9VztJqa0d9IZJbc5ccmHJWD0Sq7bvmTiqC6VMN76BsqsW255ODH3fSef4x_D4BS3BzPpM8MAPl-5Vb93pfGYbOoEzXVVxuGoZeIHAAfy7A8d7pwEbeleq4KEjZRaTxoDBUGDfNEu7loE2lXu5Iu_KWTXnTWXvJZ72puEZq01L69i1nDqX5cwFP_ZD24VafBx4KndasCPdGvdRWTmr502bj-Fg4aMI0R6SCHCNiUT2bUNRwkMeheJ7uCHZCuZQ0k15tL9IjZHkWdHo7lCc5kkvWDh26GS7t5lr2C-clXf12Vr04p6koEPqaHYS-QWqeysO3ZgE0bPChA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <https://secure-web.cisco.com/1H0DGfoWjqvWtfPHbOVzsUFsTrg89bxFuT18k2Q5AbrjgfhvkTyZnswJKggUvFS2NBKSZSqLMPeitKcFg3RImdyhVtRcK2BTCxXYulSNgvyndCVBn8FEwlOGKI1oiJzv0lDF95za3a-0SeOg9in0-O9uWMbBkTA8cPzzqbI-K5rEtKHGRknQMS9PoA3RCog1oOZ_sLgKQ8ZCI_0h0behiNqYJh8bPp44CikPqx95dE84yWjXOjVvbB_P_w9C1emEVGR_jLTXlJhFYXdEStBUCFXcDESpP6tyfBr9q_mALkD5a6EA7yZ1UDAwfCGnEgo0HRNM49k2nHo3i5HQf-krmxQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> >> . >> 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 mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1MF4VrRpcUL4tNPaYzZXJN_TaugHjriEpwuogrix64KA2RSbILH5jbyn4zZL6m9jVX2yrbI2rVWdqHBB3Fg5tlkDpTXF7enyCKZcg7v-MO1JJFU6AQDLYnYVK-zIWkFtUvawsNDck35NSFlhkv6RMLkjT_8gdO9paSMwGriUhJP6UuDymO6nluHxuujoMJz0SOT0qrezxpV5Z3bZHvyvfrf9sIRx5muBKEh9DISfS-Xm2CmMmGSVUElWqwdZEzp4lP4fn4MuyczfZcOmUbPWZrX2k7KMH-PoecPeDPn3dSXvgx65Y9ZJe7Hjqtnza8npuYAFgjMhP31ZUqWzfLKFSYA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 > https://secure-web.cisco.com/1hgRj9A22fsL9VztJqa0d9IZJbc5ccmHJWD0Sq7bvmTiqC6VMN76BsqsW255ODH3fSef4x_D4BS3BzPpM8MAPl-5Vb93pfGYbOoEzXVVxuGoZeIHAAfy7A8d7pwEbeleq4KEjZRaTxoDBUGDfNEu7loE2lXu5Iu_KWTXnTWXvJZ72puEZq01L69i1nDqX5cwFP_ZD24VafBx4KndasCPdGvdRWTmr502bj-Fg4aMI0R6SCHCNiUT2bUNRwkMeheJ7uCHZCuZQ0k15tL9IjZHkWdHo7lCc5kkvWDh26GS7t5lr2C-clXf12Vr04p6koEPqaHYS-QWqeysO3ZgE0bPChA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1hgRj9A22fsL9VztJqa0d9IZJbc5ccmHJWD0Sq7bvmTiqC6VMN76BsqsW255ODH3fSef4x_D4BS3BzPpM8MAPl-5Vb93pfGYbOoEzXVVxuGoZeIHAAfy7A8d7pwEbeleq4KEjZRaTxoDBUGDfNEu7loE2lXu5Iu_KWTXnTWXvJZ72puEZq01L69i1nDqX5cwFP_ZD24VafBx4KndasCPdGvdRWTmr502bj-Fg4aMI0R6SCHCNiUT2bUNRwkMeheJ7uCHZCuZQ0k15tL9IjZHkWdHo7lCc5kkvWDh26GS7t5lr2C-clXf12Vr04p6koEPqaHYS-QWqeysO3ZgE0bPChA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
