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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 > https://secure-web.cisco.com/1H0DGfoWjqvWtfPHbOVzsUFsTrg89bxFuT18k2Q5AbrjgfhvkTyZnswJKggUvFS2NBKSZSqLMPeitKcFg3RImdyhVtRcK2BTCxXYulSNgvyndCVBn8FEwlOGKI1oiJzv0lDF95za3a-0SeOg9in0-O9uWMbBkTA8cPzzqbI-K5rEtKHGRknQMS9PoA3RCog1oOZ_sLgKQ8ZCI_0h0behiNqYJh8bPp44CikPqx95dE84yWjXOjVvbB_P_w9C1emEVGR_jLTXlJhFYXdEStBUCFXcDESpP6tyfBr9q_mALkD5a6EA7yZ1UDAwfCGnEgo0HRNM49k2nHo3i5HQf-krmxQ/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 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.
