Re: [Freesurfer] .lta vs .dat questions
External Email - Use Caution Also - what does the "fscale" in the .lta file refer to? On Wed, Oct 18, 2023 at 1:40 PM Corinna Bauer wrote: > Thanks, Yujing. > > Do you know why the output of mri_vol2vol would be different if using the > .lta vs the .dat file? And, if the .dat file was verified/modified using > tkregister2, would the .lta file also be updated accordingly? > > Thanks > > Corinna > > On Wed, Oct 18, 2023 at 1:35 PM Huang, Yujing > wrote: > >> Hi Corinna, >> >> >> >> Here is an explanation of register.dat - >> https://secure-web.cisco.com/1LS1n_2IFmJqHufz_79O5K0eXjVtJxKQ0M6GnUF8GTuXJ1hdSOEcVCFw0R8yMW2Y1jgy8peX9T-wJQ3wK2BorIgXBj9SQO6MxLK3ix-2yrwMlihqiQOzEoHAmviNae3952L8fdk7MYa6sQQJKXTTdLP5wQ2vNtf_j38OOauga-zD9SdvPRc2oY1BY-xN_y-gHOCSBSwUQmdxnYQGGahqm2UQFD6jKJeqtTLBhV4hdDPkXGCMbiTYTXGizMklYCF2jyPoMKM3Oau76fV69ViR3BQnT22lkaONK3HyGMCcUckfJwCPvSDEpNjFD7zKGD0plVt7AGXzc5-xFqFm41YHwLQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRegisterDat >> >> >> >> You can use lta_convert to convert it to .lta - >> https://secure-web.cisco.com/12rpvh0XjUz2-jniVSUqU1AOUWpta2BodBDpKZEVJD4ENU0az5aprsFnxJ2Xq3EJljG4yku3hu6wouX8puqdN29uVnd8sNGzs8JxTjdzwsAq-aGkus8O94Lmmfrl3wWoRMxa1UxYl_yrFCHU0gR19TT_Ac-nLLZ_kkUc2hLFa6iqSxnlzi8vtoYLeR-xVZLD8fMWApj0lVt4OZ1RdySoyrigPKQczeFeFuIF1nfFHguD9X8OdW6ro7vbHilJaObjOditWRg59h3YWZPpJ_w_ptoQ4m4xYr0WC24_na0NDpMOrqhlxmOWIhYJU4fcoFONzP6wkK1g5-E6ct-kmF89Yaw/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdocs%2Fhtml%2Flta_convert.help.xml.html >> >> >> >> Best, >> >> >> >> Yujing >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer >> *Sent:* Wednesday, October 18, 2023 1:07 PM >> *To:* Mailing Freesurfer List >> *Subject:* [Freesurfer] .lta vs .dat questions >> >> >> >> *External Email - Use Caution* >> >> Hi all, >> >> >> >> Can someone please explain the difference between .lta and .dat and why >> the registration looks different using the two file types? >> >> >> >> If bbregister outputs were already checked and edited (if needed) using >> the .dat file, is there a way to convert it to .lta? >> >> >> >> Thanks >> >> Corinna >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1cCURlH2rsF7a_rdopihVolJEJYrznX-K16dBDu_UZJVhBVLtCj81G12j-H9BhtvUwla42BLONtT9PDRNg-sM5L37LuFySBFMVho0240RcPN9eH-dfT3wqRguRVMe0euRm5gsR_ZSBrAnKj9R18oQraRUGBw19RM0MllJKpdLby_WYLwR9n-yOYCk8fUKbPDjfKVM2dLMLrVZ-mpRyZwypt4QVfl1amM5bZBi5h_RASo6lhIejVdTNpcRuFHyH1M8RQiv2k8GiNoojzqy2B4vP-L7WjPEcy2dBNHhJfuxX26dQdgo4XFM2vEvOWu-VzHzvoVOCQSc9cLP-vyJ6JXXSw/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/1WXM78vaVt7PvzqIf_iooZttprzGgfe5O9ArjWbEXjGqFtIRPK80Su176VZClBBzkooCQnEg7zJivrwAT3ZGnYK7ipSs1Kar6JqLhKo_1bDWBKaoU8mGr8hfQkaLxJ0Kmaww6E-_yfj01aihxH8UYWeOfHqupUa9cT-5mu_T9Zj4-F9Mf5hLBOy0M4Z_pEWZ7LqMGXz8k_5gncM4tKqCZqV8hZXAOg-yIJSQ7568gRV_rRulWnNeBZrGZ3vfT9E_GWotLZKLlyzjB1ZmfXYYBZE9fMlz6NgJV52guAH31YgMjc4UO7kUkhn9M6KbhxNvfC9vRdpjV1j43R-Gprv8YbA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> < >> https://secure-web.cisco.com/1WXM78vaVt7PvzqIf_iooZttprzGgfe5O9ArjWbEXjGqFtIRPK80Su176VZClBBzkooCQnEg7zJivrwAT3ZGnYK7ipSs1Kar6JqLhKo_1bDWBKaoU8mGr8hfQkaLxJ0Kmaww6E-_yfj01aihxH8UYWeOfHqupUa9cT-5mu_T9Zj4-F9Mf5hLBOy0M4Z_pEWZ7LqMGXz8k_5gncM4tKqCZqV8hZXAOg-yIJSQ7568gRV_rRulWnNeBZrGZ3vfT9E_GWotLZKLlyzjB1ZmfXYYBZE9fMlz6NgJV52guAH31YgMjc4UO7kUkhn9M6KbhxNvfC9vRdpjV1j43R-Gprv8YbA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] .lta vs .dat questions
External Email - Use Caution Thanks, Yujing. Do you know why the output of mri_vol2vol would be different if using the .lta vs the .dat file? And, if the .dat file was verified/modified using tkregister2, would the .lta file also be updated accordingly? Thanks Corinna On Wed, Oct 18, 2023 at 1:35 PM Huang, Yujing wrote: > Hi Corinna, > > > > Here is an explanation of register.dat - > https://secure-web.cisco.com/1ra4diNfN_fjAekHFqsVn05LTbo_657kTJfEnoybjelcGzH0pIVdxtz010SL5pau4xOG1iywa5quVIedFVd5v4oCaqMX_8FIRjg8PrU2okrJKrvUHQCbHxM-1gSfWimysPfd44InIdIpl1z0EPQOFMumNq5xnBV1gI31KSUyrMEm4nOx4SEy94Re2OUDu8IaPNjRPNJenHwcdRgzC5cSmnwZjhxyd1P9n9-j5Y1MbzxAvnIJ_P13olBEXx0oJcrKSWHxxQLff_GMcdpx7ccr5BDX_biEvw5HUqc-H8Rsk67Tp66xYz4x14e839ZKevE6kBWy7PiDBwcAFdZVIMV90NA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRegisterDat > > > > You can use lta_convert to convert it to .lta - > https://secure-web.cisco.com/1h0zvo9fq2j9AC7lsGapA2gW2HogA1BN1EJT2UHeCOKcU3N-q24ZxsTrCQd-2d4F5kD2DdgcgmbBCtHkzlm1yw_hT6Rgrk1ZXXlF9wki1qjhS3UMnVFhbWIKDsvpCwv-nYqYfedm8dH4_Bbaux6UtK1NN5K-mPhu2QbSDWdNkJeQHuQBaath-lbHYkmUtxe1xMk33byn09AJDXqXbyWKvhPr_hITzheCAREB03CRU_yratMZHD9Ab6z4x7DEIm6DKsLMBC9kK_UVGfpHKUSi420ojYdC4F9NC8wIlyehD72MqUbkTKytE-fYJykGNSve2R39Y_NHkUqQKPA57p6TFxg/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdocs%2Fhtml%2Flta_convert.help.xml.html > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer > *Sent:* Wednesday, October 18, 2023 1:07 PM > *To:* Mailing Freesurfer List > *Subject:* [Freesurfer] .lta vs .dat questions > > > > *External Email - Use Caution* > > Hi all, > > > > Can someone please explain the difference between .lta and .dat and why > the registration looks different using the two file types? > > > > If bbregister outputs were already checked and edited (if needed) using > the .dat file, is there a way to convert it to .lta? > > > > Thanks > > Corinna > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/126CfwO1bNB3bHSlqCqf4N1K0QLpadHYENY4ftDr_0mPAt-d3W7WWfquC7ybCM-Y5Miyy6VfrPIQ_EOb1e0g1Oe_kUcHpYq9sBbqu6W3_2GBL1XPbJNKs8J5aL833gzRKGIagIfsYa_IfPsQLInhrcFOdZ89JpfYZPfKZP0G526kRy1C4Dspye0DLhNeSSNICzIz__3Emx4RAWvHAixIjgt7xIdg8htwRnBAuzoLLHj8nuSbzslEyURVSrQBhQ45bTct_vHYyhOHaK11Wzj9VKioRU0BA2GVlJe3fvLLIn4lFgX2wX2Xuvm4PzaAYK60xwyPz6cHj_nWgdu6uEkCG3g/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/1QbP9B4RFYsaZegPIlu43MVy0HaaIWl3iHsl5T-P2VK0FSfTH-Dfbkw-W3VF6Enqt2oWs0WwPn4KN9uOwzoRjV9574prZ6f2_xJEEqUnblmzHvE-L14XWhBKXbJ_a9jqNS02h_s8RxN2PV-nDeWZrVvNEgnkx8W8NbBQcCsxdpFb5svU_ROYHPZsJivwIuTAqcr_v26J_sx8zsIzSnTjqSB8TAEWjYi33R_tmW7j3bIBzW9l-pRKtYaemyCJcFabc-XpnyHRg8n87_5QVivT10igTh_-84ZZ4xFpmzsHTE51XOLkw_pbYBh7jHJFEcdjMCxk42qDYGpvqIpcubUxZ0g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1QbP9B4RFYsaZegPIlu43MVy0HaaIWl3iHsl5T-P2VK0FSfTH-Dfbkw-W3VF6Enqt2oWs0WwPn4KN9uOwzoRjV9574prZ6f2_xJEEqUnblmzHvE-L14XWhBKXbJ_a9jqNS02h_s8RxN2PV-nDeWZrVvNEgnkx8W8NbBQcCsxdpFb5svU_ROYHPZsJivwIuTAqcr_v26J_sx8zsIzSnTjqSB8TAEWjYi33R_tmW7j3bIBzW9l-pRKtYaemyCJcFabc-XpnyHRg8n87_5QVivT10igTh_-84ZZ4xFpmzsHTE51XOLkw_pbYBh7jHJFEcdjMCxk42qDYGpvqIpcubUxZ0g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] .lta vs .dat questions
External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert it to .lta? Thanks Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Postdoctoral fellow in multimodal neuroimaging
External Email - Use Caution We are seeking a full-time postdoctoral fellow with a strong background in resting state fMRI data analysis to join our team. We aim to better understand the neural correlates of visual perceptual dysfunctions observed in survivors of brain injury. We are actively working on an R01-funded project investigating the potential link between thalamocortical networks and severity of visual impairments. The multimodal project includes structural, diffusion, relaxometry, and functional MRI, in addition to behavioral correlates. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of fMRI (resting state and task), particularly focusing on network-based approaches • Strong coding skills in python, MATLAB, bash, etc. • Experience with multimodal neuroimaging datasets is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, and their C.V. to Corinna Bauer (corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure-web.cisco.com/1ly1VCBmruOLMT0T7zR9O1yCBITb75_g6M5rEL4v_nj-QPTxvCe3-MaPrRJomE1lvdst99SBeDcCPJ19CAaBmj5P_t8Etrmj7i4iJU1jrbQ93Sct5Qg5oEuUA480MsncKCDF4M6V--nQs0wCWwZ-44h04jQOPbK7WHpzixzNcX8Oj94h04JJT_lROUWxecm7rhIUm1WYTLDMEQJsqFiUDmTGsX_EWwsZpcNIUWaALqxzs1oTCSQTppR_gw9rgjZKJaIpVBR9FhgeExGKHp8hngKCcgAaGfSrYZyZsmciYSrhEzzoo3gIIH80iMToMaiuQcjn-FGXii9D4mF15JYzEAw/https%3A%2F%2Fpartners.taleo.net%2Fcareersection%2Fex%2Fjobdetail.ftl%3Fjob%3D797690 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] matlab runtime error
External Email - Use Caution Hi Andrew, I commented out the LD_LIBRARY_PATH from my .bashrc and that worked. Thanks! Corinna On Wed, Sep 1, 2021 at 10:53 PM Hoopes, Andrew wrote: > Hi Corinna, > > Do you happen to have the LD_LIBRARY_PATH environment variable set in your > shell? If so, I would unset it. LD_LIBRARY_PATH tends to mess with any > programs linked to dynamic libraries. In this case, it’s forcing freeview > to load the wrong matlab Qt libraries. > > Andrew > > > > *From: *freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Corinna Bauer < > corinna...@gmail.com> > *Date: *Wednesday, September 1, 2021 at 4:58 PM > *To: *Mailing Freesurfer List > *Subject: *[Freesurfer] matlab runtime error > > *External Email - Use Caution* > > Hi all, > > > > I ran a few subjects successfully through7.1.1, but when I got to check > the surfs in freeview I get an error about the Matlab runtime libraries > below. However, I already have those libraries and the 2014b runtime > environment installed on my Ubuntu 18.04. > > > > freeview: > /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5X11Extras.so.5: no > version information available (required by freeview) > freeview: > /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Core.so.5: no > version information available (required by freeview) > freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Gui.so.5: > no version information available (required by freeview) > freeview: > /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Widgets.so.5: no > version information available (required by freeview) > freeview: relocation error: freeview: symbol > _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not > defined in file libQt5Widgets.so.5 with link time reference > > > > I also tried re-installing the 2014b MCR, but get this message: > > fs_install_mcr R2014b > curl: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libcurl.so.4: no > version information available (required by curl) > curl: (48) An unknown option was passed in to libcurl > > > > Let me know how to best proceed. > > > > Thanks! > > > > Corinna > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1JuNRBt4pRa-DlUzxRgUW2HW7pGIYr8KWK7LPMy3VUXHJUB6q2GOt_hkmcs59HZ5ZLjf6su5txdEHCbm9oP1IY-ol3Dcxl-_sg61KpT0L51SNejUoJwQllwjMvOXYXa2hkWyHos-6oh9Ja5NwRZjFj6UouNtz8pw0v_67S0NKtU_Pq-Lolk79wiVk0jZ1As6Fhm8GpD2GUJiotddkRYG0VXE5mnCnz36KX0ym7kTlWRQ4LZSsi_YgYUZNsGvTgIGe8nj25NE_YLfQz74AeY5rvQ/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 > http://secure-web.cisco.com/193_xsi6IL32fBljIhVqQkYng0l7QITM1-EhQpnQsrXJ9RKTlytbyRz4WsENGvr1bKdhmsjZyydzpEt2f3RnIec3xB0tzcwBySVx_l3nUTfgBEf2fsxLzI2Q32Q1CrW3ZrZXl5Jic4wfNA70ieiuV2BXYhQ1eJt4RFPA2xVu3ldO6_llpAmYI-8HgOxdsMpGtS3gnCbPH17bLbX8Qfnb6drTqoXpTQSH-ovsqxCJrbmYwfvz_HGKEjQmfOAzG5GGxQPDS6jVVj21kSWGFKt-jiw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] matlab runtime error
External Email - Use Caution Hi all, I ran a few subjects successfully through7.1.1, but when I got to check the surfs in freeview I get an error about the Matlab runtime libraries below. However, I already have those libraries and the 2014b runtime environment installed on my Ubuntu 18.04. freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5X11Extras.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Core.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Gui.so.5: no version information available (required by freeview) freeview: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libQt5Widgets.so.5: no version information available (required by freeview) freeview: relocation error: freeview: symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference I also tried re-installing the 2014b MCR, but get this message: fs_install_mcr R2014b curl: /usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64/libcurl.so.4: no version information available (required by curl) curl: (48) An unknown option was passed in to libcurl Let me know how to best proceed. Thanks! Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Diffusion MRI postdoc position
External Email - Use Caution We are seeking a full-time postdoctoral fellow with experience in diffusion analysis with an emphasis on network-based approaches, NODDI, DKI, and tract-specific analysis. The NIH-funded project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin in youths with perinatal brain injury. We are seeking a candidate with the following qualifications: • Doctoral degree in computer science, neuroscience, or related field • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches are required • Strong coding skills in python, MATLAB, bash, etc. • Experience with fMRI design and analysis is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure-web.cisco.com/1PRcDuRd4mfRf2yIwKkDZ9B-oKmLA-2p68m-jCGxuMCJA8f7glCaKVcnpLSpPymTt5LL_ZZz1U6rPVyfpHRKJLCccf5seuMcS1PXZEr8k1BHYaGIcq6Uath-xRSXPCk_uk4uupQNIGbsnwLQEe311E2piHwMds55ypOBZTLDS7Yr0a_lz1E_8gIKzILQjupT047BLy37LwFR3HEC-doUZ0nu0gx4y4ghXHSKkxWNkp5qn7nGIuXcrWbbdGoPcc8ClblJDqQ7sYU3Mp6_W6eZ_Ew/https%3A%2F%2Fpartners.taleo.net%2Fcareersection%2Fmee%2Fjobdetail.ftl%3Fjob%3D3145087%26tz%3DGMT-05%253A00%26tzname%3DAmerica%252FNew_York ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data
External Email - Use Caution Hi Bruce, I am just following up on this. Were you able to get mri_normalize to run on this mp2rage data? Thanks, Corinna On Wed, May 5, 2021 at 6:50 PM Corinna Bauer wrote: > Great, thanks. The nu.mgz is attached. > > Corinna > > On Wed, May 5, 2021 at 6:47 PM Fischl, Bruce > wrote: > >> H, if you send us the data we will take a look. Just the inputs to >> mri_normalize should do it for this case >> >> Cheers >> >> Bruce >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer >> *Sent:* Wednesday, May 5, 2021 6:45 PM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage >> with MP2RAGE data >> >> >> >> *External Email - Use Caution* >> >> Hi Bruce, >> >> >> >> The nu.mgz input into mri_normalize looks ok to me (screenshot attached), >> as does the talairach registration. >> >> >> >> Corinna >> >> >> >> On Wed, May 5, 2021 at 5:39 PM Fischl, Bruce >> wrote: >> >> Can you take a look at the volume that was the input to mri_normalize and >> see if it looks ok? And check the talairach >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Corinna Bauer >> *Sent:* Wednesday, May 5, 2021 5:25 PM >> *To:* Mailing Freesurfer List >> *Subject:* [Freesurfer] error at 3d normalization pass 1 of 2 stage with >> MP2RAGE data >> >> >> >> *External Email - Use Caution* >> >> Hello all, >> >> >> >> I am trying to run recon-all on MP2RAGE data from Philips and it exits >> with errors at this point: >> >> 3d normalization pass 1 of 2 >> error: No such file or directory >> error: MRInormFindControlPoints: could not find enough control points >> >> error: No such file or directory >> error: MRInormFindControlPoints failed >> Command exited with non-zero status 253 >> >> >> >> The log file is attached. The input file was the MPRAGE generated on the >> scanner console (i.e. not the T1 map). I attached a screenshot of orig.mgz >> viewed in fsleyes. Any thoughts? >> >> >> >> Thanks! >> >> >> >> Corinna >> >> >> >> >> >> >> >> >> >> ___ >> 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/1dzAvSjb2xg057o7RyKJZrQAEUSNDKYyNvvSNj-Q1W3fj-H7rQN0_ff1fiWYt1iDlHtBScp2B2qG_7V6pAC3VnocY5eFs09ranBO0u_df2FpxmcLu365FC1Y15JadBeoa_2tWHOeKnTqTJHjpUfi4lN96S0NtVGAhYVBzbw4nNZWWu5-xDrN-dnnMOECv_nfLkTj-OQ0D12o_YyFO9czOpW-8tR_HfnXEFCu5snUTMUT62UkuGNVpVyeJsWzZsaOxlxdGZqy1QTaz8wvCA_yC6w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1QClCCeXykBScK8d5iq23hqFkPyT2qn3mpaj7VqrhnWoppw9oWwy0qLPuD9BIPjTdeJa94TGnemkL_KiFjBw1Wab0D0mWH3IJcLKpIvh3BUof3t8xND1Fyb0C0Oy81H4-qCdUJdmt38iWTc8TpxDh5_Yw1cXNpgUms9JohWuBwdgsS9W1WTq8_GErqY8walozgYWnbL4e4RZVfRBjejiWh9MVvmJuNyYihX24Ofy5tor4iJ4p6qic2UQYV5acvEbhCfxcST0sNEFjuaaYSdzHLQ/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* >> http://secure-web.cisco.com/1QIBq5EkkrXvBYedkVZBu1QSZSDY095TOl1_qa7F6M9d384V_TiBzx8rtP2y1LY0qUU937Ep76OvJeSNG8W7gn90zPnconlxQz3REgfCZywQqlAgNwXjqNdAdZihdoDU9SNgTfFRqLSzO8tdbadQfW7KqJUz31LrH45xNuWPKESmVgd98gF47tyGMjvEeOC1vEsOoTg-ordFAzjIiS67kMRUD2Sd1QZdv-7XVlY8o5eMZYbxyL0CYM0a4RndPXCYmfxcQBQ1FbWBoGZVJmbFzDA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <http://secure-web.cisco.com/1rULMMfo2yJZfoOtKTGPpqqVNGJEBAprhcfVvdoBUoB2M0U0LN5Ib1EmDrEwQfMWyMihkXLjDkVDLndLYfy5LwXkc2vTFFfgEsqlxu1Up3X5u6qkNt1teQQ3ueOG6_nKKWudRc97_roeP5hWFLwK0sDUKUgARPFXIL6ebknC7hNQA7vWbISK-LumLErCyu5lA70JfJWkS6yWDb1-Bdmr-4tEp00GK5pxZEw6q1D0rF_KaCCuOjrZWKvhLFOTDfUTDj_fwFuJkjnTG8VGbxhSYUw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fco
[Freesurfer] postdoc opportunity in relaxometry and diffusion MRI
External Email - Use Caution We are seeking a full-time postdoctoral fellow with experience in diffusion analysis with an emphasis on network-based approaches, NODDI, DKI, and tract-specific analysis. The NIH-funded project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin in youths with perinatal brain injury. We are seeking a candidate with the following qualifications: • Doctoral degree with 0-1 years of related work experience • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches are required • Experience with multicomponent T2 relaxometry • Strong coding skills in python, MATLAB, bash, etc. • Experience working with clinical pediatric populations would be preferred • Experience with psychophysical assessments of functional vision would be advantageous, but not necessary • Experience with fMRI design and analysis is a plus Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( corinna_ba...@meei.harvard.edu). Additional details can be found at: https://secure-web.cisco.com/1suYTWqeXdTkzb6aG2C5Fq7YSTkFJR7uoBAOI8t8wYVZd8zkjakk1Jk8IPnDF8YcxfQ0XllRscGtS4ExHmdOKjhSM6LrmlIidjOxjdgzZt4ZUSwp0vkpWIEj3TkHUyMXJ54ttoj5qUWf1CxqTM4qksZXH_6syzY-RUrnZ6UWUkuyTwEcvzEkcujltI-Xxf183N5jWL98ASgZERDf-hoso3bjJKMHl_7LXWEi-Nz4yzQKDMLP8QcSQ6C-63sTmHa5NCY2BvaNkgmkJnvX1YSHDlA/https%3A%2F%2Fpartners.taleo.net%2Fcareersection%2Fmee%2Fjobdetail.ftl%3Fjob%3D3145087%26tz%3DGMT-05%253A00%26tzname%3DAmerica%252FNew_York ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Postdoctoral fellowship opportunity in diffusion MRI and functional vision
External Email - Use Caution *Thalamocortical connectivity and multicomponent T2 relaxometry in youths with neonatal periventricular white matter injury* NIH-funded Postdoctoral fellowship at the Schepens Eye Research Institute of Massachusetts Eye and Ear, Harvard Medical School in Boston, MA We are seeking a full-time postdoctoral fellow to work with Dr. Corinna Bauer on an NIH-funded project investigating the impact of neonatal thalamic injury on the development of vision-processing networks in the brain and corresponding visuo-perceptual dysfunctions. The project employs structural, diffusion, and relaxometry based MRI methods to target thalamo-cortical changes in morphometry, neural networks, and MRI-based markers of myelin. The position is available beginning Spring/Summer 2021. The initial time frame will be for 18 months with the possibility of extension. *Required Qualifications:* • Doctoral degree required with 0-1 years of related work experience • Strong coding skills in python, MATLAB, bash, etc. • Advanced skills in the processing and analysis of diffusion (including connectivity, DKI, and NODDI approaches) data, particularly focusing on network-based approaches • Strong publication record in neuroimaging, with a preference for a focus on multimodal techniques in neurodevelopmental disorders • Good command of the oral and written English language • Strong organizational and data management skills • Prior experience reviewing, analyzing, and summarizing scientific literature • Excellent attention to detail and interpersonal, organizational, writing, and project management skills *Preferred Qualifications:* • Experience with multicomponent T2 relaxometry • Experience working with clinical pediatric populations • Experience with psychophysical assessments of functional vision • Experience with fMRI design and analysis Interested candidates should send a cover letter including, a brief summary of their research interests and career goals, their C.V., and the names and phone numbers of three references to Corinna Bauer ( corinna_ba...@meei.harvard.edu). Review of applications will begin immediately and continue until the position is filled. Additional details can be found at: https://secure-web.cisco.com/1aWE_5wlqXvxDWmzy4gy3dtCobaxYZF4YKpgZiy1P01DGEYZwbSg27LiCtRPK8u58v7EEM-67EcJuhyW2AP6Q1v6wG5RmoqH4CJ9iEEYoQQ5PXLQYhzIQz_pklas6d7TdAGAwTEO4k8QmQb40JhJ575qoCDxsHWY92AR9qYkk00P64zLAyKXpGTbCmNrzbIhvLZtwS6Ir6ajcaUO_J5fB6yV-tvDjHyiVvCueVg0Hm_5eVd130H8Ca4eXkAld-xnFYcvqPv9c6oXStoGvXU5mew/https%3A%2F%2Fpartners.taleo.net%2Fcareersection%2Fmee%2Fjobdetail.ftl%3Fjob%3D3145087%26tz%3DGMT-05%253A00%26tzname%3DAmerica%252FNew_York *Massachusetts Eye and Ear is proud to be an equal-opportunity employer and is committed to providing a workplace free from harassment or discrimination. All employment decisions are made without regard to race, color, age, gender, gender identification, sexual orientation, religion, marital status, sex, pregnancy or conditions related to pregnancy, national origin/ancestry, citizenship, disability, military status, genetic information, or any other basis prohibited by law. These protections extend to all management practices and decisions, including recruitment and hiring practices, appraisal systems, promotions, training, and career development programs* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Discrepancy in volume calculated for thalamic nuclei in FreeSurfer
External Email - Use Caution Hi Doug, That is helpful, thank you. Best, Corinna On Tue, Jun 30, 2020 at 10:11 AM Douglas N. Greve wrote: > Hi Corinna, this is probably due to partial volume correction. The > thalamic seg does not just count up voxels. The underlying model is a > tetrehdra mesh, and that is used to compute partial volume. > doug > > > > On 6/29/2020 6:06 PM, Corinna Bauer wrote: > > External Email - Use Caution > Hello all, > > We are working on calculating the volume of thalamic nuclei in our > participants and noticed that there is often a discrepancy in measured > volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated > for the same thalamic nucleus using fslstats -V. (Note that the nuclei are > all created in FreeSurfer, just extracted to individual .nii files > afterwards). > > For example: in one control subject, the volume of the right VPL was > measured in FreeSurfer as 264.650938 mm^3, but the same extracted label in > fslstats shows a volume of 242 mm^3. What could be causing this discrepancy? > > Thanks > > Corinna > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Discrepancy in volume calculated for thalamic nuclei in FreeSurfer
External Email - Use Caution Hello all, We are working on calculating the volume of thalamic nuclei in our participants and noticed that there is often a discrepancy in measured volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated for the same thalamic nucleus using fslstats -V. (Note that the nuclei are all created in FreeSurfer, just extracted to individual .nii files afterwards). For example: in one control subject, the volume of the right VPL was measured in FreeSurfer as 264.650938 mm^3, but the same extracted label in fslstats shows a volume of 242 mm^3. What could be causing this discrepancy? Thanks Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MNI coordinates from Thalamic nuclei
External Email - Use Caution I have them already ask masks in subject space, but I am doing connectivity analysis on a few of them and would need the MNI coordinates of the centroids for visualizing those results. Thanks! On Fri, Feb 28, 2020 at 10:29 AM Glasser, Matthew wrote: > External Email - Use Caution > > Why not represent thalamic nuclei as the actual masks? Thalamic nuclei > are not single points. > > > > Matt. > > > > *From: * on behalf of Corinna > Bauer > *Reply-To: *Freesurfer support list > *Date: *Friday, February 28, 2020 at 9:26 AM > *To: *Mailing Freesurfer List > *Subject: *[Freesurfer] MNI coordinates from Thalamic nuclei > > > > *External Email - Use Caution* > > Hi all, > > Is there a way to obtain the MNI coordinates for the thalamic nuclei? > > > > Thanks > > > > > > Corinna > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI coordinates from Thalamic nuclei
External Email - Use Caution Hi all, Is there a way to obtain the MNI coordinates for the thalamic nuclei? Thanks Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Project functional region into white matter
External Email - Use Caution Would it be best to do option 1 in the CVS space or in subject space? On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes. The 2nd would dilate in all dimensions, but you would only keep > those voxels that were in WM. but the 1st is definitely cleaner > > On 12/18/19 2:52 PM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Ok thanks! The first option sounds like it might provide a cleaner > > result, since the second would dilate in all dimensions. > > I'll let you know if I run into any trouble with it. > > > > Thanks again, > > > > Corinna > > > > > > On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > off the top of my head I can think of a couple of ways > > 1. replicate the wmparc.mgz stream. For this you will need to > > create an > > annotation from your GM ROIs by combining them into a > > ssegmenation, then > > using mri_vol2surf to create a surface-based segmentation, then using > > mris_seg2annot, then use mri_aparc2aseg to create an > > aparc+aseg.mgz type > > file, then mri_aparc2aseg again to create the wmparc.mgz type > > file. This > > will take some trial an error as the command lines are a bit picky > > (esp > > mris_seg2annot) > > 2. simple dilation of the GM ROIs followed by taking an intersection > > with the WM mask. You can use mri_binarize to create the WM mask, > > then, > > for each GM ROI, use mri_binarize with the --dilate option to > > dilate a > > few voxels, then something like fscalc wmmask.mgz and > > roidilated.mgz -o > > roidilated-in-wm.mgz > > > > > > On 12/18/19 2:33 PM, Corinna Bauer wrote: > > > > > > External Email - Use Caution > > > > > > Hi Doug, > > > Yes, I have GM ROIs in CVS space and I'd like to create a > > > corresponding WM ROI for each of them that extends 2-3 voxels > > into the WM. > > > Would it be possible to create something akin to wmparc.mgz with > > these > > > ROIs? > > > > > > Corinna > > > > > > On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > > > mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>> > > wrote: > > > > > > Hi Corinna, if I understand correctly, you basically have > > cortical GM > > > ROIs in CVS space and you want to create an ROI of the adjacent > > > WM. Is > > > that right? How far do you want to extend the ROI into WM? > > Do you > > > want > > > to do something like a wmparc.mgz? > > > doug > > > > > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Hello all, > > > > > > > > I have a series of functionally-defined ROI volumes (.nii > > > format) that > > > > I'd like to project into the white matter to then be used for > > > > tractography. > > > > > > > > So far the vols have been brought from cvs_avg35 space > > into subject > > > > space from using mri_vol2vol and the corresponding m3z file. > > > This was > > > > followed by mri_vol2vol using the registration from > bbregister > > > to get > > > > the functional regions into diffusion space. > > > > > > > > I have done this for the ROIs in their original GM volume, > but > > > would > > > > now like to also have corresponding WM volumes for > > tractography. > > > > > > > > What is the best way to go about doing this? > > > > > > > > Thanks, > > > > > > > > Corinna > > > > > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > >
Re: [Freesurfer] Project functional region into white matter
External Email - Use Caution Ok thanks! The first option sounds like it might provide a cleaner result, since the second would dilate in all dimensions. I'll let you know if I run into any trouble with it. Thanks again, Corinna On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > off the top of my head I can think of a couple of ways > 1. replicate the wmparc.mgz stream. For this you will need to create an > annotation from your GM ROIs by combining them into a ssegmenation, then > using mri_vol2surf to create a surface-based segmentation, then using > mris_seg2annot, then use mri_aparc2aseg to create an aparc+aseg.mgz type > file, then mri_aparc2aseg again to create the wmparc.mgz type file. This > will take some trial an error as the command lines are a bit picky (esp > mris_seg2annot) > 2. simple dilation of the GM ROIs followed by taking an intersection > with the WM mask. You can use mri_binarize to create the WM mask, then, > for each GM ROI, use mri_binarize with the --dilate option to dilate a > few voxels, then something like fscalc wmmask.mgz and roidilated.mgz -o > roidilated-in-wm.mgz > > > On 12/18/19 2:33 PM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > Yes, I have GM ROIs in CVS space and I'd like to create a > > corresponding WM ROI for each of them that extends 2-3 voxels into the > WM. > > Would it be possible to create something akin to wmparc.mgz with these > > ROIs? > > > > Corinna > > > > On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > Hi Corinna, if I understand correctly, you basically have cortical GM > > ROIs in CVS space and you want to create an ROI of the adjacent > > WM. Is > > that right? How far do you want to extend the ROI into WM? Do you > > want > > to do something like a wmparc.mgz? > > doug > > > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > > > External Email - Use Caution > > > > > > Hello all, > > > > > > I have a series of functionally-defined ROI volumes (.nii > > format) that > > > I'd like to project into the white matter to then be used for > > > tractography. > > > > > > So far the vols have been brought from cvs_avg35 space into subject > > > space from using mri_vol2vol and the corresponding m3z file. > > This was > > > followed by mri_vol2vol using the registration from bbregister > > to get > > > the functional regions into diffusion space. > > > > > > I have done this for the ROIs in their original GM volume, but > > would > > > now like to also have corresponding WM volumes for tractography. > > > > > > What is the best way to go about doing this? > > > > > > Thanks, > > > > > > Corinna > > > > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Project functional region into white matter
External Email - Use Caution Hi Doug, Yes, I have GM ROIs in CVS space and I'd like to create a corresponding WM ROI for each of them that extends 2-3 voxels into the WM. Would it be possible to create something akin to wmparc.mgz with these ROIs? Corinna On Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Hi Corinna, if I understand correctly, you basically have cortical GM > ROIs in CVS space and you want to create an ROI of the adjacent WM. Is > that right? How far do you want to extend the ROI into WM? Do you want > to do something like a wmparc.mgz? > doug > > On 12/18/19 9:55 AM, Corinna Bauer wrote: > > > > External Email - Use Caution > > > > Hello all, > > > > I have a series of functionally-defined ROI volumes (.nii format) that > > I'd like to project into the white matter to then be used for > > tractography. > > > > So far the vols have been brought from cvs_avg35 space into subject > > space from using mri_vol2vol and the corresponding m3z file. This was > > followed by mri_vol2vol using the registration from bbregister to get > > the functional regions into diffusion space. > > > > I have done this for the ROIs in their original GM volume, but would > > now like to also have corresponding WM volumes for tractography. > > > > What is the best way to go about doing this? > > > > Thanks, > > > > Corinna > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Project functional region into white matter
External Email - Use Caution Hello all, I have a series of functionally-defined ROI volumes (.nii format) that I'd like to project into the white matter to then be used for tractography. So far the vols have been brought from cvs_avg35 space into subject space from using mri_vol2vol and the corresponding m3z file. This was followed by mri_vol2vol using the registration from bbregister to get the functional regions into diffusion space. I have done this for the ROIs in their original GM volume, but would now like to also have corresponding WM volumes for tractography. What is the best way to go about doing this? Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thalamus_proper or whole_thalamus volume measurement?
External Email - Use Caution Dear all, For the new thalamus nuclei segmentation there is a measurement for the whole left and right thalami. The values are different from the thalamus_proper values. Which output should be reported as the volume for the whole thalamus? Thank you Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011
Great, thank you! Best, Corinna On Thu, Jun 29, 2017 at 12:09 AM, Thomas Yeo wrote: > Hi Corinna, > > You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_ > JNeurophysiol11_SplitLabels.zip?dl=0 > > Regards, > Thomas > > > On Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer > wrote: > >> Dear Dr. Yeo, >> >> Our research group is currently trying to segment the Yeo atlas into >> separate labels, but just came across this thread which indicates that you >> have already done this. Would you be willing to re-share the link to your >> previously extracted individual labels from your 7 and 17 networks? >> >> Thank you! >> >> Corinna >> >> On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo >> wrote: >> >>> Hi Annie, >>> >>> I have previously extracted individual regions from the 7 and 17 >>> networks. You can download them here >>> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol >>> 11_SplitLabels.zip?dl=0). >>> Please see the README in the folder for more explanations. There >>> should be a precuneus DMN region. >>> >>> The 17 networks consist of 114 regions that have been previously >>> published: >>> >>> 1) Krienen et al., Reconfigurable state-dependent functional coupling >>> modes cluster around a core functional architecture. Philosophical >>> Transactions of the Royal Society B, 369:20130526, 2014 >>> >>> 2) Yeo et al., Functional connectivity during rested wakefulness >>> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158, >>> 2015 >>> >>> Hope this helps. >>> >>> Cheers, >>> Thomas >>> >>> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 wrote: >>> > Hello Dr. Yeo, >>> > >>> > Thank you for your previous help and reply. We've worked out the way to >>> > switch the resolution of parcellation and successfully extracted the >>> > anatomical information using your mask derived from iFC work. >>> > >>> > However, we came across a new problem to apply the cortical mask and >>> need >>> > your kind help again. We aim to conduct a seed-based analysis to >>> investigate >>> > structural covariance based on the network defined by iFC, and find >>> your >>> > work of cortical parcellation conceptually perfectly suit our research >>> > question. Based on the current approach, however, it seemed that we >>> could >>> > only extract the anatomical information from the whole well-defined >>> network, >>> > but not the specific hub within the network (e.g., the anatomical >>> > information of the precuneus from the DMN). We wonder if you have any >>> > suggestion to resolve our problem, ie, to be specific, is there any >>> way to >>> > only extract the discrete hub information rather than the whole >>> network? >>> > >>> > We really appreciate your generous help. Thank you very much. >>> > >>> > p.s. This email would also forward to my senior colleague, Dr. >>> Hsiang-Yuan >>> > Lin, who is a child and adolescent psychiatrist doing imaging research >>> in >>> > Taiwan. >>> > >>> > >>> > 2015-05-13 19:15 GMT+08:00 陳昱潔 : >>> >> >>> >> Hi Professor Yeo : >>> >> >>> >> Thank you for helping us so much! >>> >> After mris_anatomical_stat I tried aparcstats2table to extract the >>> table. >>> >> But I failed with generating the table. >>> >> >>> >> >>> >> Best wishes, >>> >> Annie >>> >> >>> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo : >>> >> >>> >>> Hi Annie, >>> >>> >>> >>> I assume this means 5202 is your subject ID? Maybe you should check >>> if >>> >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network >>> s_N1000.annot >>> >>> exist? >>> >>> >>> >>> If so, you can run mris_anatomical_stats to generate statistics for >>> >>> the parcellation. >>> >>> >>> >>> Cheers, >>> >>> Thomas >>> >>> >>> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 wrote: >>> >>> > Hi Professor Yeo : >>> >>
Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011
Dear Dr. Yeo, Our research group is currently trying to segment the Yeo atlas into separate labels, but just came across this thread which indicates that you have already done this. Would you be willing to re-share the link to your previously extracted individual labels from your 7 and 17 networks? Thank you! Corinna On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo wrote: > Hi Annie, > > I have previously extracted individual regions from the 7 and 17 > networks. You can download them here > (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_ > JNeurophysiol11_SplitLabels.zip?dl=0). > Please see the README in the folder for more explanations. There > should be a precuneus DMN region. > > The 17 networks consist of 114 regions that have been previously published: > > 1) Krienen et al., Reconfigurable state-dependent functional coupling > modes cluster around a core functional architecture. Philosophical > Transactions of the Royal Society B, 369:20130526, 2014 > > 2) Yeo et al., Functional connectivity during rested wakefulness > predicts vulnerability to sleep deprivation. Neuroimage 111:147-158, > 2015 > > Hope this helps. > > Cheers, > Thomas > > On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 wrote: > > Hello Dr. Yeo, > > > > Thank you for your previous help and reply. We've worked out the way to > > switch the resolution of parcellation and successfully extracted the > > anatomical information using your mask derived from iFC work. > > > > However, we came across a new problem to apply the cortical mask and need > > your kind help again. We aim to conduct a seed-based analysis to > investigate > > structural covariance based on the network defined by iFC, and find your > > work of cortical parcellation conceptually perfectly suit our research > > question. Based on the current approach, however, it seemed that we could > > only extract the anatomical information from the whole well-defined > network, > > but not the specific hub within the network (e.g., the anatomical > > information of the precuneus from the DMN). We wonder if you have any > > suggestion to resolve our problem, ie, to be specific, is there any way > to > > only extract the discrete hub information rather than the whole network? > > > > We really appreciate your generous help. Thank you very much. > > > > p.s. This email would also forward to my senior colleague, Dr. > Hsiang-Yuan > > Lin, who is a child and adolescent psychiatrist doing imaging research in > > Taiwan. > > > > > > 2015-05-13 19:15 GMT+08:00 陳昱潔 : > >> > >> Hi Professor Yeo : > >> > >> Thank you for helping us so much! > >> After mris_anatomical_stat I tried aparcstats2table to extract the > table. > >> But I failed with generating the table. > >> > >> > >> Best wishes, > >> Annie > >> > >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo : > >> > >>> Hi Annie, > >>> > >>> I assume this means 5202 is your subject ID? Maybe you should check if > >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_ > 7Networks_N1000.annot > >>> exist? > >>> > >>> If so, you can run mris_anatomical_stats to generate statistics for > >>> the parcellation. > >>> > >>> Cheers, > >>> Thomas > >>> > >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 wrote: > >>> > Hi Professor Yeo : > >>> > After I rechecked the directory and run again mri_surf2surf > >>> > I got the result: > >>> > "Saving target data > >>> > Converting to target annot > >>> > Saving to target annot > >>> > > >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_ > 7Networks_N1000.annot" > >>> > The file of 5202/label didn't come out with > >>> > lh.Yeo2011_7Networks_N1000.annot > >>> > But it seems succeed, right? > >>> > How can I get the stat of this parcellation ? > >>> > > >>> > Thank you very much! > >>> > > >>> > Best wishes, > >>> > Annie > >>> > > >>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo : > >>> > > >>> >> Hi Annie, > >>> >> > >>> >> mri_surf2surf is complaining that it cannot write out the > annotation. > >>> >> > >>> >> Just to clarify, is your subject called test_run_allindex? In other > >>> >> words, is the variable s equal to test_run_allindex? > >>> >> > >>> >> Does the directory "/home/annie/test_run_allindex/label/" exist? If > >>> >> not, then you first need to create the directory first, and then > >>> >> mri_surf2surf can write the resulting annotation file into the > >>> >> directory. > >>> >> > >>> >> Cheers, > >>> >> Thomas > >>> >> > >>> >> On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 wrote: > >>> >> > Hi Professor Yeo : > >>> >> > > >>> >> >We tried the code > >>> >> >>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh > >>> >> >>> --sval-annot > >>> >> >>> > >>> >> >>> > >>> >> >>> > >>> >> >>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_ > 7Networks_N1000.annot > >>> >> >>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot > >>> >> > However there came an error of "could not write annot file > >>> >> > /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_ > N1000.annot > >>> >> > No suc
Re: [Freesurfer] mri_cvs_register failure from missing shared lib
The comman was mri_cvs_register --mov MAE_06072013 --mni (because labels in MNI space were mapping incorrectly to subject space -- see this thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52786.html ) The log is attached. I killed the command once I saw the errors. Thanks! Corinna On Tue, Apr 25, 2017 at 2:46 PM, Z K wrote: > Hi Corinna, > > Its been awhile since Ive used Ubuntu12.04. Infact its End of Life date > is 3 days away ;) > > Can you please send me the command and the log file which gives the > exact error. Thanks. > > -Zeke > > On 04/25/2017 01:49 PM, Corinna Bauer wrote: > > Hi Zeke, > > > > I am also having this same problem. Even after completing the steps you > > listed above. I am running Ubuntu 12.04. > > > > Any suggetions? > > > > Thanks > > > > On Wed, May 28, 2014 at 1:50 PM, Z K > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > > > You will need to install libboost v1.41 onto your system. You should > be > > able to install it using yum: > > > > $>yum install boost-devel > > > > However, its possible that the version you get thru this method may > be > > incompatible with the version required by freesurfer. If the above > does > > not fix your issue, then download libboost > > (http://www.boost.org/users/history/version_1_41_0.html > > <http://www.boost.org/users/history/version_1_41_0.html>) and untar > > it. Then: > > > > >cd libboost_folder > > >mkdir libraries > > >./bootstrap.sh --prefix=./libraries > > >./bjam install > > >cd libraries/lib > > > ln -s libboost_program_options.so.1.41.0 > > libboost_program_options.so.5 > > >export > > LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/ > lib:$LD_LIBRARY_PATH > > > > Hope this helps and feel free to contact me if your having issues > > getting it to work. > > > > -Zeke > > > > On 05/28/2014 12:17 PM, Michael Waskom wrote: > > > Hi, I had mri_cvs_register die on me when it couldn't find a shared > > > library. Relevant bit is (full log is attached): > > > > > > mris_resample: error while loading shared libraries: > > > libboost_program_options.so.5: cannot open shared object file: No > such > > > file or directory > > > > > > Freesurfer bugr info: > > > > > > > > > > > > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 > > > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > > > > > RedHat release: Red Hat Enterprise Linux Server release 6.3 > (Santiago) > > > > > > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 > > > > > > -- > > > > > > Any thoughts on how to proceed? Thanks! > > > > > > Michael > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . 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. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > htt
Re: [Freesurfer] mri_cvs_register failure from missing shared lib
Hi Zeke, I am also having this same problem. Even after completing the steps you listed above. I am running Ubuntu 12.04. Any suggetions? Thanks On Wed, May 28, 2014 at 1:50 PM, Z K wrote: > You will need to install libboost v1.41 onto your system. You should be > able to install it using yum: > > $>yum install boost-devel > > However, its possible that the version you get thru this method may be > incompatible with the version required by freesurfer. If the above does > not fix your issue, then download libboost > (http://www.boost.org/users/history/version_1_41_0.html) and untar it. > Then: > > >cd libboost_folder > >mkdir libraries > >./bootstrap.sh --prefix=./libraries > >./bjam install > >cd libraries/lib > > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5 > >export > LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH > > Hope this helps and feel free to contact me if your having issues > getting it to work. > > -Zeke > > On 05/28/2014 12:17 PM, Michael Waskom wrote: > > Hi, I had mri_cvs_register die on me when it couldn't find a shared > > library. Relevant bit is (full log is attached): > > > > mris_resample: error while loading shared libraries: > > libboost_program_options.so.5: cannot open shared object file: No such > > file or directory > > > > Freesurfer bugr info: > > > > > > > > FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > > > RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) > > > > Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 > > > > -- > > > > Any thoughts on how to proceed? Thanks! > > > > Michael > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] volume in native space of .vtk file in mni152 space
Hi Antonin,
Thank you for your input. I will give mri_cvs_register a try.
Best,
Corinna
On Mon, Apr 24, 2017 at 10:24 AM, Antonin Skoch wrote:
> Dear Corinna,
>
> I am not sure what is (or whether is) something wrong with your commands,
> but in any case I would be cautious of interpretation of results using such
> method, mainly from following reasons:
>
> 1.
> mni152reg uses 12 DOF whole-brain registration. You cannot expect to get
> perfect alignment of subcortical regions using such crude transform. To
> obtain more precise transform, I would use either registration targeted
> specifically to subcortical regions (e.g. using first_flirt in FSL, which
> is, however, still affine only), or use mri_cvs_register.
>
> 2.
> Due to no reasonable contrast within thalamus to allow to distinguish the
> nuclei using even state-of-the-art MR imaging, such registration-based
> atlas method would by necessity be a simple transfer of predefined atlas
> onto the subject space, with no information to guide the alignment within
> the thalamus itself (it would basically be a best-guiess of where these
> nuclei might be, with no scope for subject-specific refinement).
>
> Antonin Skoch
>
>
> Hi al, Just wondering if anyone has any suggestionsto my previous question
> as to why the volume from mni152 space would be rotated, even though the
> MNI152 to subject T1 alignment looks good?
>
> As a recap, here are my commands:
>
> mni152reg --s ${subject} --1
>
> tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ
> /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg
> ${reg_file}
>
> mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ
> /home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg
> ${reg_file} --inv --o ${out_dir}/lh_global.nii.gz
>
> tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov
> ${out_dir}/lh_global.nii.gz -fminmax .5 1
>
> ___
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
[Freesurfer] volume in native space of .vtk file in mni152 space
Dear all, I have a series of .vtk files in MNI152 1mm space from an external thalamus atlas outlining specific thalamic nuclei. I would like to put these into native subject space and calculate the volume from each nuclei. I would imagine that I would do the following: 1. run mni152reg --s --1 on each subject 2. mri_vol2vol --mov mni152space_atlas_file.nii.gz -- targ subject/mri/orig.mgz --reg subject/mri/mni152.orig.mgz.reg --inv --o newoutputfile_subject_space But then I am not certain how to calculate the volume of the new output file. Suggestions? Thanks! Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] seed to seed resting state?
Is there a way to implement it in an earlier version? On Tue, Mar 7, 2017 at 9:36 PM, Douglas Greve wrote: > yes, v6 > > On 3/7/17 8:18 PM, Jinsong Tang wrote: > > Hi Doug， > > I am also interested in seed to seed resting state analysis. > > It seems no fcseedcor command in Freesurfer v5.3.? Is it command in v6.0? > > Thanks and best, > > Jinsong > > > > > On Mon, Mar 6, 2017 at 10:13 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Try fcseedcor. Run with -help to get docs >> >> >> On 03/06/2017 09:52 AM, Corinna Bauer wrote: >> > Hi, just following up on this question to see if there were any >> > suggestions for how to best complete seed to seed RS analysis in >> > FreeSurfer. >> > >> > Thanks! >> > >> > Corinna >> > >> > On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer > > <mailto:corinna...@gmail.com>> wrote: >> > >> > Hi all, >> > >> > I was just wondering if it was possible to do seed to seed resting >> > state analysis in freesurfer, rather than seed to voxel? I am >> > wanting to examine connectivity within specific Yeo networks, >> > using a spherical ROI as a seed. The spherical ROI will be >> > generated from one of the peak areas of activation listed in the >> > original 7 network Yeo paper. >> > >> > Thanks >> > >> > Corinna >> > >> > >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 <(617)%20724-2358> >> Fax: 617-726-7422 <(617)%20726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . 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. >> >> > > > -- > Jinsong Tang, MD > Institute of Mental Health > The Second Xiangya Hospital , Central South University > 139 Renmin Road, Changsha Hunan 410011, P.R. China > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] seed to seed resting state?
Hi, just following up on this question to see if there were any suggestions for how to best complete seed to seed RS analysis in FreeSurfer. Thanks! Corinna On Thu, Mar 2, 2017 at 12:09 PM, Corinna Bauer wrote: > Hi all, > > I was just wondering if it was possible to do seed to seed resting state > analysis in freesurfer, rather than seed to voxel? I am wanting to examine > connectivity within specific Yeo networks, using a spherical ROI as a seed. > The spherical ROI will be generated from one of the peak areas of > activation listed in the original 7 network Yeo paper. > > Thanks > > Corinna > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] seed to seed resting state?
Hi all, I was just wondering if it was possible to do seed to seed resting state analysis in freesurfer, rather than seed to voxel? I am wanting to examine connectivity within specific Yeo networks, using a spherical ROI as a seed. The spherical ROI will be generated from one of the peak areas of activation listed in the original 7 network Yeo paper. Thanks Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster
Should be, so long as it is the uncorrected value. Is that the CWPmax? On Mon, Oct 3, 2016 at 2:57 PM, Douglas N Greve wrote: > In the table produced by glmfit-sim, the maximum vertex-wise uncorrected > -log10(p) is given. Is that enough? > > > On 10/03/2016 02:55 PM, Corinna Bauer wrote: > > Hi all, just following up on my previous question. For the purposes of > > showing uncorrected p-values <0.005 as well as the corrected results > > (via mri_glmfit-sim) I would like to get the table of uncorrected > > p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir > > --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but > > there has gone through the simulations. I would like the raw p-values > > from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd > > file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex > > --glmdir rh.thick.noreg.sm08.glmdir > > > > What command would I use? > > > > Thanks > > Corinna > > > > > > On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer > <mailto:corinna...@gmail.com>> wrote: > > > > Hello all, > > > > I would like to get a table of the uncorrected p-values to compare > > with the corrected ones obtained using mri_glmfit-sim. I tried the > > following, which outputs a table of clusters and their vertices, > > but it does not include p-values. Is there a flag that I shoudl > > include to output the p-values? > > > > mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi > > lh --surf white --annot aparc --no-adjust --bonferroni 2 > > --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot > > cache.uncorr.abs.sig.ocn.annot --cwsig > > cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum > > cache.uncorr.abs.sig.ocn.dat > > > > Thanks > > > > corinna > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Output uncorrected p-values using mri_surfcluster
Hi all, just following up on my previous question. For the purposes of showing uncorrected p-values <0.005 as well as the corrected results (via mri_glmfit-sim) I would like to get the table of uncorrected p-values. I have tried using mri_glmfit-sim --glmdir results.glmdir --cache 2.3 abs --cwp 1 --2spaces and it does output p-values, but there has gone through the simulations. I would like the raw p-values from this step: mri_glmfit --y rh.noreg.thickness.08B.mgh --fsgd file.fsgd dods --C diff_noreg.mtx --surf fsaverage rh --cortex --glmdir rh.thick.noreg.sm08.glmdir What command would I use? Thanks Corinna On Wed, Sep 21, 2016 at 4:31 PM, Corinna Bauer wrote: > Hello all, > > I would like to get a table of the uncorrected p-values to compare with > the corrected ones obtained using mri_glmfit-sim. I tried the following, > which outputs a table of clusters and their vertices, but it does not > include p-values. Is there a flag that I shoudl include to output the > p-values? > > mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh > --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn > cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot > --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum > cache.uncorr.abs.sig.ocn.dat > > Thanks > > corinna > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Output uncorrected p-values using mri_surfcluster
Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values? mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat Thanks corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit
Yes, I agree completely. We are using DODS and it is clear that we have different results depending on which type of ICV we use. The question is... which type of ICV correction for DODS is the most statistically sound? demean across all groups, no demeaning, or demean within groups separately. What would you recommend. On Mon, Aug 29, 2016 at 3:33 PM, Douglas N Greve wrote: > If there was not an interaction between group and ICV, I would say to > use DOSS where demeaning does not make a difference. Since there is an > interaction, you have to use DODS, but the interpretation is no longer > easy. If you do not demean, then you are implictly testing for a > difference at ICV=0 (this is what "regressing out" means). If you > demean, you are implicitly testing at ICV=MeanICV. The problem is that > the results can change depending on the ICV you test it at. > > > On 08/29/2016 02:53 PM, Corinna Bauer wrote: > > Sorry for not specifying. Yes, we are looking at difference in volume > > between the two groups using DODS. What is the most statistically > > sound... raw values, demeaning across the entire sample, or demeaning > > with groups separately? FYI, I exported the ICV values to SAS and > > there is a significant different between the two groups for ICV. > > > > > > > > On Mon, Aug 29, 2016 at 2:48 PM, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > not sure what you are testing, but if you are, eg, looking at the > > difference between two groups regressing out ICV, then it can make a > > huge difference > > > > > > On 08/29/2016 12:36 PM, Corinna Bauer wrote: > > > Hello all, > > > > > > I am wondering why results would change completely for between > group > > > volume analysis when using demeaned/mean-centered ICV compared to > > > using ICV as a covariate in mri_glmfit? See the figures below. > > > > > > Does demeaning the covariate inherently change the results > > comapred to > > > the raw covariate values? > > > > > > Thanks > > > > > > Corinna > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . 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. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu >
Re: [Freesurfer] Results different between mean-centered and raw covariates -- glm_fit
Sorry for not specifying. Yes, we are looking at difference in volume between the two groups using DODS. What is the most statistically sound... raw values, demeaning across the entire sample, or demeaning with groups separately? FYI, I exported the ICV values to SAS and there is a significant different between the two groups for ICV. On Mon, Aug 29, 2016 at 2:48 PM, Douglas N Greve wrote: > not sure what you are testing, but if you are, eg, looking at the > difference between two groups regressing out ICV, then it can make a > huge difference > > > On 08/29/2016 12:36 PM, Corinna Bauer wrote: > > Hello all, > > > > I am wondering why results would change completely for between group > > volume analysis when using demeaned/mean-centered ICV compared to > > using ICV as a covariate in mri_glmfit? See the figures below. > > > > Does demeaning the covariate inherently change the results comapred to > > the raw covariate values? > > > > Thanks > > > > Corinna > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Results different between mean-centered and raw covariates -- glm_fit
Hello all, I am wondering why results would change completely for between group volume analysis when using demeaned/mean-centered ICV compared to using ICV as a covariate in mri_glmfit? See the figures below. Does demeaning the covariate inherently change the results comapred to the raw covariate values? Thanks Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] errors in wm and pial boundaries
Hello, Have you been able to look at the data I sent over yet? It would be great to get a sense of what we can or cannot do to correct the boundaries. Thanks Corinna On Wed, May 25, 2016 at 12:05 PM, Corinna Bauer wrote: > Hi Bruce, just checking in to see if you have had an opportunity to take a > look at the data I sent over? > > Thanks > > Corinna > > On Wed, May 18, 2016 at 6:19 PM, Corinna Bauer > wrote: > >> Sure. I'm uploading now. The above is approximately slice 75, although >> the control points/wm surface problem is seen throughout in this subject. >> >> Thanks >> >> Corinna >> >> On Tue, May 17, 2016 at 3:46 PM, Bruce Fischl > > wrote: >> >>> Hi Corinna >>> >>> it's hard to tell what's going on from a single slice. If you upload the >>> subject and tell us the specific coordinates that you see problems in we >>> will take a look >>> >>> cheers >>> Bruce >>> On Tue, 17 May 2016, Corinna Bauer wrote: >>> >>> Hello all,We are analyzing data from our collaborators and are running >>>> into >>>> some difficulties with the accuracy of the pial and wm boundaries. The >>>> wm.mgz appears to follow the actual WM, independent of the wm surface >>>> boundary. Attached is an example showing two types of problems. >>>> 1. the WM surface is inaccurate regardless of the number of control >>>> points >>>> used. >>>> 2. The pial surface is inaccurate, missing a bunch of the sulcal and >>>> gyral >>>> patterns of the left parietal lobe (see area around cursor). >>>> >>>> For completeness, I have also included the wm.mgz at the same slice. >>>> >>>> I should mention that these problems has been occurring in multiple >>>> subjects. >>>> >>>> Any suggestions?? >>>> >>>> Thanks >>>> >>>> Corinna >>>> >>>> >>> ___ >>> 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 Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . 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. >>> >>> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] errors in wm and pial boundaries
Hi Bruce, just checking in to see if you have had an opportunity to take a look at the data I sent over? Thanks Corinna On Wed, May 18, 2016 at 6:19 PM, Corinna Bauer wrote: > Sure. I'm uploading now. The above is approximately slice 75, although the > control points/wm surface problem is seen throughout in this subject. > > Thanks > > Corinna > > On Tue, May 17, 2016 at 3:46 PM, Bruce Fischl > wrote: > >> Hi Corinna >> >> it's hard to tell what's going on from a single slice. If you upload the >> subject and tell us the specific coordinates that you see problems in we >> will take a look >> >> cheers >> Bruce >> On Tue, 17 May 2016, Corinna Bauer wrote: >> >> Hello all,We are analyzing data from our collaborators and are running >>> into >>> some difficulties with the accuracy of the pial and wm boundaries. The >>> wm.mgz appears to follow the actual WM, independent of the wm surface >>> boundary. Attached is an example showing two types of problems. >>> 1. the WM surface is inaccurate regardless of the number of control >>> points >>> used. >>> 2. The pial surface is inaccurate, missing a bunch of the sulcal and >>> gyral >>> patterns of the left parietal lobe (see area around cursor). >>> >>> For completeness, I have also included the wm.mgz at the same slice. >>> >>> I should mention that these problems has been occurring in multiple >>> subjects. >>> >>> Any suggestions?? >>> >>> Thanks >>> >>> Corinna >>> >>> >> ___ >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . 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. >> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] errors in wm and pial boundaries
Sure. I'm uploading now. The above is approximately slice 75, although the control points/wm surface problem is seen throughout in this subject. Thanks Corinna On Tue, May 17, 2016 at 3:46 PM, Bruce Fischl wrote: > Hi Corinna > > it's hard to tell what's going on from a single slice. If you upload the > subject and tell us the specific coordinates that you see problems in we > will take a look > > cheers > Bruce > On Tue, 17 May 2016, Corinna Bauer wrote: > > Hello all,We are analyzing data from our collaborators and are running into >> some difficulties with the accuracy of the pial and wm boundaries. The >> wm.mgz appears to follow the actual WM, independent of the wm surface >> boundary. Attached is an example showing two types of problems. >> 1. the WM surface is inaccurate regardless of the number of control points >> used. >> 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral >> patterns of the left parietal lobe (see area around cursor). >> >> For completeness, I have also included the wm.mgz at the same slice. >> >> I should mention that these problems has been occurring in multiple >> subjects. >> >> Any suggestions?? >> >> Thanks >> >> Corinna >> >> > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] errors in wm and pial boundaries
Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface is inaccurate regardless of the number of control points used. 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral patterns of the left parietal lobe (see area around cursor). For completeness, I have also included the wm.mgz at the same slice. I should mention that these problems has been occurring in multiple subjects. Any suggestions?? Thanks Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mris_make_surfaces dimensions error
Hi Bruce, I checked and it is indeed a volume file with 256x256x256 size. The full command line was: mris_make_surfaces -cover_seg edited_ribbon.mgz subject_id lh Thanks Corinna On Sat, Feb 20, 2016 at 1:38 PM, Bruce Fischl wrote: > Hi Corinna > > can you send us your full command line? Sounds like you are using a > surface overlay as the cover_seg parameter instead of a volume one. Try > running mri_info on it to make sure it is a volume (i.e. 256x256x256). If > not, you will need to sample it into the volume with mri_surf2vol > > thanks > Bruce > > On Thu, 18 Feb 2016, Corinna Bauer > wrote: > > > Hello all, > > I am attempting to reshape the pial surfaces to fill the new boundaries > in > > my edited ribbon.mgz file. I am using mris_make_surfaces with the > -cover_seg > > flag but keep getting this error: > > ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 > > height=1. > > > > Any suggestions? > > > > Thanks! > > Corinna > > > > FYI: I am trying to reshape the pial boundary based off this previous > > thread. > > > https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/04134 > > 8.html > > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] mris_make_surfaces dimensions error
Hello all, I am attempting to reshape the pial surfaces to fill the new boundaries in my edited ribbon.mgz file. I am using mris_make_surfaces with the -cover_seg flag but keep getting this error: ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2 height=1. Any suggestions? Thanks! Corinna FYI: I am trying to reshape the pial boundary based off this previous thread. https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2014-November/041348.html ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] pial edits in subject with severe atrophy
Hi Bruce, I exported the ribbon.mgz to itksnap and was able to edit the grey matter to include the atrophic frontal areas. I am wondering if there is a way to have these edits reflected in the pial surface? Thanks. Corinna On Wed, Feb 10, 2016 at 4:02 PM, Corinna Bauer wrote: > ok thanks. > > On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl > wrote: > >> not to my knowledge, but others may have developed something >> Bruce >> On Wed, 10 Feb >> 2016, Corinna Bauer wrote: >> >> > Thanks, Bruce. >> > In an earlier thread from '09 with a similar problem( >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html >> > ), it was mentioned that there was a method being developed to edit the >> > surface mesh. Is that option still available and would it help? Since >> this >> > step in our analysis stream is central to everything else, we are >> willing to >> > try whatever it takes. >> > >> > Corinna >> > >> > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> > wrote: >> > Sorry Corinna >> > >> > I meant to answer this the first time but it slipped through the >> > cracks. >> > I doubt there is much you can do if there is that big a lesion. >> > If the >> > topology is wrong and you can't see tissue in those regions it's >> > going to >> > be very hard >> > Bruce >> > >> > >> > On Wed, 10 Feb 2016, >> > Corinna Bauer wrote: >> > >> > > Dear Experts, >> > > >> > > I have a subject with severe atrophy in bilateral frontal and >> > parietal >> > > regions and after many rounds of edits to the brainmask, >> > wm.mgz, and control >> > > points, these regions are still left uncaptured. Is there a >> > way to edit the >> > > pial surface to include these grey matter regions? I am >> > hesitant to draw >> > > them in via the wm surface since there is no definite WM >> > present. >> > > >> > > I do have a FLAIR also on this subject. >> > > >> > > I've attached a couple examples. >> > > >> > > Thanks! >> > > >> > > Corinna >> > > >> > > >> > ___ >> > 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 Partners Compliance >> > HelpLine at >> > http://www.partners.org/complianceline . 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. >> > >> > >> > >> > >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] pial edits in subject with severe atrophy
ok thanks. On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl wrote: > not to my knowledge, but others may have developed something > Bruce > On Wed, 10 Feb > 2016, Corinna Bauer wrote: > > > Thanks, Bruce. > > In an earlier thread from '09 with a similar problem( > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html > > ), it was mentioned that there was a method being developed to edit the > > surface mesh. Is that option still available and would it help? Since > this > > step in our analysis stream is central to everything else, we are > willing to > > try whatever it takes. > > > > Corinna > > > > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > wrote: > > Sorry Corinna > > > > I meant to answer this the first time but it slipped through the > > cracks. > > I doubt there is much you can do if there is that big a lesion. > > If the > > topology is wrong and you can't see tissue in those regions it's > > going to > > be very hard > > Bruce > > > > > > On Wed, 10 Feb 2016, > > Corinna Bauer wrote: > > > > > Dear Experts, > > > > > > I have a subject with severe atrophy in bilateral frontal and > > parietal > > > regions and after many rounds of edits to the brainmask, > > wm.mgz, and control > > > points, these regions are still left uncaptured. Is there a > > way to edit the > > > pial surface to include these grey matter regions? I am > > hesitant to draw > > > them in via the wm surface since there is no definite WM > > present. > > > > > > I do have a FLAIR also on this subject. > > > > > > I've attached a couple examples. > > > > > > Thanks! > > > > > > Corinna > > > > > > > > ___ > > 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 Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . 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. > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] pial edits in subject with severe atrophy
I should mention that the aseg file captures the GM outside the pial surface. On Wed, Feb 10, 2016 at 1:23 PM, Corinna Bauer wrote: > Thanks, Bruce. > In an earlier thread from '09 with a similar problem ( > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html), > it was mentioned that there was a method being developed to edit the > surface mesh. Is that option still available and would it help? Since this > step in our analysis stream is central to everything else, we are willing > to try whatever it takes. > > Corinna > > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl > wrote: > >> Sorry Corinna >> >> I meant to answer this the first time but it slipped through the cracks. >> I doubt there is much you can do if there is that big a lesion. If the >> topology is wrong and you can't see tissue in those regions it's going to >> be very hard >> Bruce >> >> >> On Wed, 10 Feb 2016, >> Corinna Bauer wrote: >> >> > Dear Experts, >> > >> > I have a subject with severe atrophy in bilateral frontal and parietal >> > regions and after many rounds of edits to the brainmask, wm.mgz, and >> control >> > points, these regions are still left uncaptured. Is there a way to edit >> the >> > pial surface to include these grey matter regions? I am hesitant to draw >> > them in via the wm surface since there is no definite WM present. >> > >> > I do have a FLAIR also on this subject. >> > >> > I've attached a couple examples. >> > >> > Thanks! >> > >> > Corinna >> > >> > >> ___ >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . 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. >> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] pial edits in subject with severe atrophy
Thanks, Bruce. In an earlier thread from '09 with a similar problem ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html), it was mentioned that there was a method being developed to edit the surface mesh. Is that option still available and would it help? Since this step in our analysis stream is central to everything else, we are willing to try whatever it takes. Corinna On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl wrote: > Sorry Corinna > > I meant to answer this the first time but it slipped through the cracks. > I doubt there is much you can do if there is that big a lesion. If the > topology is wrong and you can't see tissue in those regions it's going to > be very hard > Bruce > > > On Wed, 10 Feb 2016, > Corinna Bauer wrote: > > > Dear Experts, > > > > I have a subject with severe atrophy in bilateral frontal and parietal > > regions and after many rounds of edits to the brainmask, wm.mgz, and > control > > points, these regions are still left uncaptured. Is there a way to edit > the > > pial surface to include these grey matter regions? I am hesitant to draw > > them in via the wm surface since there is no definite WM present. > > > > I do have a FLAIR also on this subject. > > > > I've attached a couple examples. > > > > Thanks! > > > > Corinna > > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] pial edits in subject with severe atrophy
Dear Experts, I have a subject with severe atrophy in bilateral frontal and parietal regions and after many rounds of edits to the brainmask, wm.mgz, and control points, these regions are still left uncaptured. Is there a way to edit the pial surface to include these grey matter regions? I am hesitant to draw them in via the wm surface since there is no definite WM present. I do have a FLAIR also on this subject. I've attached a couple examples. Thanks! Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] segmentation errors in subject with severe atrophy
Dear all, We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that it is captured within the surfs? Because we have other modalities that use the Desikan atlas, this is an important first step. I have attached a few figures for examples. Thanks!! ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] aparc labels to grey white ratio
Hi all,
What command would I use to apply the aparc labels to a different surface
(e.g. to $h.ratio.mgh)??
The ratio file was created as follows:
mri_vol2surf --src ${nu_mgz} --projfrac +0.35 --surf white --hemi lh
--out ${subj_dir}/mri/lh.white.projfrac.pos35.mgh --regheader ${subject}
--noreshape
mri_vol2surf --src ${nu_mgz} --projdist -1 --surf white --hemi lh --out
${subj_dir}/mri/lh.white.projdist.neg1.mgh --regheader ${subject}
--noreshape
fscalc ${subj_dir}/mri/lh.white.projfrac.pos35.mgh div
${subj_dir}/mri/lh.white.projdist.neg1.mgh -o ${subj_dir}/mri/lh.ratio.mgh
Thanks
Corinna
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full
Thanks, Doug. On Tue, Feb 3, 2015 at 10:37 AM, Douglas Greve wrote: > Hi Corinna, > > In each iteration, the mc-full replaces your data (--y) with white > gaussian noise, smoothes it, then computes the GLM and p-values from the t > or F-test. The mc-z ignores your data entirely and creates a single frame > of WGN in each iteration, smoothes it, rescales it back to a z, then > converts the z to a p. This is much faster because it only has one frame vs > how many you have in your data. It is less accurate because a p-value map > from a smoothed z-map is not the same as computing the glm. It has been a > while, but I remember the mc-z as being more conservative, but it is much > much faster. > > doug > > > On 2/3/15 10:12 AM, Corinna Bauer wrote: > > Hi all, > I am wondering what the specific reasons might be for choosing to run the > mc-z simulation compared to mc-full? What are the pros and cons for each > method for looking at group morphometry differences? > > Thanks > > Corinna > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] mri_glmfit-sim mc-z comapred to mc-full
Hi all, I am wondering what the specific reasons might be for choosing to run the mc-z simulation compared to mc-full? What are the pros and cons for each method for looking at group morphometry differences? Thanks Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] strange artefact in T1 - stripe pattern
We actually ran it through the processing stream and only the middle of the brain made it into the wm.mgz and the surfaces. On Thu, Oct 23, 2014 at 12:49 PM, Bruce Fischl wrote: > Hi Corinna > > it's hard to say. It's quite noisy, but you should give it a try > > Bruce > On Thu, 23 > Oct 2014, Corinna Bauer wrote: > > > Hello, > > I am analysing some structural data for collaborators and one of the > > datasets has a strange artefact in it. Is there any way to adjust for the > > intensity bands or is this a lost cause? > > > > Thanks, > > > > Corinna > > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Transform labels in Diffusion space into MNI space
Hi Doug,
That still gives sag rotated -90 degrees, axial shows up as a coronal
rotated 180 deg, and coronal shows up as axial.
Corinna
On Wed, Oct 15, 2014 at 11:17 AM, Douglas N Greve wrote:
>
> Sorry, I gave you a bad command line. Try this
>
> mri_matrix_multiply -im MAE_06072013/register.dat -iim
> MAE_06072013/mri/mni152.orig.mgz.reg -om MAE_06072013/newmnireg.dat
>
> doug
>
>
> On 10/15/2014 10:33 AM, Corinna Bauer wrote:
> > I tried your suggestion first and the registration was off, whereby
> > the axial and coronal were switched and sagittal was rotated 90 degrees.
> >
> > Corinna
> >
> > On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > I'm not sure what is in that file. Try doing it the way that I
> > suggested and see if it works.
> > doug
> >
> >
> >
> > On 10/15/14 10:29 AM, Corinna Bauer wrote:
> >> Doug, instead of using the register.dat (which was generated from
> >> bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl
> >> --reg register.dat), I had to use the registration file generated
> >> from the mri_vol2vol step where the orig T1 is put into dti space:
> >> mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz
> >> --reg register.dat --inv --o ${mri_indtispace}.
> >>
> >> mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> >> MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
> >>
> >> Corinna
> >>
> >> On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer
> >> mailto:corinna...@gmail.com>> wrote:
> >>
> >> Hi Doug,
> >>
> >> I'm not sure why, but the registration is off. In
> >> tkregister2, the "coronal" appears as an axial slice and vice
> >> versa, while the sagittal is rotated 90 degrees compared to
> >> the target. I did the following:
> >> 1. mni152reg --s MAE_06072013
> >> 2. tkregister2 --mov
> >>
>
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
> >> --targ
> >> /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
> >> --reg
> >>
>
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
> >> 3. tkregister2 --mov
> >> MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
> >> MAE_06072013/register.dat --surf
> >>
> >> Up until this point, everything looks good and well registered.
> >>
> >> 4. mri_matrix_multiply -im
> >> MAE_06072013/mri/mni152.orig.mgz.reg -iim
> >> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
> >>
> >>
> >> Corinna
> >>
> >> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve
> >> >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >>
> >>
> >> Hi Corinna, once you do #1, you can concatenate the
> >> register.dat with the mni152.2mm.reg.dat like this
> >>
> >> mri_matrix_multipy -im mnireg.dat -iim register.dat -o
> >> newreg.dat
> >>
> >> Check
> >> tkregister2 --mov dti.nii --targ
> >> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
> >>
> >> mri_vol2vol --mov dti.nii --targ
> >> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg
> >> newreg.dat --o dti.in.mni.nii
> >>
> >> doug
> >>
> >>
> >>
> >> On 10/14/14 2:57 PM, Corinna Bauer wrote:
> >>> Hello all,
> >>> I am wanting to put labels currently in diffusion space
> >>> into MNI space. Does this make sense or is there a more
> >>> straight forward way?
> >>>
> >>> 1. mni152reg the subject's structural into MNI space
> >>> 2. inverse transform the MNI in the the subject's T1 space
> >>> 3. Use bbregister to align the DTI to the T1 space
> >>> 4. inverse transform the MNI into DTI space using
> >>> mri_vol2vol using the registration from step 3?
Re: [Freesurfer] Transform labels in Diffusion space into MNI space
I tried your suggestion first and the registration was off, whereby the
axial and coronal were switched and sagittal was rotated 90 degrees.
Corinna
On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve
wrote:
>
> I'm not sure what is in that file. Try doing it the way that I suggested
> and see if it works.
> doug
>
>
>
> On 10/15/14 10:29 AM, Corinna Bauer wrote:
>
> Doug, instead of using the register.dat (which was generated from
> bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg
> register.dat), I had to use the registration file generated from the
> mri_vol2vol step where the orig T1 is put into dti space:
> mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg
> register.dat --inv --o ${mri_indtispace}.
>
> mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
>
> Corinna
>
> On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer
> wrote:
>
>> Hi Doug,
>>
>> I'm not sure why, but the registration is off. In tkregister2, the
>> "coronal" appears as an axial slice and vice versa, while the sagittal is
>> rotated 90 degrees compared to the target. I did the following:
>> 1. mni152reg --s MAE_06072013
>> 2. tkregister2 --mov
>> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
>> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
>> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
>> 3. tkregister2 --mov
>> MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
>> MAE_06072013/register.dat --surf
>>
>> Up until this point, everything looks good and well registered.
>>
>> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
>> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>>
>>
>> Corinna
>>
>> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Corinna, once you do #1, you can concatenate the register.dat with
>>> the mni152.2mm.reg.dat like this
>>>
>>> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>>>
>>> Check
>>> tkregister2 --mov dti.nii --targ
>>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>>
>>> mri_vol2vol --mov dti.nii --targ
>>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>>> dti.in.mni.nii
>>>
>>> doug
>>>
>>>
>>>
>>> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>>
>>> Hello all,
>>> I am wanting to put labels currently in diffusion space into MNI space.
>>> Does this make sense or is there a more straight forward way?
>>>
>>> 1. mni152reg the subject's structural into MNI space
>>> 2. inverse transform the MNI in the the subject's T1 space
>>> 3. Use bbregister to align the DTI to the T1 space
>>> 4. inverse transform the MNI into DTI space using mri_vol2vol using the
>>> registration from step 3?
>>>
>>> Cheers,
>>>
>>> Corinna
>>>
>>>
>>> ___
>>> Freesurfer mailing
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
>>> 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 Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . 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.
>>>
>>>
>>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo
Re: [Freesurfer] Transform labels in Diffusion space into MNI space
I'm pretty sure it came from mni152reg. Here are the last few lines of the mni152 reg output: Final tkRAS-to-tkRAS Matrix is: 1.013 0.045 0.047 -1.659; 0.062 -0.209 -1.043 -15.101; -0.025 0.933 -0.227 33.122; 0.000 0.000 0.000 1.000; Vox2Vox Matrix is: 2.025 0.094 -0.090 36.461; -0.049 -0.455 -1.865 206.757; -0.124 2.086 -0.418 23.848; 0.000 0.000 0.000 1.000; Resampling Output registration matrix is identity INFO: writing registration to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.lta transformed matrix: 1.000 0.000 -0.000 -1.566; -0.000 -0.000 -1.000 -23.577; 0.000 1.000 -0.000 9.029; 0.000 0.000 0.000 1.000; transformed matrix: 0.500 0.000 0.000 -18.500; 0.000 0.500 0.000 -9.500; 0.000 0.000 0.500 -18.500; 0.000 0.000 0.000 1.000; INFO: writing registration matrix to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg To check registration, run: tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg mri_vol2vol done On Wed, Oct 15, 2014 at 10:28 AM, Douglas Greve wrote: > > Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg > ... > doug > > > On 10/15/14 10:19 AM, Corinna Bauer wrote: > > Hi Doug, > > I'm not sure why, but the registration is off. In tkregister2, the > "coronal" appears as an axial slice and vice versa, while the sagittal is > rotated 90 degrees compared to the target. I did the following: > 1. mni152reg --s MAE_06072013 > 2. tkregister2 --mov > /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz > --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg > /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg > 3. tkregister2 --mov > MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg > MAE_06072013/register.dat --surf > > Up until this point, everything looks good and well registered. > > 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim > MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat > > > Corinna > > On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve > wrote: > >> >> Hi Corinna, once you do #1, you can concatenate the register.dat with the >> mni152.2mm.reg.dat like this >> >> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat >> >> Check >> tkregister2 --mov dti.nii --targ >> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat >> >> mri_vol2vol --mov dti.nii --targ >> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o >> dti.in.mni.nii >> >> doug >> >> >> >> On 10/14/14 2:57 PM, Corinna Bauer wrote: >> >> Hello all, >> I am wanting to put labels currently in diffusion space into MNI space. >> Does this make sense or is there a more straight forward way? >> >> 1. mni152reg the subject's structural into MNI space >> 2. inverse transform the MNI in the the subject's T1 space >> 3. Use bbregister to align the DTI to the T1 space >> 4. inverse transform the MNI into DTI space using mri_vol2vol using the >> registration from step 3? >> >> Cheers, >> >> Corinna >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . 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. >> >> > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer
Re: [Freesurfer] Transform labels in Diffusion space into MNI space
Doug, instead of using the register.dat (which was generated from
bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg
register.dat), I had to use the registration file generated from the
mri_vol2vol step where the orig T1 is put into dti space:
mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg
register.dat --inv --o ${mri_indtispace}.
mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
Corinna
On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer
wrote:
> Hi Doug,
>
> I'm not sure why, but the registration is off. In tkregister2, the
> "coronal" appears as an axial slice and vice versa, while the sagittal is
> rotated 90 degrees compared to the target. I did the following:
> 1. mni152reg --s MAE_06072013
> 2. tkregister2 --mov
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
> 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz
> --reg MAE_06072013/register.dat --surf
>
> Up until this point, everything looks good and well registered.
>
> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>
>
> Corinna
>
> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve > wrote:
>
>>
>> Hi Corinna, once you do #1, you can concatenate the register.dat with the
>> mni152.2mm.reg.dat like this
>>
>> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>>
>> Check
>> tkregister2 --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>
>> mri_vol2vol --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>> dti.in.mni.nii
>>
>> doug
>>
>>
>>
>> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>
>>Hello all,
>> I am wanting to put labels currently in diffusion space into MNI space.
>> Does this make sense or is there a more straight forward way?
>>
>> 1. mni152reg the subject's structural into MNI space
>> 2. inverse transform the MNI in the the subject's T1 space
>> 3. Use bbregister to align the DTI to the T1 space
>> 4. inverse transform the MNI into DTI space using mri_vol2vol using the
>> registration from step 3?
>>
>> Cheers,
>>
>> Corinna
>>
>>
>> ___
>> Freesurfer mailing
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Transform labels in Diffusion space into MNI space
Hi Doug, I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf Up until this point, everything looks good and well registered. 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat Corinna On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve wrote: > > Hi Corinna, once you do #1, you can concatenate the register.dat with the > mni152.2mm.reg.dat like this > > mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat > > Check > tkregister2 --mov dti.nii --targ > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat > > mri_vol2vol --mov dti.nii --targ > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o > dti.in.mni.nii > > doug > > > > On 10/14/14 2:57 PM, Corinna Bauer wrote: > >Hello all, > I am wanting to put labels currently in diffusion space into MNI space. > Does this make sense or is there a more straight forward way? > > 1. mni152reg the subject's structural into MNI space > 2. inverse transform the MNI in the the subject's T1 space > 3. Use bbregister to align the DTI to the T1 space > 4. inverse transform the MNI into DTI space using mri_vol2vol using the > registration from step 3? > > Cheers, > > Corinna > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Transform labels in Diffusion space into MNI space
Hello all, I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way? 1. mni152reg the subject's structural into MNI space 2. inverse transform the MNI in the the subject's T1 space 3. Use bbregister to align the DTI to the T1 space 4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3? Cheers, Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mris_divide_parcellation for white matter
Doug, that worked very well, thanks.
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --wmparc-dmax 2 --o ${subj_dir}/mri/wmdivided.nii --annot
aparc.split
mri_annotation2label --ctab new.rh.ctab --subject ${subject} --hemi rh
--annotation aparc.split --outdir ${subj_dir}/smaller_labels
mri_extract_label ${subj_dir}/mri/wmdivided.nii 3001
${subj_dir}/smaller_labels/wm-lh-bankssts.nii
On Mon, Jul 7, 2014 at 1:05 PM, Corinna Bauer wrote:
> great, thanks! I'll give that a try and let you know how it goes.
>
>
> On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Right, this is going to be a problem. One of the things you can do is to
>> use the --ctab option of mri_annotation2label to create a colortable,
>> something like
>>
>> mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
>> --annotation newannot --outdir junk
>>
>> You can do this for both hemis, then concatenate them together along
>> with the ROIs from the subcortical. Then take the two new.?h.ctabs and
>> add 3000
>> to the indices and change the name to be wm- instead of ctx- and include
>> those in the new ctab
>>
>> clunky, but it should work
>>
>> doug
>>
>>
>> On 07/07/2014 12:29 PM, Corinna Bauer wrote:
>> > the new white matter divided labels. I was not able to extract the
>> > labels using the matching grey matter names, but was able to do so
>> > using the label number seen in the tools from tkmedit. Seeing as there
>> > are over 100 labels, is there a more efficient way?
>> >
>> >
>> > On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > The name of which label?
>> >
>> > On 07/02/2014 02:00 PM, Corinna Bauer wrote:
>> > > Whereby the label name is derived from which, the GM labels? i.e.
>> > > lh.rostralmiddlefrontal_div3
>> > >
>> > >
>> > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
>> > > mailto:fis...@nmr.mgh.harvard.edu>
>> > <mailto:fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote:
>> > >
>> > > yes, or mri_binarize --match
>> > >
>> > >
>> > > cheers
>> > > Bruce
>> > >
>> > >
>> > > On Wed, 2 Jul 2014, Corinna Bauer wrote:
>> > >
>> > > And then for breaking the individual labels up, would
>> > > mri_extract_label be
>> > > the best option?
>> > >
>> > >
>> > > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
>> > > > > <mailto:fis...@nmr.mgh.harvard.edu>
>> > <mailto:fis...@nmr.mgh.harvard.edu
>> > <mailto:fis...@nmr.mgh.harvard.edu>>>
>> > > wrote:
>> > > Hi Corinna
>> > >
>> > > you need to give some output extension so it knows
>> > what file
>> > > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>> > >
>> > > cheers
>> > > Bruce
>> > >
>> > > On Wed, 2 Jul 2014, Corinna Bauer wrote:
>> > >
>> > > Hi Bruce,
>> > >
>> > > I am trying to do just that using the
>> following
>> > > command line:
>> > > mri_aparc2aseg --s ${subject} --labelwm
>> > --hypo-as-wm
>> > > --rip-unknown --volmask
>> > > --o ${subj_dir}/mri/wmdivided --annot
>> > aparc.split
>> > >
>> > > After the slice labeling, I get the following:
>> > >
>> > > Used brute-force search on 872 voxels
>> > > Fixing Parahip LH WM
>> > > Found 0 clusters
>> > > Fixing Parahip RH WM
>> > > Found 0 clusters
>> > > Writing output aseg to
>> > >
>> >
Re: [Freesurfer] mris_divide_parcellation for white matter
great, thanks! I'll give that a try and let you know how it goes.
On Mon, Jul 7, 2014 at 12:50 PM, Douglas N Greve
wrote:
>
> Right, this is going to be a problem. One of the things you can do is to
> use the --ctab option of mri_annotation2label to create a colortable,
> something like
>
> mri_annotation2label --ctab new.lh.ctab --s subject --hemi lh
> --annotation newannot --outdir junk
>
> You can do this for both hemis, then concatenate them together along
> with the ROIs from the subcortical. Then take the two new.?h.ctabs and
> add 3000
> to the indices and change the name to be wm- instead of ctx- and include
> those in the new ctab
>
> clunky, but it should work
>
> doug
>
>
> On 07/07/2014 12:29 PM, Corinna Bauer wrote:
> > the new white matter divided labels. I was not able to extract the
> > labels using the matching grey matter names, but was able to do so
> > using the label number seen in the tools from tkmedit. Seeing as there
> > are over 100 labels, is there a more efficient way?
> >
> >
> > On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > The name of which label?
> >
> > On 07/02/2014 02:00 PM, Corinna Bauer wrote:
> > > Whereby the label name is derived from which, the GM labels? i.e.
> > > lh.rostralmiddlefrontal_div3
> > >
> > >
> > > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> > > mailto:fis...@nmr.mgh.harvard.edu>
> > <mailto:fis...@nmr.mgh.harvard.edu
> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > yes, or mri_binarize --match
> > >
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Wed, 2 Jul 2014, Corinna Bauer wrote:
> > >
> > > And then for breaking the individual labels up, would
> > > mri_extract_label be
> > > the best option?
> > >
> > >
> > > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
> > > > <mailto:fis...@nmr.mgh.harvard.edu>
> > <mailto:fis...@nmr.mgh.harvard.edu
> > <mailto:fis...@nmr.mgh.harvard.edu>>>
> > > wrote:
> > > Hi Corinna
> > >
> > > you need to give some output extension so it knows
> > what file
> > > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
> > >
> > > cheers
> > > Bruce
> > >
> > > On Wed, 2 Jul 2014, Corinna Bauer wrote:
> > >
> > > Hi Bruce,
> > >
> > > I am trying to do just that using the following
> > > command line:
> > > mri_aparc2aseg --s ${subject} --labelwm
> > --hypo-as-wm
> > > --rip-unknown --volmask
> > > --o ${subj_dir}/mri/wmdivided --annot
> > aparc.split
> > >
> > > After the slice labeling, I get the following:
> > >
> > > Used brute-force search on 872 voxels
> > > Fixing Parahip LH WM
> > > Found 0 clusters
> > > Fixing Parahip RH WM
> > > Found 0 clusters
> > > Writing output aseg to
> > >
> > > /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
> > > unknown file type for file
> > >
> > > (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
> > > subject = FSH_09062013
> > > annotation = wmdivided
> > > hemi = lh
> > > outdir =
> > >
> > > /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
> > > surface = white
> > >
> > > Any suggestions?
> > >
> > > Thanks,
> > > Corinna
> > >
> > >
> > >
> > > On Tue, Jul 1, 2014 at
Re: [Freesurfer] mris_divide_parcellation for white matter
the new white matter divided labels. I was not able to extract the labels
using the matching grey matter names, but was able to do so using the label
number seen in the tools from tkmedit. Seeing as there are over 100 labels,
is there a more efficient way?
On Mon, Jul 7, 2014 at 12:08 PM, Douglas N Greve
wrote:
> The name of which label?
>
> On 07/02/2014 02:00 PM, Corinna Bauer wrote:
> > Whereby the label name is derived from which, the GM labels? i.e.
> > lh.rostralmiddlefrontal_div3
> >
> >
> > On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >
> > yes, or mri_binarize --match
> >
> >
> > cheers
> > Bruce
> >
> >
> > On Wed, 2 Jul 2014, Corinna Bauer wrote:
> >
> > And then for breaking the individual labels up, would
> > mri_extract_label be
> > the best option?
> >
> >
> > On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> > Hi Corinna
> >
> > you need to give some output extension so it knows what
> file
> > type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
> >
> > cheers
> > Bruce
> >
> > On Wed, 2 Jul 2014, Corinna Bauer wrote:
> >
> > Hi Bruce,
> >
> > I am trying to do just that using the following
> > command line:
> > mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm
> > --rip-unknown --volmask
> > --o ${subj_dir}/mri/wmdivided --annot aparc.split
> >
> > After the slice labeling, I get the following:
> >
> > Used brute-force search on 872 voxels
> > Fixing Parahip LH WM
> > Found 0 clusters
> > Fixing Parahip RH WM
> > Found 0 clusters
> > Writing output aseg to
> >
> > /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
> > unknown file type for file
> >
> > (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
> > subject = FSH_09062013
> > annotation = wmdivided
> > hemi = lh
> > outdir =
> >
> > /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
> > surface = white
> >
> > Any suggestions?
> >
> > Thanks,
> > Corinna
> >
> >
> >
> > On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl
> > > <mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> > Hi Corinna
> >
> > not really, as that is a surface-based
> > utility. You could divide
> > the
> > cortical labels and then recrate the wmparc
> > from it, which might
> > do what
> > you want.
> >
> > cheers
> > Bruce
> >
> >
> > On Tue, 1 Jul 2014, Corinna
> > Bauer wrote:
> >
> > > hello,
> > > I was wondering if it was possible to use
> > mris_divide_parcellation on white
> > > matter labels.
> > >
> > > Thanks,
> > >
> > > Corinna
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > <mailto: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
> >
Re: [Freesurfer] mris_divide_parcellation for white matter
I figured it out. Thanks for your help!
On Wed, Jul 2, 2014 at 2:00 PM, Corinna Bauer wrote:
> Whereby the label name is derived from which, the GM labels? i.e.
> lh.rostralmiddlefrontal_div3
>
>
> On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
> wrote:
>
>> yes, or mri_binarize --match
>>
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>>
>> And then for breaking the individual labels up, would mri_extract_label
>>> be
>>> the best option?
>>>
>>>
>>> On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>> Hi Corinna
>>>
>>> you need to give some output extension so it knows what file
>>> type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>>>
>>> cheers
>>> Bruce
>>>
>>> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>>>
>>> Hi Bruce,
>>>
>>> I am trying to do just that using the following
>>> command line:
>>> mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm
>>> --rip-unknown --volmask
>>> --o ${subj_dir}/mri/wmdivided --annot aparc.split
>>>
>>> After the slice labeling, I get the following:
>>>
>>> Used brute-force search on 872 voxels
>>> Fixing Parahip LH WM
>>> Found 0 clusters
>>> Fixing Parahip RH WM
>>> Found 0 clusters
>>> Writing output aseg to
>>> /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
>>> unknown file type for file
>>> (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
>>> subject = FSH_09062013
>>> annotation = wmdivided
>>> hemi = lh
>>> outdir =
>>> /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
>>> surface = white
>>>
>>> Any suggestions?
>>>
>>> Thanks,
>>> Corinna
>>>
>>>
>>>
>>> On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl
>>>
>>> wrote:
>>> Hi Corinna
>>>
>>> not really, as that is a surface-based
>>> utility. You could divide
>>> the
>>> cortical labels and then recrate the wmparc
>>> from it, which might
>>> do what
>>> you want.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Tue, 1 Jul 2014, Corinna
>>> Bauer wrote:
>>>
>>> > hello,
>>> > I was wondering if it was possible to use
>>> mris_divide_parcellation on white
>>> > matter labels.
>>> >
>>> > Thanks,
>>> >
>>> > Corinna
>>> >
>>> >
>>> ___
>>> 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
>>> Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . 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.
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer m
Re: [Freesurfer] mris_divide_parcellation for white matter
Whereby the label name is derived from which, the GM labels? i.e.
lh.rostralmiddlefrontal_div3
On Wed, Jul 2, 2014 at 11:45 AM, Bruce Fischl
wrote:
> yes, or mri_binarize --match
>
>
> cheers
> Bruce
>
>
> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>
> And then for breaking the individual labels up, would mri_extract_label be
>> the best option?
>>
>>
>> On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl > >
>> wrote:
>> Hi Corinna
>>
>> you need to give some output extension so it knows what file
>> type to write (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>>
>> cheers
>> Bruce
>>
>> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>>
>> Hi Bruce,
>>
>> I am trying to do just that using the following
>> command line:
>> mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm
>> --rip-unknown --volmask
>> --o ${subj_dir}/mri/wmdivided --annot aparc.split
>>
>> After the slice labeling, I get the following:
>>
>> Used brute-force search on 872 voxels
>> Fixing Parahip LH WM
>> Found 0 clusters
>> Fixing Parahip RH WM
>> Found 0 clusters
>> Writing output aseg to
>> /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
>> unknown file type for file
>> (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
>> subject = FSH_09062013
>> annotation = wmdivided
>> hemi = lh
>> outdir =
>> /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
>> surface = white
>>
>> Any suggestions?
>>
>> Thanks,
>> Corinna
>>
>>
>>
>> On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl
>>
>> wrote:
>> Hi Corinna
>>
>> not really, as that is a surface-based
>> utility. You could divide
>> the
>> cortical labels and then recrate the wmparc
>> from it, which might
>> do what
>> you want.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 1 Jul 2014, Corinna
>> Bauer wrote:
>>
>> > hello,
>> > I was wondering if it was possible to use
>> mris_divide_parcellation on white
>> > matter labels.
>> >
>> > Thanks,
>> >
>> > Corinna
>> >
>> >
>> ___
>> 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
>> Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>>
>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dis
Re: [Freesurfer] mris_divide_parcellation for white matter
And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl
wrote:
> Hi Corinna
>
> you need to give some output extension so it knows what file type to write
> (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>
> cheers
> Bruce
>
>
> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>
> Hi Bruce,
>>
>> I am trying to do just that using the following command line:
>> mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
>> --volmask
>> --o ${subj_dir}/mri/wmdivided --annot aparc.split
>>
>> After the slice labeling, I get the following:
>>
>> Used brute-force search on 872 voxels
>> Fixing Parahip LH WM
>> Found 0 clusters
>> Fixing Parahip RH WM
>> Found 0 clusters
>> Writing output aseg to
>> /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
>> unknown file type for file
>> (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
>> subject = FSH_09062013
>> annotation = wmdivided
>> hemi = lh
>> outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
>> surface = white
>>
>> Any suggestions?
>>
>> Thanks,
>> Corinna
>>
>>
>>
>> On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl
>> wrote:
>> Hi Corinna
>>
>> not really, as that is a surface-based utility. You could divide
>> the
>> cortical labels and then recrate the wmparc from it, which might
>> do what
>> you want.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 1 Jul 2014, Corinna
>> Bauer wrote:
>>
>> > hello,
>> > I was wondering if it was possible to use
>> mris_divide_parcellation on white
>> > matter labels.
>> >
>> > Thanks,
>> >
>> > Corinna
>> >
>> >
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>>
>>
> ___
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mris_divide_parcellation for white matter
Hi Bruce,
I am trying to do just that using the following command line:
mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
--volmask --o ${subj_dir}/mri/wmdivided --annot aparc.split
After the slice labeling, I get the following:
Used brute-force search on 872 voxels
Fixing Parahip LH WM
Found 0 clusters
Fixing Parahip RH WM
Found 0 clusters
Writing output aseg to
/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
unknown file type for file
(/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
subject = FSH_09062013
annotation = wmdivided
hemi = lh
outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
surface = white
Any suggestions?
Thanks,
Corinna
On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl
wrote:
> Hi Corinna
>
> not really, as that is a surface-based utility. You could divide the
> cortical labels and then recrate the wmparc from it, which might do what
> you want.
>
> cheers
> Bruce
>
>
> On Tue, 1 Jul 2014, Corinna
> Bauer wrote:
>
> > hello,
> > I was wondering if it was possible to use mris_divide_parcellation on
> white
> > matter labels.
> >
> > Thanks,
> >
> > Corinna
> >
> >
> ___
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
[Freesurfer] mris_divide_parcellation for white matter
hello, I was wondering if it was possible to use mris_divide_parcellation on white matter labels. Thanks, Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] longitudinal recon-all -long error
Hi Martin, Neither freeview nor tkmedit could open the 001.mgz file. It could not read 262144 bytes at slice 4. At this point is my best option to re-run this time point from the beginning? Corinna On Mon, Apr 28, 2014 at 9:18 AM, Martin Reuter wrote: > Hi Corinna, > > try to open > > /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz > > in freeview to see if maybe the file is corrupted. > > Best, Martin > > > > On 04/25/2014 03:46 PM, Corinna Bauer wrote: > > Hello, > I am on the recon-all -long step of the longitudinal processing stream and > the final time point exits with errors at the mri_convert stage. > > mri_convert -at > /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta > -odt uchar -rt cubic > /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz > /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz > > > mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz): > could not read 262144 bytes at slice 4 > > I still have plenty of space left on the drive > > > total used free sharedbuffers cached > Mem: 16348132 148565241491608 0 5349166193928 > -/+ buffers/cache:81276808220452 > Swap: 16690172 573232 16116940 > > > > Any suggestions? The two previous timepoints finished without error. > > > Corinna > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] longitudinal recon-all -long error
Hello, I am on the recon-all -long step of the longitudinal processing stream and the final time point exits with errors at the mri_convert stage. mri_convert -at /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta -odt uchar -rt cubic /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz): could not read 262144 bytes at slice 4 I still have plenty of space left on the drive total used free sharedbuffers cached Mem: 16348132 148565241491608 0 5349166193928 -/+ buffers/cache:81276808220452 Swap: 16690172 573232 16116940 Any suggestions? The two previous timepoints finished without error. Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
no, I was in subjects_dir. Updated the command to this and it works now.
thanks.
mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown
--volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split
On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve wrote:
>
> Are you in the folder just above the mri folder?
>
> On 04/10/2014 11:20 AM, Corinna Bauer wrote:
> > Hi Doug,
> > Following the example in recon-all.log, I tried this: mri_aparc2aseg
> > --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
> > mri/wmdivided.mgz --annot aparc.split
> >
> > and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1):
> > could not open file
> >
> >
> >
> > On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Use mri_aparc2aseg with the --labelwm option. Look in the
> > recon-all.log
> > file for an example command line that generates wmparc.mgz
> >
> > doug
> >
> > On 04/10/2014 09:52 AM, Corinna Bauer wrote:
> > > For creating corresponding wm segmentations to the rois derived
> from
> > > mris_divide_parcellation, should mri_aparc2wmseg be used or should
> I
> > > follow the steps outlined in this posting
> > >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
> > > ?
> > >
> > > Thanks
> > >
> > > Corinna
> > >
> > >
> > > On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer
> > mailto:corinna...@gmail.com>
> > > <mailto:corinna...@gmail.com <mailto:corinna...@gmail.com>>>
> wrote:
> > >
> > > Perfect. Thanks!
> > >
> > >
> > > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
> > > > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > >
> > > you'll need to figure it out from the volume itself by
> > loading
> > > the seg
> > > with both -seg and -aux. When you find the label you want,
> > > click on it
> > > and the aux value in the control window will tell you
> > what the
> > > id is
> > >
> > > doug
> > >
> > > On 04/09/2014 09:41 AM, Corinna Bauer wrote:
> > > > In the mri_extract_label, there is a label number. Where
> > > would I find
> > > > this for the new labels?
> > > >
> > > > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
> 2035
> > > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
> > > >
> > > >
> > > > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
> > > > > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote:
> > > >
> > > > yep, exactly
> > > >
> > > >
> > > > On 4/8/14 6:00 PM, Corinna Bauer wrote:
> > > >> Hi Doug,
> > > >> After I have the labels then in each subject's T1
> > > space, I will
> > > >> need to then put them into diffusion and resting
> > state
> > > space.
> > > >>
> > > >> I already have scripts that put the parcellations
> > into
> > > >> subject-specific diffusion/resting state space
> (using
> > > bbregister,
> > > >> tkregister2, mri_vol2vol (using the inverse
> > > registration from
> > > >> bbregister to put the T1 into diffusion space),
> > > mri_extract_label
> > > >>
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg --s
FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not
open file
On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve wrote:
> Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
> file for an example command line that generates wmparc.mgz
>
> doug
>
> On 04/10/2014 09:52 AM, Corinna Bauer wrote:
> > For creating corresponding wm segmentations to the rois derived from
> > mris_divide_parcellation, should mri_aparc2wmseg be used or should I
> > follow the steps outlined in this posting
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
> > ?
> >
> > Thanks
> >
> > Corinna
> >
> >
> > On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer > <mailto:corinna...@gmail.com>> wrote:
> >
> > Perfect. Thanks!
> >
> >
> > On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >
> >
> > you'll need to figure it out from the volume itself by loading
> > the seg
> > with both -seg and -aux. When you find the label you want,
> > click on it
> > and the aux value in the control window will tell you what the
> > id is
> >
> > doug
> >
> > On 04/09/2014 09:41 AM, Corinna Bauer wrote:
> > > In the mri_extract_label, there is a label number. Where
> > would I find
> > > this for the new labels?
> > >
> > > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
> > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
> > >
> > >
> > > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
> > > > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > yep, exactly
> > >
> > >
> > > On 4/8/14 6:00 PM, Corinna Bauer wrote:
> > >> Hi Doug,
> > >> After I have the labels then in each subject's T1
> > space, I will
> > >> need to then put them into diffusion and resting state
> > space.
> > >>
> > >> I already have scripts that put the parcellations into
> > >> subject-specific diffusion/resting state space (using
> > bbregister,
> > >> tkregister2, mri_vol2vol (using the inverse
> > registration from
> > >> bbregister to put the T1 into diffusion space),
> > mri_extract_label
> > >> (extract labels from aparc+aseg.mgz), and then
> > mri_label2vol
> > >> (register each of the extracted labels into diffusion
> > space).
> > >> Would a similar approach work for the new labels?
> > >>
> > >> Corinna
> > >>
> > >>
> > >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
> > >> > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >>
> > >>
> > >> Exactly what you have described won't work very
> > well because
> > >> it would be
> > >> in the volume. I would divide up the parcellations in
> > >> fsaverage space
> > >> like you've done, then map the parcellation to each
> > subject using
> > >> mri_surf2surf (--sval-annot, see example 6)
> > >>
> > >> doug
> > >>
> > >> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> > >> > Hello all,
> > >> >
> > >> > I am planning to use mris_divide_parcellation to
> > split the
> > >> Desikan
> > >>
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer wrote:
> Perfect. Thanks!
>
>
> On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> you'll need to figure it out from the volume itself by loading the seg
>> with both -seg and -aux. When you find the label you want, click on it
>> and the aux value in the control window will tell you what the id is
>>
>> doug
>>
>> On 04/09/2014 09:41 AM, Corinna Bauer wrote:
>> > In the mri_extract_label, there is a label number. Where would I find
>> > this for the new labels?
>> >
>> > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
>> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
>> >
>> >
>> > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > yep, exactly
>> >
>> >
>> > On 4/8/14 6:00 PM, Corinna Bauer wrote:
>> >> Hi Doug,
>> >> After I have the labels then in each subject's T1 space, I will
>> >> need to then put them into diffusion and resting state space.
>> >>
>> >> I already have scripts that put the parcellations into
>> >> subject-specific diffusion/resting state space (using bbregister,
>> >> tkregister2, mri_vol2vol (using the inverse registration from
>> >> bbregister to put the T1 into diffusion space), mri_extract_label
>> >> (extract labels from aparc+aseg.mgz), and then mri_label2vol
>> >> (register each of the extracted labels into diffusion space).
>> >> Would a similar approach work for the new labels?
>> >>
>> >> Corinna
>> >>
>> >>
>> >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
>> >> mailto:gr...@nmr.mgh.harvard.edu>>
>> wrote:
>> >>
>> >>
>> >> Exactly what you have described won't work very well because
>> >> it would be
>> >> in the volume. I would divide up the parcellations in
>> >> fsaverage space
>> >> like you've done, then map the parcellation to each subject
>> using
>> >> mri_surf2surf (--sval-annot, see example 6)
>> >>
>> >> doug
>> >>
>> >> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
>> >> > Hello all,
>> >> >
>> >> > I am planning to use mris_divide_parcellation to split the
>> >> Desikan
>> >> > atlas into smaller ROIs, but will need the new ROIs to be
>> >> consistent
>> >> > between subjects.
>> >> >
>> >> > Can I achieve this if I register each subject to fsaverage
>> >> space and
>> >> > then apply the inverse transform to the divided
>> >> parcellations (which
>> >> > are currently done on the fsaverage brain)?
>> >> >
>> >> > If so, for extracting each label, what would be used for
>> >> the label
>> >> > number?
>> >> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
>> >> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>> >> >
>> >> >
>> >> > Thanks
>> >> >
>> >> > Corinna
>> >> >
>> >> >
>> >> > ___
>> >> > Freesurfer mailing list
>> >> > Freesurfer@nmr.mgh.harvard.edu
>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >> --
>> >> Douglas N. Greve, Ph.D.
>> >> MGH-NMR Center
>> >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> >> Phone Number: 617-724-2358
>> >> Fax:
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
wrote:
>
> you'll need to figure it out from the volume itself by loading the seg
> with both -seg and -aux. When you find the label you want, click on it
> and the aux value in the control window will tell you what the id is
>
> doug
>
> On 04/09/2014 09:41 AM, Corinna Bauer wrote:
> > In the mri_extract_label, there is a label number. Where would I find
> > this for the new labels?
> >
> > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
> >
> >
> > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > yep, exactly
> >
> >
> > On 4/8/14 6:00 PM, Corinna Bauer wrote:
> >> Hi Doug,
> >> After I have the labels then in each subject's T1 space, I will
> >> need to then put them into diffusion and resting state space.
> >>
> >> I already have scripts that put the parcellations into
> >> subject-specific diffusion/resting state space (using bbregister,
> >> tkregister2, mri_vol2vol (using the inverse registration from
> >> bbregister to put the T1 into diffusion space), mri_extract_label
> >> (extract labels from aparc+aseg.mgz), and then mri_label2vol
> >> (register each of the extracted labels into diffusion space).
> >> Would a similar approach work for the new labels?
> >>
> >> Corinna
> >>
> >>
> >> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
> >> mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >>
> >>
> >> Exactly what you have described won't work very well because
> >> it would be
> >> in the volume. I would divide up the parcellations in
> >> fsaverage space
> >> like you've done, then map the parcellation to each subject
> using
> >> mri_surf2surf (--sval-annot, see example 6)
> >>
> >> doug
> >>
> >> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> >> > Hello all,
> >> >
> >> > I am planning to use mris_divide_parcellation to split the
> >> Desikan
> >> > atlas into smaller ROIs, but will need the new ROIs to be
> >> consistent
> >> > between subjects.
> >> >
> >> > Can I achieve this if I register each subject to fsaverage
> >> space and
> >> > then apply the inverse transform to the divided
> >> parcellations (which
> >> > are currently done on the fsaverage brain)?
> >> >
> >> > If so, for extracting each label, what would be used for
> >> the label
> >> > number?
> >> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
> >> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
> >> >
> >> >
> >> > Thanks
> >> >
> >> > Corinna
> >> >
> >> >
> >> > ___
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> >> Outgoing:
> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.e
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Should I make up my own LUT for the new ROIs that specifies some colour and
label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer wrote:
> It looks like the FreeSurferColorLUT.txt does not contain the label number
> for the newly created labels (divided from the desikan atlas).
>
>
> On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl
> wrote:
>
>> $FREESURFER_HOME/FreeSurferColorLUT.txt
>>
>> cheers
>> Bruce
>> On Wed, 9 Apr 2014, Corinna Bauer
>> wrote:
>>
>> > In the mri_extract_label, there is a label number. Where would I find
>> this
>> > for the new labels?
>> >
>> > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
>> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
>> >
>> >
>> > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu>
>> > wrote:
>> > yep, exactly
>> >
>> > On 4/8/14 6:00 PM, Corinna Bauer wrote:
>> > Hi Doug,
>> > After I have the labels then in each subject's T1 space, I
>> > will need to then put them into diffusion and resting
>> > state space.
>> >
>> > I already have scripts that put the parcellations into
>> > subject-specific diffusion/resting state space (using
>> > bbregister, tkregister2, mri_vol2vol (using the inverse
>> > registration from bbregister to put the T1 into diffusion
>> > space), mri_extract_label (extract labels from
>> > aparc+aseg.mgz), and then mri_label2vol (register each of
>> > the extracted labels into diffusion space). Would a
>> > similar approach work for the new labels?
>> >
>> > Corinna
>> >
>> >
>> > On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
>> > wrote:
>> >
>> > Exactly what you have described won't work very well
>> > because it would be
>> > in the volume. I would divide up the parcellations
>> > in fsaverage space
>> > like you've done, then map the parcellation to each
>> > subject using
>> > mri_surf2surf (--sval-annot, see example 6)
>> >
>> > doug
>> >
>> > On 04/08/2014 04:54 PM, Corinna Bauer wrote:
>> > > Hello all,
>> > >
>> > > I am planning to use mris_divide_parcellation to
>> > split the Desikan
>> > > atlas into smaller ROIs, but will need the new
>> > ROIs to be consistent
>> > > between subjects.
>> > >
>> > > Can I achieve this if I register each subject to
>> > fsaverage space and
>> > > then apply the inverse transform to the divided
>> > parcellations (which
>> > > are currently done on the fsaverage brain)?
>> > >
>> > > If so, for extracting each label, what would be
>> > used for the label
>> > > number?
>> > > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
>> > *2035*
>> > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>> > >
>> > >
>> > > Thanks
>> > >
>> > > Corinna
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > >
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu
>> > Phone Number: 617-724-2358
>> > Fax: 617-726-7422
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > Outgoing:
>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >
>> > ___
>> > 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 informati
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl wrote:
> $FREESURFER_HOME/FreeSurferColorLUT.txt
>
> cheers
> Bruce
> On Wed, 9 Apr 2014, Corinna Bauer
> wrote:
>
> > In the mri_extract_label, there is a label number. Where would I find
> this
> > for the new labels?
> >
> > i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii
> >
> >
> > On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve <
> gr...@nmr.mgh.harvard.edu>
> > wrote:
> > yep, exactly
> >
> > On 4/8/14 6:00 PM, Corinna Bauer wrote:
> > Hi Doug,
> > After I have the labels then in each subject's T1 space, I
> > will need to then put them into diffusion and resting
> > state space.
> >
> > I already have scripts that put the parcellations into
> > subject-specific diffusion/resting state space (using
> > bbregister, tkregister2, mri_vol2vol (using the inverse
> > registration from bbregister to put the T1 into diffusion
> > space), mri_extract_label (extract labels from
> > aparc+aseg.mgz), and then mri_label2vol (register each of
> > the extracted labels into diffusion space). Would a
> > similar approach work for the new labels?
> >
> > Corinna
> >
> >
> > On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
> > wrote:
> >
> > Exactly what you have described won't work very well
> > because it would be
> > in the volume. I would divide up the parcellations
> > in fsaverage space
> > like you've done, then map the parcellation to each
> > subject using
> > mri_surf2surf (--sval-annot, see example 6)
> >
> > doug
> >
> > On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> > > Hello all,
> > >
> > > I am planning to use mris_divide_parcellation to
> > split the Desikan
> > > atlas into smaller ROIs, but will need the new
> > ROIs to be consistent
> > > between subjects.
> > >
> > > Can I achieve this if I register each subject to
> > fsaverage space and
> > > then apply the inverse transform to the divided
> > parcellations (which
> > > are currently done on the fsaverage brain)?
> > >
> > > If so, for extracting each label, what would be
> > used for the label
> > > number?
> > > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
> > *2035*
> > > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
> > >
> > >
> > > Thanks
> > >
> > > Corinna
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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 Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . 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.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> >
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve wrote:
> yep, exactly
>
>
> On 4/8/14 6:00 PM, Corinna Bauer wrote:
>
> Hi Doug,
> After I have the labels then in each subject's T1 space, I will need to
> then put them into diffusion and resting state space.
>
> I already have scripts that put the parcellations into subject-specific
> diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
> (using the inverse registration from bbregister to put the T1 into
> diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
> and then mri_label2vol (register each of the extracted labels into
> diffusion space). Would a similar approach work for the new labels?
>
> Corinna
>
>
> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve > wrote:
>
>>
>> Exactly what you have described won't work very well because it would be
>> in the volume. I would divide up the parcellations in fsaverage space
>> like you've done, then map the parcellation to each subject using
>> mri_surf2surf (--sval-annot, see example 6)
>>
>> doug
>>
>> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
>> > Hello all,
>> >
>> > I am planning to use mris_divide_parcellation to split the Desikan
>> > atlas into smaller ROIs, but will need the new ROIs to be consistent
>> > between subjects.
>> >
>> > Can I achieve this if I register each subject to fsaverage space and
>> > then apply the inverse transform to the divided parcellations (which
>> > are currently done on the fsaverage brain)?
>> >
>> > If so, for extracting each label, what would be used for the label
>> > number?
>> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
>> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>> >
>> >
>> > Thanks
>> >
>> > Corinna
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.
I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the inverse registration from bbregister to put the T1 into
diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
and then mri_label2vol (register each of the extracted labels into
diffusion space). Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
wrote:
>
> Exactly what you have described won't work very well because it would be
> in the volume. I would divide up the parcellations in fsaverage space
> like you've done, then map the parcellation to each subject using
> mri_surf2surf (--sval-annot, see example 6)
>
> doug
>
> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> > Hello all,
> >
> > I am planning to use mris_divide_parcellation to split the Desikan
> > atlas into smaller ROIs, but will need the new ROIs to be consistent
> > between subjects.
> >
> > Can I achieve this if I register each subject to fsaverage space and
> > then apply the inverse transform to the divided parcellations (which
> > are currently done on the fsaverage brain)?
> >
> > If so, for extracting each label, what would be used for the label
> > number?
> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
> >
> >
> > Thanks
> >
> > Corinna
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
[Freesurfer] mris_divide_parcellation same divisions between subjects
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan atlas
into smaller ROIs, but will need the new ROIs to be consistent between
subjects.
Can I achieve this if I register each subject to fsaverage space and then
apply the inverse transform to the divided parcellations (which are
currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.
[Freesurfer] Discrepancy between volume generated by aparcstats2table and mri_segstats
Hello all, I have noticed a discrepancy in the volumes generated by aparcstats2table and mri_segstats using aparc+aseg. Which is correct? I am using version 5.3. Thanks, Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] Talairach failure in 5.3 but not in 5.2
Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects. Any suggestions? Corinna # #@# Talairach Fri Feb 28 12:39:50 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align # #@# Talairach Fri Feb 28 12:40:51 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri Feb 28 12:41:10 EST 2014 tmpdir is transforms/tmp.talairach.30730 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.30730/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.13732e-09, 3.72529e-09) j_ras = (-3.72529e-09, -1.45519e-11, -1) k_ras = (2.6057e-10, 1, 1.45519e-11) writing to transforms/tmp.talairach.30730/src.mnc... mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.30730/src.mnc transforms/talairach.auto.xfm Fri Feb 28 12:41:27 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #@# Talairach Failure Detection Fri Feb 28 12:41:28 EST 2014 /home/bauer/freesurfer_subjects/symmetry/MWP_04182013/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0012, pval=0. < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux bauer 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MWP_04182013 exited with ERRORS ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] expand GM label into white matter
Hi Doug, I don't see anywhere a seg.mgz. mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 Corinna On Tue, Nov 5, 2013 at 11:38 AM, Corinna Bauer wrote: > I think that the first option you provided is more along the lines of what > I'm looking for. Thanks > > Corinna > > > On Mon, Nov 4, 2013 at 5:37 PM, Douglas N Greve > wrote: > >> Yes. As Bruce mentioned you can also use the program that creates the >> wmparc (mri_aparc2aseg). You can look in the recon-all.log file for the >> command line (there will be two in there, one to create aparc+aseg and one >> to create wmparc). You can run this command with --wmparc-dmax to set the >> maximum distance from cortex to dilate the voxels. Make sure to name the >> output something other than wmparc.mgz so you don't overwrite what is >> there. When it is done, there will be a WM label for each cortical label. >> Is this what you want? It won't do this for subcortical structures. >> doug >> >> >> On 11/04/2013 12:25 PM, Corinna Bauer wrote: >> >>> ok thanks, I'll give that a try. I would have to do that for each of the >>> segmentations of interest and I get the number from the LUT? >>> >>> >>> On Mon, Nov 4, 2013 at 11:47 AM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> There is not a single command to do it, but you could do something >>> like >>> >>> mri_binarize --i aparc+aseg.mgz --wm --o wmmask.mgz # mask of >>> white matter >>> mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 >>> mri_binarize --i seg.mgz --match 17 --dilate 2 --o mask17.dil2.mgz # >>> mask of seg 17 dilated by 2 voxels >>> fscalc wmmask.mgz and mask17.dil2.mgz --o mask17.dil2.wm.mgz # seg >>> 17 >>> inside WM >>> mri_concat mask17.mgz mask17.dil2.wm.mgz --sum --o mask17+wm.mgz >>> # seg >>> 17 plus dilation into WM >>> >>> doug >>> >>> >>> On 11/04/2013 11:38 AM, Corinna Bauer wrote: >>> > Hello all, >>> > Is there a way to expand a GM label into the white matter by n >>> voxels? >>> > >>> > Corinna >>> > >>> > >>> > ___ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@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 Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . 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. >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] expand GM label into white matter
I think that the first option you provided is more along the lines of what I'm looking for. Thanks Corinna On Mon, Nov 4, 2013 at 5:37 PM, Douglas N Greve wrote: > Yes. As Bruce mentioned you can also use the program that creates the > wmparc (mri_aparc2aseg). You can look in the recon-all.log file for the > command line (there will be two in there, one to create aparc+aseg and one > to create wmparc). You can run this command with --wmparc-dmax to set the > maximum distance from cortex to dilate the voxels. Make sure to name the > output something other than wmparc.mgz so you don't overwrite what is > there. When it is done, there will be a WM label for each cortical label. > Is this what you want? It won't do this for subcortical structures. > doug > > > On 11/04/2013 12:25 PM, Corinna Bauer wrote: > >> ok thanks, I'll give that a try. I would have to do that for each of the >> segmentations of interest and I get the number from the LUT? >> >> >> On Mon, Nov 4, 2013 at 11:47 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> There is not a single command to do it, but you could do something >> like >> >> mri_binarize --i aparc+aseg.mgz --wm --o wmmask.mgz # mask of >> white matter >> mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 >> mri_binarize --i seg.mgz --match 17 --dilate 2 --o mask17.dil2.mgz # >> mask of seg 17 dilated by 2 voxels >> fscalc wmmask.mgz and mask17.dil2.mgz --o mask17.dil2.wm.mgz # seg 17 >> inside WM >> mri_concat mask17.mgz mask17.dil2.wm.mgz --sum --o mask17+wm.mgz >> # seg >> 17 plus dilation into WM >> >> doug >> >> >> On 11/04/2013 11:38 AM, Corinna Bauer wrote: >> > Hello all, >> > Is there a way to expand a GM label into the white matter by n >> voxels? >> > >> > Corinna >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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 Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . 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. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] expand GM label into white matter
ok thanks, I'll give that a try. I would have to do that for each of the segmentations of interest and I get the number from the LUT? On Mon, Nov 4, 2013 at 11:47 AM, Douglas N Greve wrote: > > There is not a single command to do it, but you could do something like > > mri_binarize --i aparc+aseg.mgz --wm --o wmmask.mgz # mask of white matter > mri_binarize --i seg.mgz --match 17 --o mask17.mgz # mask of seg 17 > mri_binarize --i seg.mgz --match 17 --dilate 2 --o mask17.dil2.mgz # > mask of seg 17 dilated by 2 voxels > fscalc wmmask.mgz and mask17.dil2.mgz --o mask17.dil2.wm.mgz # seg 17 > inside WM > mri_concat mask17.mgz mask17.dil2.wm.mgz --sum --o mask17+wm.mgz # seg > 17 plus dilation into WM > > doug > > > On 11/04/2013 11:38 AM, Corinna Bauer wrote: > > Hello all, > > Is there a way to expand a GM label into the white matter by n voxels? > > > > Corinna > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] expand GM label into white matter
Hello all, Is there a way to expand a GM label into the white matter by n voxels? Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] aparcstats2table error
Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.stats is not found or is too small to be a valid statsfile The statsfile is there and is not empty. Subject names are all in this format ABC_12345678 Any suggestions? Thanks Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Fornix labelled as corpus callosum in patient with periventricular leukomalacia
Hi Bruce, I was just wondering if you had any suggestions on how to fix the corpus callosum labels? Corinna On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer wrote: > In general, it mostly looks ok. There are regions which are labelled as > hypointensities, but should be CSF or gray matter, particularly around the > parieto-occipital fissure (see attached). Much of the fornix and corpus > callosum is also just labelled as left/right cerebral white matter. > > > > > On Wed, Aug 14, 2013 at 11:37 AM, Bruce Fischl > wrote: > >> Hi Corinna >> >> how does the rest of the aseg.mgz look? Is it accurate? >> Bruce >> >> On Wed, 14 Aug 2013, Corinna Bauer wrote: >> >> Hello all, >>> I am examining diffusion tracking in the corpus callosum of individuals >>> with >>> periventricular leukomalacia (PVL). The corpus callosum is particularly >>> small and the anterior and mid-anterior labels are being applied to the >>> fornix (see attached Fornix_labelled_as_CC.png). The midposterior and >>> posterior look ok, while the central is very small, maybe one voxel in >>> size. >>> >>> The wm segmentation, seen with ?l.white, also shows segmentation defaults >>> with the anterior corpus callosum (see attached images). I tried to >>> correct >>> this using control points, which you can see did not fix the >>> segmentation. >>> >>> Any suggestions? >>> >>> Corinna >>> >>> >>> >>> >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> 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. >> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] epi correction of fmri data
oh great. Is there a way to get this to work with FSL 5? On Fri, May 3, 2013 at 1:11 PM, Douglas N Greve wrote: > It needs to be 0 to 4095, see below > > --ph phasevolid > > Phase volume from the B0 fieldmap (if the phases from Echo1, Echo2 are > available instead of their difference). These are assumed to be scaled > between 0 to 4095 for -pi to pi. Eg, ph.ext, where ext is either nii, > nii.gz, or img. Not with --complex or with --dph. > > This is made to work with the default Siemens field map. Note that you can > also use complex inputs instead of mag and phase > > doug > > > > > > On 05/03/2013 01:05 PM, Corinna Bauer wrote: > >> Should the phase image be in rads? and does the magnitude image need to >> be skull-stripped first? >> >> >> On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer > corinna...@gmail.com>> wrote: >> >> thanks Doug, I will give that a try. >> >> >> On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put >> it in >> the bold folder, eg: >> >> epidewarp.fsl \ >> --mag mag.nii.gz \ >> --dph dphase.nii.gz \ >> --tediff YOUR_TE_DIFF --esp YOUR_ESP \ >> --vsm bold/b0dcmap.nii.gz >> >> When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the >> command lines. >> >> doug >> >> >> On 05/03/2013 12:16 PM, Corinna Bauer wrote: >> >> Yes, I am using FSFAST. >> >> >> On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu>>> >> wrote: >> >> >> Hi Corinna, are you using FSFAST? If not, are you >> still going to the >> surface? >> doug >> >> On 05/03/2013 11:07 AM, Corinna Bauer wrote: >> > Is there a way to correct fmri data for epi >> distortions in >> freesurfer? >> > Or does the data need to be first fun through FSL's >> B0 unwarping? >> > >> > Corinna >> > >> > >> > __**_ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu >> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> >> Phone Number: 617-724-2358 >> > >> Fax: 617-726-7422 > >> > >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedr
Re: [Freesurfer] epi correction of fmri data
Should the phase image be in rads? and does the magnitude image need to be skull-stripped first? On Fri, May 3, 2013 at 12:30 PM, Corinna Bauer wrote: > thanks Doug, I will give that a try. > > > On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in >> the bold folder, eg: >> >> epidewarp.fsl \ >> --mag mag.nii.gz \ >> --dph dphase.nii.gz \ >> --tediff YOUR_TE_DIFF --esp YOUR_ESP \ >> --vsm bold/b0dcmap.nii.gz >> >> When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the >> command lines. >> >> doug >> >> >> On 05/03/2013 12:16 PM, Corinna Bauer wrote: >> >>> Yes, I am using FSFAST. >>> >>> >>> On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu>> >>> wrote: >>> >>> >>> Hi Corinna, are you using FSFAST? If not, are you still going to the >>> surface? >>> doug >>> >>> On 05/03/2013 11:07 AM, Corinna Bauer wrote: >>> > Is there a way to correct fmri data for epi distortions in >>> freesurfer? >>> > Or does the data need to be first fun through FSL's B0 unwarping? >>> > >>> > Corinna >>> > >>> > >>> > __**_ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesur...@nmr.mgh.**harvard.edu >>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu >>> > >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> Outgoing: >>> >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu > >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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 Partners >>> Compliance HelpLine at >>> >>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >>> 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. >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] epi correction of fmri data
thanks Doug, I will give that a try. On Fri, May 3, 2013 at 12:27 PM, Douglas N Greve wrote: > Create the B0 voxel shift map. Call it b0dcmap.nii.gz and put it in > the bold folder, eg: > > epidewarp.fsl \ > --mag mag.nii.gz \ > --dph dphase.nii.gz \ > --tediff YOUR_TE_DIFF --esp YOUR_ESP \ > --vsm bold/b0dcmap.nii.gz > > When you run mkanalysis-sess and preproc-sess, add "-b0dc" to the > command lines. > > doug > > > On 05/03/2013 12:16 PM, Corinna Bauer wrote: > >> Yes, I am using FSFAST. >> >> >> On Fri, May 3, 2013 at 12:08 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> >> Hi Corinna, are you using FSFAST? If not, are you still going to the >> surface? >> doug >> >> On 05/03/2013 11:07 AM, Corinna Bauer wrote: >> > Is there a way to correct fmri data for epi distortions in >> freesurfer? >> > Or does the data need to be first fun through FSL's B0 unwarping? >> > >> > Corinna >> > >> > >> > __**_ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu >> > >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu > >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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 Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> 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. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] epi correction of fmri data
Is there a way to correct fmri data for epi distortions in freesurfer? Or does the data need to be first fun through FSL's B0 unwarping? Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] mkbrainmask error with libmeshclass.so
actually, on closer look, adding those lines to the FSL config did not fix the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works. I am not sure why, but to call anything from fsl I have to first put fsl5.0- first. On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer wrote: > That's alright. I had to add these lines to my .bashrc file > # get FSL config loaded > if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then > . /usr/share/fsl/5.0/etc/fslconf/fsl.sh; > fi > > but now, I get this error when running preproc-sess -per-run -fwhm 3 > -force -so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs > > /usr/local/freesurfer/subjects/symmetry/functional > mri_convert ERROR: could not determine file for > /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask > lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii > > > > > > On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve > wrote: > >> Hi Corinna, I hate to pass the buck, but I think you'll have to contact >> the FSL people to get it sorted out. >> doug >> >> >> >> On 4/16/13 9:31 AM, Corinna Bauer wrote: >> >> Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared >> object file: No such file or directory. >> >> >> >> On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Corinna, if you just run bet2 at the command line, do you get the >>> same error? >>> doug >>> >>> On 04/12/2013 03:56 PM, Corinna Bauer wrote: >>> > Hello all, when running preproc-sess, I got this error message: >>> > ERROR: could not determine file for >>> > >>> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain >>> > Try running mkbrainmask-sess with -per-run >>> > >>> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . >>> > -fsd bold >>> > m) and got the output below, which shows a problem with a shared >>> library? >>> > >>> > Any suggestions? >>> > >>> > Corinna >>> > >>> > >>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test >>> > Fri Apr 12 15:53:14 EDT 2013 >>> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil >>> > 1 -nerode 0 >>> > FSLMATHS fslmaths.fsl >>> > Scratch Dir is /tmp/mkbrainmask_9634 >>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii >>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii >>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>> > reading from template.nii.gz... >>> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >>> > i_ras = (-0.996119, -0.0108587, 0.0873391) >>> > j_ras = (0.000562893, 0.991553, 0.129698) >>> > k_ras = (0.0880098, -0.129244, 0.9877) >>> > writing to /tmp/mkbrainmask_9634/in.nii... >>> > # -- Using FSL's BET to Extract Brain-- # >>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >>> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f >>> 0.1 >>> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: >>> > libmeshclass.so: cannot open shared object file: No such file or >>> directory >>> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o >>> > /tmp/mkbrainmask_9634/brain_mask.nii >>> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii >>> > >>> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >>> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >>> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min >>> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii >>> > sysname Linux >>> > hostname lotfi >>> > machine x86_64 >>> > user bauer >>> > >>> > input /tmp/mkbrainmask_9634/brain_mask.nii >>> > frame 0 >>> > nErode3d 0 >>> > nErode2d 0 >>> > output /tmp/mkbrainmask_9634/brain_mask.nii >>> > Binarizing based on threshold >>> > min0.01 >>> > max
Re: [Freesurfer] mkbrainmask error with libmeshclass.so
That's alright. I had to add these lines to my .bashrc file # get FSL config loaded if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then . /usr/share/fsl/5.0/etc/fslconf/fsl.sh; fi but now, I get this error when running preproc-sess -per-run -fwhm 3 -force -so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs /usr/local/freesurfer/subjects/symmetry/functional mri_convert ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve wrote: > Hi Corinna, I hate to pass the buck, but I think you'll have to contact > the FSL people to get it sorted out. > doug > > > > On 4/16/13 9:31 AM, Corinna Bauer wrote: > > Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared > object file: No such file or directory. > > > > On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> Hi Corinna, if you just run bet2 at the command line, do you get the >> same error? >> doug >> >> On 04/12/2013 03:56 PM, Corinna Bauer wrote: >> > Hello all, when running preproc-sess, I got this error message: >> > ERROR: could not determine file for >> > >> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain >> > Try running mkbrainmask-sess with -per-run >> > >> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . >> > -fsd bold >> > m) and got the output below, which shows a problem with a shared >> library? >> > >> > Any suggestions? >> > >> > Corinna >> > >> > >> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test >> > Fri Apr 12 15:53:14 EDT 2013 >> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil >> > 1 -nerode 0 >> > FSLMATHS fslmaths.fsl >> > Scratch Dir is /tmp/mkbrainmask_9634 >> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii >> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii >> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> > reading from template.nii.gz... >> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 >> > i_ras = (-0.996119, -0.0108587, 0.0873391) >> > j_ras = (0.000562893, 0.991553, 0.129698) >> > k_ras = (0.0880098, -0.129244, 0.9877) >> > writing to /tmp/mkbrainmask_9634/in.nii... >> > # -- Using FSL's BET to Extract Brain-- # >> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f >> 0.1 >> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: >> > libmeshclass.so: cannot open shared object file: No such file or >> directory >> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o >> > /tmp/mkbrainmask_9634/brain_mask.nii >> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii >> > >> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold >> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min >> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii >> > sysname Linux >> > hostname lotfi >> > machine x86_64 >> > user bauer >> > >> > input /tmp/mkbrainmask_9634/brain_mask.nii >> > frame 0 >> > nErode3d 0 >> > nErode2d 0 >> > output /tmp/mkbrainmask_9634/brain_mask.nii >> > Binarizing based on threshold >> > min0.01 >> > max+infinity >> > binval1 >> > binvalnot 0 >> > >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>
Re: [Freesurfer] mkbrainmask error with libmeshclass.so
Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared object file: No such file or directory. On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve wrote: > Hi Corinna, if you just run bet2 at the command line, do you get the > same error? > doug > > On 04/12/2013 03:56 PM, Corinna Bauer wrote: > > Hello all, when running preproc-sess, I got this error message: > > ERROR: could not determine file for > > > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain > > Try running mkbrainmask-sess with -per-run > > > > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . > > -fsd bold > > m) and got the output below, which shows a problem with a shared library? > > > > Any suggestions? > > > > Corinna > > > > > > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test > > Fri Apr 12 15:53:14 EDT 2013 > > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil > > 1 -nerode 0 > > FSLMATHS fslmaths.fsl > > Scratch Dir is /tmp/mkbrainmask_9634 > > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold > > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii > > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from template.nii.gz... > > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-0.996119, -0.0108587, 0.0873391) > > j_ras = (0.000562893, 0.991553, 0.129698) > > k_ras = (0.0880098, -0.129244, 0.9877) > > writing to /tmp/mkbrainmask_9634/in.nii... > > # -- Using FSL's BET to Extract Brain-- # > > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold > > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f > 0.1 > > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: > > libmeshclass.so: cannot open shared object file: No such file or > directory > > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o > > /tmp/mkbrainmask_9634/brain_mask.nii > > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii > > > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold > > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min > > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii > > sysname Linux > > hostname lotfi > > machine x86_64 > > user bauer > > > > input /tmp/mkbrainmask_9634/brain_mask.nii > > frame 0 > > nErode3d 0 > > nErode2d 0 > > output /tmp/mkbrainmask_9634/brain_mask.nii > > Binarizing based on threshold > > min0.01 > > max+infinity > > binval1 > > binvalnot 0 > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . 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. > > ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
[Freesurfer] mkbrainmask error with libmeshclass.so
Hello all, when running preproc-sess, I got this error message: ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain Try running mkbrainmask-sess with -per-run I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . -fsd bold m) and got the output below, which shows a problem with a shared library? Any suggestions? Corinna /usr/local/freesurfer/subjects/symmetry/lindsay/first_test Fri Apr 12 15:53:14 EDT 2013 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_9634 /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996119, -0.0108587, 0.0873391) j_ras = (0.000562893, 0.991553, 0.129698) k_ras = (0.0880098, -0.129244, 0.9877) writing to /tmp/mkbrainmask_9634/in.nii... # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f 0.1 /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii sysname Linux hostname lotfi machine x86_64 user bauer input /tmp/mkbrainmask_9634/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_9634/brain_mask.nii Binarizing based on threshold min0.01 max+infinity binval1 binvalnot 0 ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] bbregister error with hardi data
Ok I adjusted the bbregister file to say fsvol.mgz in the location you specified and got this error a bit later on in the bbregister output: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry cd /usr/local/freesurfer/subjects/symmetry/lindsay /usr/local/freesurfer/bin/bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti --init-fsl --reg register.dat $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii mri_convert hardi/ffiltered_func_data_01.nii.gz ./tmp.bbregister.15807/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from hardi/ffiltered_func_data_01.nii.gz... TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.991204, -0.025762, 0.129811) j_ras = (-0.0259819, 0.999662, 0) k_ras = (0.129768, 0.00337275, 0.991539) writing to ./tmp.bbregister.15807/template.nii... fslregister --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask ERROR: Flag --fsvol.mgz unrecognized. --s lindsay --mov ./tmp.bbregister.15807/template.nii --reg ./tmp.bbregister.15807/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.15807/fslregister --dof 6 --fsvol.mgz brainmask mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/reg.init.dat --out-reg ./tmp.bbregister.15807/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/reg.init.dat mri_segreg --mov ./tmp.bbregister.15807/template.nii --init-reg ./tmp.bbregister.15807/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.15807/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open ./tmp.bbregister.15807/bbr.pass1.dat Cleaning up Started at Mon Mar 25 13:24:53 EDT 2013 Ended at Mon Mar 25 13:25:00 EDT 2013 BBR-Run-Time-Sec 7 bbregister Done To check results, run: tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat --surf On Mon, Mar 25, 2013 at 1:22 PM, Douglas N Greve wrote: > > Corinna, can you edit $FREESURFER_HOME/bin/**bbregister? If so, change > the following line > > From > set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ > --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ > --dof $FSLDOF --fsvol $fsvol) > To > set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \ > --niters 1 --maxangle 90 --tmp $tmpdir/fslregister \ > --dof $FSLDOF --fsvol $fsvol.mgz) > > It is just the very last part that is changed where I added ".mgz" to > $fsvol > > Re-run bbregister and let me know if this works. > > doug > > > > On 03/25/2013 01:11 PM, Corinna Bauer wrote: > >> yes, this file exists. >> >> >> On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> Can you verify that >> /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz >> exists? >> doug >> >> >> On 03/25/2013 12:55 PM, Corinna Bauer wrote: >> >> sure. Here is the dng.log. >> >> Corinna >> >> On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >>> >> wrote: >> >> >> Hi Corinna, can you run >> >> fslregister --debug --s lindsay --mov >> hardi/ffiltered_func_data_01.**nii.gz --reg fsl.reg.dat >> --niters 1 >> --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 >> --fsvol >> brainmask |& tee dng.log >> >> and send me the dng.log? >> >> doug >> >> >> On 03/25/2013 12:39 PM, Corinna Bauer wrote: >> > Hello all, >> > >> > I am attempting to run bbregister on 4D HARDI data that >>
Re: [Freesurfer] bbregister error with hardi data
yes, this file exists.
On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve
wrote:
> Can you verify that
> /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz
> exists?
> doug
>
>
> On 03/25/2013 12:55 PM, Corinna Bauer wrote:
>
>> sure. Here is the dng.log.
>>
>> Corinna
>>
>> On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.**edu>>
>> wrote:
>>
>>
>> Hi Corinna, can you run
>>
>> fslregister --debug --s lindsay --mov
>> hardi/ffiltered_func_data_01.**nii.gz --reg fsl.reg.dat --niters 1
>> --maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol
>> brainmask |& tee dng.log
>>
>> and send me the dng.log?
>>
>> doug
>>
>>
>> On 03/25/2013 12:39 PM, Corinna Bauer wrote:
>> > Hello all,
>> >
>> > I am attempting to run bbregister on 4D HARDI data that has already
>> > been motion, eddy, and epi-distortion corrected in fsl. I run
>> the command:
>> > bbregister --s lindsay --mov hardi/ffiltered_func_data_01.**nii.gz
>> --dti
>> > --init-fsl --reg register.dat and get a number of errors that
>> seem to
>> > begin in the mri_convert section as seen below.
>> > Any insight?
>> >
>> > Cheers,
>> > Corinna
>> >
>> > FREESURFER_HOME /usr/local/freesurfer
>> > mri_convert hardi/ffiltered_func_data_01.**nii.gz
>> > ./tmp.bbregister.15356/**template.nii
>> > mri_convert hardi/ffiltered_func_data_01.**nii.gz
>> > ./tmp.bbregister.15356/**template.nii
>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> > reading from hardi/ffiltered_func_data_01.**nii.gz...
>> > TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (-0.991204, -0.025762, 0.129811)
>> > j_ras = (-0.0259819, 0.999662, 0)
>> > k_ras = (0.129768, 0.00337275, 0.991539)
>> > writing to ./tmp.bbregister.15356/**template.nii...
>> > fslregister --s lindsay --mov ./tmp.bbregister.15356/**template.nii
>> > --reg ./tmp.bbregister.15356/reg.**init.dat --niters 1 --maxangle
>> 90
>> > --nobetmov --tmp ./tmp.bbregister.15356/**fslregister --dof 6
>> --fsvol
>> > brainmask
>> >
>> > Log file is ./tmp.bbregister.15356/reg.**init.dat.fslregister.log
>> >
>> > Mon Mar 25 12:22:23 EDT 2013
>> > --s lindsay --mov ./tmp.bbregister.15356/**template.nii --reg
>> > ./tmp.bbregister.15356/reg.**init.dat --niters 1 --maxangle 90
>> > --nobetmov --tmp ./tmp.bbregister.15356/**fslregister --dof 6
>> --fsvol
>> > brainmask
>> > $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>> > lotfi
>> > Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC
>> > 2013 x86_64 x86_64 x86_64 GNU/Linux
>> > nIters 1
>> > --**
>> > /usr/local/freesurfer/**subjects/symmetry/lindsay
>> > mri_convert ERROR: could not determine file for
>> > /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**ERROR:
>> > ./tmp.bbregister.15356/**fslregister/refvol.**fslregister.nii
>> > mri_convert ERROR: could not determine file for
>> > /usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**ERROR:
>> > ./tmp.bbregister.15356/**fslregister/refvol.**fslregister.nii
>> >
>> > mri_convert: extra arguments ("not" and following)
>> >
>> > type mri_convert -u for usage
>> >
>> > --**
>> > /usr/local/freesurfer/**subjects/symmetry/lindsay
>> > mri_convert ./tmp.bbregister.15356/**template.nii
>> > ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii
>> --frame 0
>> > mri_convert ./tmp.bbregister.15356/**template.nii
>> > ./tmp.bbregister.15356/**fslregister/movvol.**fslregister.nii
>> --frame 0
>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> > reading from ./tmp.bbregister.15356/**template.nii...
>> > TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (-0.991204, -0.025762, 0.129811)
>> > j_ras = (-0.0259819, 0.999662, 0)
>> > k_ras = (0.1297
[Freesurfer] bbregister error with hardi data
Hello all,
I am attempting to run bbregister on 4D HARDI data that has already been
motion, eddy, and epi-distortion corrected in fsl. I run the command:
bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti
--init-fsl --reg register.dat and get a number of errors that seem to begin
in the mri_convert section as seen below.
Any insight?
Cheers,
Corinna
FREESURFER_HOME /usr/local/freesurfer
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15356/template.nii
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15356/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from hardi/ffiltered_func_data_01.nii.gz...
TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.991204, -0.025762, 0.129811)
j_ras = (-0.0259819, 0.999662, 0)
k_ras = (0.129768, 0.00337275, 0.991539)
writing to ./tmp.bbregister.15356/template.nii...
fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg
./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log
Mon Mar 25 12:22:23 EDT 2013
--s lindsay --mov ./tmp.bbregister.15356/template.nii --reg
./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
lotfi
Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--
/usr/local/freesurfer/subjects/symmetry/lindsay
mri_convert ERROR: could not determine file for
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
--
/usr/local/freesurfer/subjects/symmetry/lindsay
mri_convert ./tmp.bbregister.15356/template.nii
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0
mri_convert ./tmp.bbregister.15356/template.nii
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.bbregister.15356/template.nii...
TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.991204, -0.025762, 0.129811)
j_ras = (-0.0259819, 0.999662, 0)
k_ras = (0.129768, 0.00337275, 0.991539)
keeping frame 0
writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii...
Mov determinant is -6.125
/usr/local/freesurfer/subjects/symmetry/lindsay
tkregister2_cmdl --mov
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg
./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout
./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
reg file ./tmp.bbregister.15356/fslregister/reg0.15393.dat
LoadVol0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/orig.mgz
Ttarg:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
Tmov:
-1.750 0.000 0.000 112.000;
0.000 0.000 2.000 -60.000;
0.000 -1.750 0.000 112.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
Input registration matrix (computed)
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
---
Input registration matrix
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
Determinant 1
subject = lindsay
RegMat ---
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -6.125, ref det = -1
Mon Mar 25 12:22:34 EDT 2013
/usr/local/freesurfer/subjects/symmetry/lindsay
flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
-in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256
-cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-
[Freesurfer] error in longitudinal template creation
Hi all, I was creating the longitudinal template for a subject when I got this error while on the third time point. Is this a memory problem or is it something else? Thanks, Corinna Resolution: 0 Iteration(single-prec): 1 -- diff. to prev. transform: 0.0425184 Iteration(single-prec): 2mri_robust_template(63717) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 186th slice Cannot allocate memory Darwin killiany-240-97.bumc.bu.edu 11.3.0 Darwin Kernel Version 11.3.0: Thu Jan 12 18:47:41 PST 2012; root:xnu-1699.24.23~1/RELEASE_X86_64 x86_64 recon-all -s 006_S_0498_template exited with ERRORS at Wed Jun 6 15:58:30 EDT 2012 ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Problem creating longitudinal template file
Hi Martin,
I think this is what you're looking for. If not, let me know.
recon-all -base 137_S_0158_template -tp
/Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/24mos/137_S_0158/mri/norm.mgz
-tp
/Applications/freesurfer/subjects/corinna/ADNI/36mos/137_S_0158/mri/norm.mgz
-all
So it will create this for each of the subjects.
There are folders for each time point and then the subjects within those
folders.
Corinna
On Mon, May 14, 2012 at 10:29 PM, Martin Reuter wrote:
> Hi corinna,
> Can you send the corresponding call to recon-all that your script
> generates?
>
> Best Martin
>
> On May 14, 2012, at 18:27, Corinna Bauer wrote:
>
> Hello all,
> I am trying to create a template for longitudinal processing and am
> running into some problems generating the file. I have many subjects so I
> am running a batch script. I am using version 5.1.0
>
> Any suggestions?
>
> Thanks!
> Corinna
>
> Here is my script:
> #!/bin/tcsh
> setenv FREESURFER_HOME /Applications/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template
>
> set subjects=`cat $1`
>
> foreach subject ($subjects)
>
> echo " Processing $subject
> -"
> set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/
> set
> template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri
> set
> tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz
> set
> tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz
> set
> tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz
>set
> tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz
> #set nu_mgz=${subj_dir}/mri/nu.mgz
>
> recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos}
> -tp ${tp_24mos} -tp ${tp_36mos} -all
>
> end
>
>
>
> Here is my output:
> Processing 137_S_0631 -
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is
> /Applications/freesurfer/subjects/corinna/ADNI/template
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin <http://ebrcb-dhcp-240-126.bumc.bu.edu>
> ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue
> Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
> #
> #@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template
> \n mri_robust_template --mov
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> --lta
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
> --template
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
> --average 1 --sat 4.685 \n
> $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
>
> --mov: Using
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> as movable/source volume.
> --mov: Using
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> as movable/source volume.
> --mov: Using
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> as movable/source volume.
> --mov: Using
> /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
> as movable/source volume.
> Total: 4 input volumes
> --lta: Will output LTA transforms
> --template: Using
> /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
> as template output volume.
> --a
[Freesurfer] Problem creating longitudinal template file
Hello all,
I am trying to create a template for longitudinal processing and am running
into some problems generating the file. I have many subjects so I am
running a batch script. I am using version 5.1.0
Any suggestions?
Thanks!
Corinna
Here is my script:
#!/bin/tcsh
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template
set subjects=`cat $1`
foreach subject ($subjects)
echo " Processing $subject
-"
set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/
set
template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri
set
tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz
set
tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz
set
tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz
set
tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz
#set nu_mgz=${subj_dir}/mri/nu.mgz
recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos} -tp
${tp_24mos} -tp ${tp_36mos} -all
end
Here is my output:
Processing 137_S_0631 -
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is
/Applications/freesurfer/subjects/corinna/ADNI/template
Actual FREESURFER_HOME /Applications/freesurfer
Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2:
Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
#
#@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template
\n mri_robust_template --mov
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
--lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta
--template
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
--average 1 --sat 4.685 \n
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
--mov: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz
as movable/source volume.
Total: 4 input volumes
--lta: Will output LTA transforms
--template: Using
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz
as template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source
'/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'...
mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz,
-1): could not open file
MultiRegistration::loadMovables: could not open input volume
/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz.
Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2:
Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
recon-all -s 137_S_0631_template exited with ERRORS at Mon May 14 18:21:23
EDT 2012
For more details, see the log file
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
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 Partners Compliance HelpLine at
http://www.partners.org/
Re: [Freesurfer] fscalc size mismatch error
Would the best solution be to average the frames of the first file or can I specify just one frame? Corinna On Mon, Jul 11, 2011 at 1:17 PM, Corinna Bauer wrote: > Looks like it is because one of the files has multiple frames. > > mri_info first file: > > Volume information for wm.reg.pet.mgz > type: MGH > dimensions: 256 x 256 x 256 x 6 >voxel sizes: 1., 1., 1. > type: FLOAT (3) >fov: 256.000 >dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees >nframes: 6 >PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > -4.7658 > : x_a = 0., y_a = 0., z_a = 1., c_a = > 75.9533 > : x_s = 0., y_s = -1., z_s = 0., c_s = > 4.7458 > > talairach xfm : > /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 123.2342 > 0. 0. 1. -52.0467 > 0. -1. 0. 132.7458 > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. 0. 0. 123.2342 >-0. -0. -1. 132.7458 >-0. 1. -0.52.0467 > 0. 0. 0. 1. > > > and second file: > > Volume information for wm.pet_binarized.mgz > type: MGH > dimensions: 256 x 256 x 256 >voxel sizes: 1., 1., 1. > type: INT (1) >fov: 256.000 >dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees >nframes: 1 >PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > -4.7658 > : x_a = 0., y_a = 0., z_a = 1., c_a = > 75.9533 > : x_s = 0., y_s = -1., z_s = 0., c_s = > 4.7458 > > talairach xfm : > /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 123.2342 > 0. 0. 1. -52.0467 > 0. -1. 0. 132.7458 > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. 0. 0. 123.2342 >-0. -0. -1. 132.7458 >-0. 1. -0.52.0467 > 0. 0. 0. 1. > > > > > On Mon, Jul 11, 2011 at 12:51 PM, Rudolph Pienaar < > rudo...@nmr.mgh.harvard.edu> wrote: > >> (forgot to cc the list)... >> >> >> In general, that error means the number of elements in your first input is >> not equal to the number of element in your second. >> >> Can you run the command and copy-paste the output into an email? Also, run >> 'mris_calc' with '--verbosity 10'. That will print out additional (useful) >> information. >> >> >> >> On 7/11/11 12:25 , Corinna Bauer wrote: >> >>> When running fscalc, I get the following error on some of my subjects >>> but not all of them, >>> >>> mris_calc: >>> Sorry, but I seem to have encountered an error. >>> While checking on input filetype sizes, >>> I found a size mismatch, i.e. len(input1)!=len(input2) >>> >>> Any suggestions? >>> >>> Thanks, >>> Corinna >>> >>> >>> __**_ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >> >> >> -- >> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> 149 (2301) 13th Street, Charlestown, MA 02129 USA >>
Re: [Freesurfer] fscalc size mismatch error
Looks like it is because one of the files has multiple frames. mri_info first file: Volume information for wm.reg.pet.mgz type: MGH dimensions: 256 x 256 x 256 x 6 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 6 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. and second file: Volume information for wm.pet_binarized.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. On Mon, Jul 11, 2011 at 12:51 PM, Rudolph Pienaar < rudo...@nmr.mgh.harvard.edu> wrote: > (forgot to cc the list)... > > > In general, that error means the number of elements in your first input is > not equal to the number of element in your second. > > Can you run the command and copy-paste the output into an email? Also, run > 'mris_calc' with '--verbosity 10'. That will print out additional (useful) > information. > > > > On 7/11/11 12:25 , Corinna Bauer wrote: > >> When running fscalc, I get the following error on some of my subjects >> but not all of them, >> >> mris_calc: >> Sorry, but I seem to have encountered an error. >> While checking on input filetype sizes, >> I found a size mismatch, i.e. len(input1)!=len(input2) >> >> Any suggestions? >> >> Thanks, >> Corinna >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > > -- > Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street, Charlestown, MA 02129 USA > > > 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 Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > 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. > > ___ 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.
[Freesurfer] fscalc size mismatch error
When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
