External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g... 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/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT... . 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.
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use Caution
Hi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output On 11/9/2021 6:05 AM, Yangwen Xu wrote:External Email - Use Caution Hello FreeSurfer Developers, I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1. I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem? Thanks for the help, Yangwen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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
External Email - Use Caution
Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
[image: Screenshot 2021-11-09 at 16.47.58.png]
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use CautionHi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqT... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqT... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19... http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqT... 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/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19... . 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.
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of:
mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:51 AM, Yangwen Xu wrote:
External Email - Use Caution
Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
Screenshot 2021-11-09 at 16.47.58.png
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii On 11/9/2021 10:17 AM, Yangwen Xu wrote:External Email - Use Caution Hi Douglas, Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information. export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii 7.2.0 setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii Best, Yangwen On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: please send your command line and terminal output On 11/9/2021 6:05 AM, Yangwen Xu wrote:External Email - Use Caution Hello FreeSurfer Developers, I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1. I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem? Thanks for the help, Yangwen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19Em49WmTx5F5dqiIbtyRystWvz0Cqz2zN7xUOHT9ndBIassXBjmeNv7Bv_vahfRTornELOx5Wg1mpCbkgHzxzQ0Fetm53czvyBDfZWYmgTrNwYszHicgVHck4jbYxmPw5lQ2Bj2Tzb6ISo5o2Eptt0JVmNStFNWbiey0landOloKy0P2RVtP86-vplolpz3KRvcXEFa2mRFhu84bCxmemZX6pfkXR6sz_p53Em_M75bw8gNFDvo4URwDgSOcpdWNp2FBXqIMcJu0ti1ivp/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
External Email - Use Caution
Hi Douglas,
This time, I tried to smooth one single image. Here occurs the error that the number of surface vertices (10242) and the number of value vertices (1) do not match. However, the image we want to smooth indeed has 10242 vertices. [image: Screenshot 2021-11-09 at 23.43.57.png]
The following is the command line and the terminal output.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
sysname Darwin hostname Yangwens-MBP.homenet.telecomitalia.it machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 10242 Number of value vertices = 1
On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of:
mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:51 AM, Yangwen Xu wrote:
External Email - Use CautionYes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
[image: Screenshot 2021-11-09 at 16.47.58.png]
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use CautionHi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ' ,InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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/1BQWpUfki32Q7Uh8XUQ102YbMZayHZR1BDikrgb7WaUeKr8m... http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/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/1BQWpUfki32Q7Uh8XUQ102YbMZayHZR1BDikrgb7WaUeKr8m... http://secure-web.cisco.com/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19Em49WmTx5F5dqiIbtyRystWvz0Cqz2zN7xUOHT9ndBIassXBjmeNv7Bv_vahfRTornELOx5Wg1mpCbkgHzxzQ0Fetm53czvyBDfZWYmgTrNwYszHicgVHck4jbYxmPw5lQ2Bj2Tzb6ISo5o2Eptt0JVmNStFNWbiey0landOloKy0P2RVtP86-vplolpz3KRvcXEFa2mRFhu84bCxmemZX6pfkXR6sz_p53Em_M75bw8gNFDvo4URwDgSOcpdWNp2FBXqIMcJu0ti1ivp/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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94... 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/1BQWpUfki32Q7Uh8XUQ102YbMZayHZR1BDikrgb7WaUeKr8m... . 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.
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
Note: this is the 3rd time I've made the request, please just do what I ask you to do -- it will be easier for all of us
On 11/9/2021 5:46 PM, Yangwen Xu wrote:
External Email - Use Caution
Hi Douglas,
This time, I tried to smooth one single image. Here occurs the error that the number of surface vertices (10242) and the number of value vertices (1) do not match. However, the image we want to smooth indeed has 10242 vertices. Screenshot 2021-11-09 at 23.43.57.png
The following is the command line and the terminal output.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
sysname Darwin hostname Yangwens-MBP.homenet.telecomitalia.it http://secure-web.cisco.com/1JPOys9ZFTolrfjOMdYEUVgoHCJRf4bs0PNNt0Qk40rOKrSZirkG3-EDkwDv3PCO0XMOHXXm6HCwaN5xVXHAPnZkdigUlNkwaimwBbB_fNVBp-5foBmiRcCksPaPL6YTSQll1mWd3zmZeL-9_pAH0WwrDas0QqPz_hmSMgKMbBDQZ6ndRMk3XT7ZXxlSmzEsd7bDfvxOhloqMUtPKkYcV3PlVDL8pKo_fEODEvp0jEVoWocsdoYZNkIh5JJw7i5T_bXPSUlClj2m1HVXGYApkuhvi93k1LDoQPd17NJK-wJkrb4ergXI5qzFHcbsyxfam/http%3A%2F%2FYangwens-MBP.homenet.telecomitalia.it machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 10242 Number of value vertices = 1
On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of: mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii On 11/9/2021 10:51 AM, Yangwen Xu wrote:External Email - Use Caution Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information: Screenshot 2021-11-09 at 16.47.58.png Do I need to transfer the images to you? On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii On 11/9/2021 10:17 AM, Yangwen Xu wrote:External Email - Use Caution Hi Douglas, Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information. export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii 7.2.0 setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii Best, Yangwen On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: please send your command line and terminal output On 11/9/2021 6:05 AM, Yangwen Xu wrote:External Email - Use Caution Hello FreeSurfer Developers, I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',InputImagePath,' --fwhm 6 --tval ', OutputImagePath The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1. I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem? Thanks for the help, Yangwen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19Em49WmTx5F5dqiIbtyRystWvz0Cqz2zN7xUOHT9ndBIassXBjmeNv7Bv_vahfRTornELOx5Wg1mpCbkgHzxzQ0Fetm53czvyBDfZWYmgTrNwYszHicgVHck4jbYxmPw5lQ2Bj2Tzb6ISo5o2Eptt0JVmNStFNWbiey0landOloKy0P2RVtP86-vplolpz3KRvcXEFa2mRFhu84bCxmemZX6pfkXR6sz_p53Em_M75bw8gNFDvo4URwDgSOcpdWNp2FBXqIMcJu0ti1ivp/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94Gr6SWFYn0NcXfVAJL02qpwhBI4vQ9kg80SFmJFO4C-o-7hQX58bK5GsHo-qw9-k7AxoY9y3U_ncwx1LM-bay8k8OOLXB4tgMQZltJcfkZQ6WMny0vnqfq6zHVd1AuQeKFadiEzLaOQ56CD7kAp3iYZBuewDEB8Sw8d1kGdqd18kmUSkQiinkcD7xgROQb-uxwzn9PvwIBeoA37iqR1leaJlABWhWItKZlzId_PXlnSrLFMaxiiPxmGqIrN_iJ95Thn13QA6AoFXnz7N8Gb/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1-edkXsKUZk2YfrHFwiVgc-YYUBolUdpf23gRhvLzaW8b94Gr6SWFYn0NcXfVAJL02qpwhBI4vQ9kg80SFmJFO4C-o-7hQX58bK5GsHo-qw9-k7AxoY9y3U_ncwx1LM-bay8k8OOLXB4tgMQZltJcfkZQ6WMny0vnqfq6zHVd1AuQeKFadiEzLaOQ56CD7kAp3iYZBuewDEB8Sw8d1kGdqd18kmUSkQiinkcD7xgROQb-uxwzn9PvwIBeoA37iqR1leaJlABWhWItKZlzId_PXlnSrLFMaxiiPxmGqIrN_iJ95Thn13QA6AoFXnz7N8Gb/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://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1BQWpUfki32Q7Uh8XUQ102YbMZayHZR1BDikrgb7WaUeKr8mlFPFrPiPH328O3AQVHZSSBbcV2aHJQLHATP79jSCrbD2kNqSvL_nShVvTfH5pYNF-czJGa78aJvYIMDaOaNkZuOsRTnRIvY77leMyUudt0yowD6oiGO1e0yA56yenluHRxk3YAWZqygZhS4IT4lqYGEWpw0qVH2VwRylk6NadcDE2pFb8p8Embzmi1GiGysuVCUUlIENONuZAWuP6ANag9DmLL8vDLBd5P9UPFWV2F4KtVAlromAWfK7LUP-Hbf5QwCCBB0730OGXgR9m/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
External Email - Use Caution
Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information when I run the gifti function in matlab:
gifti('sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii')
ans =
struct with fields:
cdata: [10242×475 single]
On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of:
mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:51 AM, Yangwen Xu wrote:
External Email - Use CautionYes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
[image: Screenshot 2021-11-09 at 16.47.58.png]
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use CautionHi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ' ,InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RPqmi18tSLQEFOsNkBdKvPr4OKabzkyUxkouEbQEmUv4bd... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RPqmi18tSLQEFOsNkBdKvPr4OKabzkyUxkouEbQEmUv4bd... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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/1T8nxWztjXYSGQi3DD2mioa20HpohtmpQrbjNZN5r3naB7TU... http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RPqmi18tSLQEFOsNkBdKvPr4OKabzkyUxkouEbQEmUv4bd... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RPqmi18tSLQEFOsNkBdKvPr4OKabzkyUxkouEbQEmUv4bd... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/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/1T8nxWztjXYSGQi3DD2mioa20HpohtmpQrbjNZN5r3naB7TU... http://secure-web.cisco.com/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19Em49WmTx5F5dqiIbtyRystWvz0Cqz2zN7xUOHT9ndBIassXBjmeNv7Bv_vahfRTornELOx5Wg1mpCbkgHzxzQ0Fetm53czvyBDfZWYmgTrNwYszHicgVHck4jbYxmPw5lQ2Bj2Tzb6ISo5o2Eptt0JVmNStFNWbiey0landOloKy0P2RVtP86-vplolpz3KRvcXEFa2mRFhu84bCxmemZX6pfkXR6sz_p53Em_M75bw8gNFDvo4URwDgSOcpdWNp2FBXqIMcJu0ti1ivp/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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1RPqmi18tSLQEFOsNkBdKvPr4OKabzkyUxkouEbQEmUv4bd... 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/1T8nxWztjXYSGQi3DD2mioa20HpohtmpQrbjNZN5r3naB7TU... . 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.
External Email - Use Caution
Hi Douglas,
This time, I tried to smooth one single image. Here occurs the error that the number of surface vertices (10242) and the number of value vertices (1) do not match. However, the image we want to smooth indeed has 10242 vertices.
gifti('sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii')
ans =
struct with fields:
cdata: [10242×1 single]
The following is the command line and the terminal output.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii
sysname Darwin hostname Yangwens-MBP.homenet.telecomitalia.it http://secure-web.cisco.com/1Bxh1LxDpf84_UUsWbnEJmVqkqMJOlk8biJkblvvTz8Us6CQXwOVYuf_JACN0gvieqqcR1Omkl98ldlylWp0KmM5qh1cNtz9I0yzbsuD2_d8OfH9rn94Czvj5G0NgtYOwZRCQMswqvJROktDqG17GYkxwPAJlw8rFIwA7-69jDaIaMguXi6LZMRo4cObPxt1CdGOWYPiyPfpU4ytb_Ss9lX8VkQjbWbWXo58QmXK6vVNxuEuizltMMim3QTwX_dKP_3JkuIj0sfOVwIuvd5m1hkNxq6W62KC_B7bWKSITIMeIYmaXeK-6qBemZTQDoqUD/http%3A%2F%2Fyangwens-mbp.homenet.telecomitalia.it%2F machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/SeedBasedRSFC/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Smoothing/UA-Intersect-L-ILOTC/sub-eb01/sub-eb01_space-fsaverage5_hemi-L_Seed-UA-Intersect-L-ILOTC_RSFC_Smoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 10242 Number of value vertices = 1
On Wed, 10 Nov 2021 at 17:40, Yangwen Xu yangwen.xu@unitn.it wrote:
Yes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information when I run the gifti function in matlab:
gifti('sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii')
ans =
struct with fields:
cdata: [10242×475 single]On Tue, 9 Nov 2021 at 19:10, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of:
mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:51 AM, Yangwen Xu wrote:
External Email - Use CautionYes! It's simply a gifti image with 10242 vertices and 475 time points. The following is the information:
[image: Screenshot 2021-11-09 at 16.47.58.png]
Do I need to transfer the images to you?
On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I have a feeling that it may be ignoring the extra frames in the gii file. Can you send the result of mri_info sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii
On 11/9/2021 10:17 AM, Yangwen Xu wrote:
External Email - Use CautionHi Douglas,
Thanks for the reply. Here are my command line and the output from the terminal. Please tell me if you need further information.
export FREESURFER_HOME=/Applications/freesurfer/7.2.0 export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
7.2.0
setenv SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects cd /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii --fwhm 6 --tval /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
sysname Darwin hostname Yangwens-MacBook-Pro.local machine x86_64 user yangwenxu srcsubject = fsaverage5 srcval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRF/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFiltered.func.gii srctype = trgsubject = fsaverage5 trgval = /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 6 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/7.2.0/subjects/fsaverage5/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 6.000000, std = 2.547965, with 2 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label NN smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii
Best, Yangwen
On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
please send your command line and terminal output
On 11/9/2021 6:05 AM, Yangwen Xu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ' ,InputImagePath,' --fwhm 6 --tval ', OutputImagePath
The Input Image is 10242 (number of vertices) * 475 (number of time points) in the func.gii format. The output image is supposed to be in the same dimensions. However, it only smoothed the image of the first time point, i.e., the dimension of the output Image is 10242 * 1.
I have implemented this before but never met this problem. The only difference seems that I am now using freesurfer-darwin-macOS-7.2.0. Does anyone have any thoughts on how to solve this problem?
Thanks for the help, Yangwen
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1kvF4ts3APegR7_3diu-F4AZB3m5HHiTD-wX1Tj9B5IAfQY... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1kvF4ts3APegR7_3diu-F4AZB3m5HHiTD-wX1Tj9B5IAfQY... https://secure-web.cisco.com/1FTt7kHO9Vv8m0kxPlU3kpWEaiE36K137l9GCNhZ2ZDY_1g_b1tdjtj-8hmC9ZWI5-ynvSU1DwueNBpT0fvtWwQCsmTDQHhAvUpEU2CuiHT9220SsrQXCfNJ8C3F0084hbsUdwoEv-JPC6aSz1DqeYBWIXtoQz7VZ36557Xc_my52BWYnpdr5ufUkbZD5LnYAk8jt10SimIC9E3sDZEqmoZZ1pqQo-eLwziTWuxbkZuUtFv2qxLZhVSSkPok7QI1pEcztMtFxgGhvbxOvznusZ_r5io_r0kmOzn_G0_dKM4Zs7l33IdrwSCcmsct6MBNnr3r8LPivGDBIlKjLodhArw/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/1ixQIKFfJ5yRhZ5ZM8Y6JOgdoIF4M9_evppO0TpIiHVKSM7n... http://secure-web.cisco.com/1btUqv4KLksFwJnP0cx_vM9oiuLzt2IjgvfQLDxJ314n5NyT9SrQukJxq3AVjZo93E_ooig3w6_jSi14IPHNNmcKv_vAgG3tyFEnJEOj_-aGxGdZb5kq5ubnqVYLjjf3qC9VuxBYdBKD1b9etcrdzWt0Eid4-adYLpZ9jqeXTNy54zYGMUULgWqBkKP6kyOeH5KsURf4lV1xopclFhj_M1e6xfs4Ra8ULv8J07V6MbNxs0bBrx96f17FsvXJ9CwVFRWSo83OVBNMri4GaA2xqTFS_2cTuHWx0cGXeCrN8GTi8d9wMX55McpIg945W0AE83ywqt_VSixIJtINoJ5K-NA/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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1kvF4ts3APegR7_3diu-F4AZB3m5HHiTD-wX1Tj9B5IAfQY... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1kvF4ts3APegR7_3diu-F4AZB3m5HHiTD-wX1Tj9B5IAfQY... https://secure-web.cisco.com/1aAoXBY4O-Pqbc-U7RYzI0WaozgMU0FbvalBj9XxKRw9ZqTuQGJjL0WOFeLBG-7ZIiwwbLIA5MId5GIEvNihDOA0IBHWiXveCkGb_iv2aqHOXwlsYdp56elaeIkurxz8ffqpzq8EyeaV6lSJBUQWroR86JHcUDq3BBSG7rDk0WkpQW6gxmd3z4gdtawlgXaiFHz3l6wK6ZUXgFDhbx2TaXoX4qXE0w1OBy2JrQorZnD3n-lTnwM_ciT0wgBZK2KbJSn93lAVTe1GtnfrDua54S6Ap5LuEllJsVL_BGMVbbvoPxhpEyLG7IvijsUFlwfgi/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/1ixQIKFfJ5yRhZ5ZM8Y6JOgdoIF4M9_evppO0TpIiHVKSM7n... http://secure-web.cisco.com/1-LDUU-p4zB__CijtGUToaAOabnw_JpyzWzP4lMQwoUmmP19Em49WmTx5F5dqiIbtyRystWvz0Cqz2zN7xUOHT9ndBIassXBjmeNv7Bv_vahfRTornELOx5Wg1mpCbkgHzxzQ0Fetm53czvyBDfZWYmgTrNwYszHicgVHck4jbYxmPw5lQ2Bj2Tzb6ISo5o2Eptt0JVmNStFNWbiey0landOloKy0P2RVtP86-vplolpz3KRvcXEFa2mRFhu84bCxmemZX6pfkXR6sz_p53Em_M75bw8gNFDvo4URwDgSOcpdWNp2FBXqIMcJu0ti1ivp/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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kvF4ts3APegR7_3diu-F4AZB3m5HHiTD-wX1Tj9B5IAfQY... 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/1ixQIKFfJ5yRhZ5ZM8Y6JOgdoIF4M9_evppO0TpIiHVKSM7n... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Yangwen Xu