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Hello FreeSurfer Developers,
I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error :
Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ?
Thank you very much for your help,
Marine
By default, mri_glmfit will exclude any voxels where there is even a single data point that is 0. It looks like all your voxels fall into that category. If this is really ok and you want to analyze voxels where some data points are 0, then add --no-prune.
On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:
Hello FreeSurfer Developers,
I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error :
Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ?
Thank you very much for your help,
Marine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Douglas,
Thank you very much for your answer. Actually, I looked a little bit deeper into the problem, and found out that when I project the MTR of each subject on the surface, all my MTR values are correct and well projected. But once I run mris_preproc to bring everything to fsaverage; all values go to zero. I think that this is linked to the fact that all my MTR values are below 0.5 and that there is a round. So I tried to run mris_preproc again after multiplying the MTR images for 100; and by doing so the values on fsaverage were correct, but all integer. Is there a way to tell mris_preproc to treat the values as float and not to round them?
Thank you again for your kind help.
Marine
2018-06-06 16:20 GMT+02:00 Douglas Greve dgreve@mgh.harvard.edu:
By default, mri_glmfit will exclude any voxels where there is even a single data point that is 0. It looks like all your voxels fall into that category. If this is really ok and you want to analyze voxels where some data points are 0, then add --no-prune.
On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:
Hello FreeSurfer Developers,
I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error :
Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input
I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ?
Thank you very much for your help,
Marine
Freesurfer mailing listFreesurfer@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.
There should not be any rounding in mris_preproc, so I don't know why it is behaving in that way.
On 06/08/2018 05:12 AM, Marine Boudot de la Motte wrote:
Dear Douglas,
Thank you very much for your answer. Actually, I looked a little bit deeper into the problem, and found out that when I project the MTR of each subject on the surface, all my MTR values are correct and well projected. But once I run mris_preproc to bring everything to fsaverage; all values go to zero. I think that this is linked to the fact that all my MTR values are below 0.5 and that there is a round. So I tried to run mris_preproc again after multiplying the MTR images for 100; and by doing so the values on fsaverage were correct, but all integer. Is there a way to tell mris_preproc to treat the values as float and not to round them?
Thank you again for your kind help.
Marine
2018-06-06 16:20 GMT+02:00 Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>:
By default, mri_glmfit will exclude any voxels where there is even a single data point that is 0. It looks like all your voxels fall into that category. If this is really ok and you want to analyze voxels where some data points are 0, then add --no-prune. On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:Hello FreeSurfer Developers, I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error : Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ? Thank you very much for your help, Marine _______________________________________________ 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>_______________________________________________ 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> 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.
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Douglas Greve -
Douglas N. Greve
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Marine Boudot de la Motte