Dear Freesurfer experts,
I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
However, I am getting an error " dimension mismatch between source and mask".
Could someone please let me know how to solve this problem?
Best, Maria
Hi Maria
are they in register? If so you can do:
mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz
cheers Bruce
On Mon, 10 Apr 2017, Maria Hakonen wrote:
Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
However, I am getting an error " dimension mismatch between source and mask".
Could someone please let me know how to solve this problem?
Best, Maria
Hi Bruce,
Thank you for the reply! I have now tried:
mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh --tal --talres 2
mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal --talres 2
mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz
mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz
mri_convert masked_fmri.mgz masked_fmri.nii
I got:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from masked_fmri.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to masked_fmri.nii...
However, when I opened the masked_fmri.nii in fslview, the masked_fmri seems to be empty (intensity is zero and no brain is shown).
I would need to get a matrix containing voxels in the grey matter at all time points. Could you please let me know what I am doing wrong above? Or is there some better way to do this? I am new with Freesurfer, so sorry if my questions are trivial.
Best,
Maria
2017-04-10 17:28 GMT+03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Maria
are they in register? If so you can do:
mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz
cheers Bruce
On Mon, 10 Apr 2017, Maria Hakonen wrote:
Dear Freesurfer experts,
I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
However, I am getting an error " dimension mismatch between source and mask".
Could someone please let me know how to solve this problem?
Best, Maria
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.
You should only need those first two commands (+ the mri_mask). Use --interp nearest with the ribbon
On 04/10/2017 12:27 PM, Maria Hakonen wrote:
Hi Bruce,
Thank you for the reply! I have now tried:
mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh --tal --talres 2
mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal --talres 2
mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz
mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz
mri_convert masked_fmri.mgz masked_fmri.nii
I got:
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from masked_fmri.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to masked_fmri.nii...
However, when I opened the masked_fmri.nii in fslview, the masked_fmri seems to be empty (intensity is zero and no brain is shown).
I would need to get a matrix containing voxels in the grey matter at all time points. Could you please let me know what I am doing wrong above? Or is there some better way to do this? I am new with Freesurfer, so sorry if my questions are trivial.
Best,
Maria
2017-04-10 17:28 GMT+03:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Maria are they in register? If so you can do: mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz cheers Bruce On Mon, 10 Apr 2017, Maria Hakonen wrote: Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz However, I am getting an error " dimension mismatch between source and mask". Could someone please let me know how to solve this problem? Best, Maria _______________________________________________ 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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Probably you'll want to use mri_vol2vol so that you can incorporate your registration between the fMRI and the anatomical
On 04/10/2017 10:28 AM, Bruce Fischl wrote:
Hi Maria
are they in register? If so you can do:
mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz
cheers Bruce
On Mon, 10 Apr 2017, Maria Hakonen wrote:
Dear Freesurfer experts, I have tried to mask fMRI data with grey matter mask as follows: mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
However, I am getting an error " dimension mismatch between source and mask".
Could someone please let me know how to solve this problem?
Best, Maria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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