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Hi there,
I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame.
I have done the following steps for achieving this: 1. ran recon-all on its anatomical volume. 2. register the fMRI series with the anatomical volume by using bbregister. 3. assign values from volumes to each surface vertex through the command mri_vol2surf.
I have got a result of mapping the 4D volumes intensities onto its surfaces but there are 35.5% vertices assigned 0 value in every time frame.
I am wondering is the ratio reasonable and how could I improve the result? I guess resolution would be one of reasons causing the high 0 value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3.
Many thanks for your help.
Best, An
35% sounds high to me. Did you actually check the registration
You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used
On 11/21/19 10:03 AM, An wrote:
External Email - Use Caution
Hi there,
I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame.
I have done the following steps for achieving this:
- ran recon-all on its anatomical volume.
- register the fMRI series with the anatomical volume by using
bbregister. 3. assign values from volumes to each surface vertex through the command mri_vol2surf.
I have got a result of mapping the 4D volumes intensities onto its surfaces but there are 35.5% vertices assigned 0 value in every time frame.
I am wondering is the ratio reasonable and how could I improve the result? I guess resolution would be one of reasons causing the high 0 value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3.
Many thanks for your help.
Best, An
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Prof. Greve,
Thanks for your reply. I do it in the following steps: 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s subjid -all 2. register the fMRI series with the anatomical volume by using bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat 3. assign values from volumes to each surface vertex through the command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz --srcreg register.dat --hemi lh
I also attached the registered image after step2. It looks like they are not perfectly aligned. Is there anyway to improve that and also the final result?
Many thanks.
Best, An [image: image.png]
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月21日周四 下午12:42写道：
35% sounds high to me. Did you actually check the registration
You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used
On 11/21/19 10:03 AM, An wrote:
External Email - Use CautionHi there,
I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame.
I have done the following steps for achieving this:
- ran recon-all on its anatomical volume.
- register the fMRI series with the anatomical volume by using
bbregister. 3. assign values from volumes to each surface vertex through the command mri_vol2surf.
I have got a result of mapping the 4D volumes intensities onto its surfaces but there are 35.5% vertices assigned 0 value in every time frame.
I am wondering is the ratio reasonable and how could I improve the result? I guess resolution would be one of reasons causing the high 0 value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3.
Many thanks for your help.
Best, An
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give the full command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI
On 11/21/19 1:20 PM, An wrote:
External Email - Use Caution
Hi Prof. Greve,
Thanks for your reply. I do it in the following steps:
- ran recon-all on the anatomical volume: recon-all -i MRI.nii -s
subjid -all 2. register the fMRI series with the anatomical volume by using bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat 3. assign values from volumes to each surface vertex through the command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz --srcreg register.dat --hemi lh
I also attached the registered image after step2. It looks like they are not perfectly aligned. Is there anyway to improve that and also the final result?
Many thanks.
Best, An image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午12:42写道：
35% sounds high to me. Did you actually check the registration You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used On 11/21/19 10:03 AM, An wrote: > > External Email - Use Caution > > Hi there, > > I want to map the intensities of the fMRI 4D volumes onto its surface > in order to get the functional values on each vertex in each frame. > > I have done the following steps for achieving this: > 1. ran recon-all on its anatomical volume. > 2. register the fMRI series with the anatomical volume by using > bbregister. > 3. assign values from volumes to each surface vertex through the > command mri_vol2surf. > > I have got a result of mapping the 4D volumes intensities onto its > surfaces but there are 35.5% vertices assigned 0 value in every time > frame. > > I am wondering is the ratio reasonable and how could I improve the > result? I guess resolution would be one of reasons causing the high 0 > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > Many thanks for your help. > > Best, > An > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The image in the previous email uses the command tkregisterfv to visualize the registration result after step2 bbregister, where I uncheck the boxes of the surface layers. The full command of my bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat --t1. I attached both the registration result with checking the boxes of the surface layers and my final result mapped onto surface below. The log file is also attached to this email, please take a look at your convenience.
Many thanks.
Best, An
[image: image.png] [image: image.png]
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月21日周四 下午2:49写道：
It is hard to say from that image, but it does not look registered to me.
- your bbregister command is not valid as it is, please give the full
command
- please send the bbregister log file
- to look at the registration, use tkregisterfv. It will show the
surfaces over the fMRI
On 11/21/19 1:20 PM, An wrote:
External Email - Use CautionHi Prof. Greve,
Thanks for your reply. I do it in the following steps:
- ran recon-all on the anatomical volume: recon-all -i MRI.nii -s
subjid -all 2. register the fMRI series with the anatomical volume by using bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat 3. assign values from volumes to each surface vertex through the command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz --srcreg register.dat --hemi lh
I also attached the registered image after step2. It looks like they are not perfectly aligned. Is there anyway to improve that and also the final result?
Many thanks.
Best, An image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午12:42写道：
35% sounds high to me. Did you actually check the registration You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used On 11/21/19 10:03 AM, An wrote: > > External Email - Use Caution > > Hi there, > > I want to map the intensities of the fMRI 4D volumes onto its surface > in order to get the functional values on each vertex in each frame. > > I have done the following steps for achieving this: > 1. ran recon-all on its anatomical volume. > 2. register the fMRI series with the anatomical volume by using > bbregister. > 3. assign values from volumes to each surface vertex through the > command mri_vol2surf. > > I have got a result of mapping the 4D volumes intensities onto its > surfaces but there are 35.5% vertices assigned 0 value in every time > frame. > > I am wondering is the ratio reasonable and how could I improve the > result? I guess resolution would be one of reasons causing the high 0 > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > Many thanks for your help. > > Best, > An > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Why are you using --t1? If this is fmri, it should be --t2
On 11/21/19 3:27 PM, An wrote:
External Email - Use Caution
The image in the previous email uses the command tkregisterfv to visualize the registration result after step2 bbregister, where I uncheck the boxes of the surface layers. The full command of my bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat --t1. I attached both the registration result with checking the boxes of the surface layers and my final result mapped onto surface below. The log file is also attached to this email, please take a look at your convenience.
Many thanks.
Best, An
image.png image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午2:49写道：
It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give the full command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI On 11/21/19 1:20 PM, An wrote: > > External Email - Use Caution > > Hi Prof. Greve, > > Thanks for your reply. I do it in the following steps: > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s > subjid -all > 2. register the fMRI series with the anatomical volume by using > bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat > 3. assign values from volumes to each surface vertex through the > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz > --srcreg register.dat --hemi lh > > I also attached the registered image after step2. It looks like they > are not perfectly aligned. Is there anyway to improve that and also > the final result? > > Many thanks. > > Best, > An > image.png > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> 于2019年11月21日周四 下午12:42写道： > > 35% sounds high to me. Did you actually check the registration > > You can always load the the fMRI as an overlay in freeview, try > tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz > Also, please include command lines you used > > On 11/21/19 10:03 AM, An wrote: > > > > External Email - Use Caution > > > > Hi there, > > > > I want to map the intensities of the fMRI 4D volumes onto its > surface > > in order to get the functional values on each vertex in each frame. > > > > I have done the following steps for achieving this: > > 1. ran recon-all on its anatomical volume. > > 2. register the fMRI series with the anatomical volume by using > > bbregister. > > 3. assign values from volumes to each surface vertex through the > > command mri_vol2surf. > > > > I have got a result of mapping the 4D volumes intensities onto its > > surfaces but there are 35.5% vertices assigned 0 value in every > time > > frame. > > > > I am wondering is the ratio reasonable and how could I improve the > > result? I guess resolution would be one of reasons causing the > high 0 > > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > > > Many thanks for your help. > > > > Best, > > An > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Prof. Greve,
Thanks for the correction. Here are the results when I ran bbregister with --t2. It's still does not well registered. The log file is attached in this email.
Also, I was just informed that the fMRI 4D series and the MRI are not scanned in the same day. Is it possible to register them in freesurfer.
Many thanks.
Best, An [image: image.png]
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月21日周四 下午3:54写道：
Why are you using --t1? If this is fmri, it should be --t2
On 11/21/19 3:27 PM, An wrote:
External Email - Use CautionThe image in the previous email uses the command tkregisterfv to visualize the registration result after step2 bbregister, where I uncheck the boxes of the surface layers. The full command of my bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat --t1. I attached both the registration result with checking the boxes of the surface layers and my final result mapped onto surface below. The log file is also attached to this email, please take a look at your convenience.
Many thanks.
Best, An
image.png image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午2:49写道：
It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give the full command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI On 11/21/19 1:20 PM, An wrote: > > External Email - Use Caution > > Hi Prof. Greve, > > Thanks for your reply. I do it in the following steps: > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s > subjid -all > 2. register the fMRI series with the anatomical volume by using > bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat > 3. assign values from volumes to each surface vertex through the > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz > --srcreg register.dat --hemi lh > > I also attached the registered image after step2. It looks like they > are not perfectly aligned. Is there anyway to improve that and also > the final result? > > Many thanks. > > Best, > An > image.png > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> 于2019年11月21日周四 下午12:42写道： > > 35% sounds high to me. Did you actually check the registration > > You can always load the the fMRI as an overlay in freeview, try > tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz > Also, please include command lines you used > > On 11/21/19 10:03 AM, An wrote: > > > > External Email - Use Caution > > > > Hi there, > > > > I want to map the intensities of the fMRI 4D volumes onto its > surface > > in order to get the functional values on each vertex in each frame. > > > > I have done the following steps for achieving this: > > 1. ran recon-all on its anatomical volume. > > 2. register the fMRI series with the anatomical volume by using > > bbregister. > > 3. assign values from volumes to each surface vertex through the > > command mri_vol2surf. > > > > I have got a result of mapping the 4D volumes intensities onto its > > surfaces but there are 35.5% vertices assigned 0 value in every > time > > frame. > > > > I am wondering is the ratio reasonable and how could I improve the > > result? I guess resolution would be one of reasons causingthe
> high 0 > > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > > > Many thanks for your help. > > > > Best, > > An > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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What is the blue? The best way to dispaly it is to show the fMRI in gray scale with the surfaces overlaid on it. What exactly is the input pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz? How was it created? Can you verify that the orientation is correct? You can load it in FreeView
On 11/21/19 4:35 PM, An wrote:
External Email - Use Caution
Hi Prof. Greve,
Thanks for the correction. Here are the results when I ran bbregister with --t2. It's still does not well registered. The log file is attached in this email.
Also, I was just informed that the fMRI 4D series and the MRI are not scanned in the same day. Is it possible to register them in freesurfer.
Many thanks.
Best, An image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午3:54写道：
Why are you using --t1? If this is fmri, it should be --t2 On 11/21/19 3:27 PM, An wrote: > > External Email - Use Caution > > The image in the previous email uses the command tkregisterfv to > visualize the registration result after step2 bbregister, where I > uncheck the boxes of the surface layers. The full command of my > bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat > --t1. > I attached both the registration result with checking the boxes of the > surface layers and my final result mapped onto surface below. > The log file is also attached to this email, please take a look at > your convenience. > > Many thanks. > > Best, > An > > image.png image.png > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> 于2019年11月21日周四 下午2:49写道： > > It is hard to say from that image, but it does not look registered > to me. > - your bbregister command is not valid as it is, please give the full > command > - please send the bbregister log file > - to look at the registration, use tkregisterfv. It will show the > surfaces over the fMRI > > On 11/21/19 1:20 PM, An wrote: > > > > External Email - Use Caution > > > > Hi Prof. Greve, > > > > Thanks for your reply. I do it in the following steps: > > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s > > subjid -all > > 2. register the fMRI series with the anatomical volume by using > > bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat > > 3. assign values from volumes to each surface vertex through the > > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz > > --srcreg register.dat --hemi lh > > > > I also attached the registered image after step2. It looks like > they > > are not perfectly aligned. Is there anyway to improve that and also > > the final result? > > > > Many thanks. > > > > Best, > > An > > image.png > > > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > 于2019年11月21日周四 下午12:42写道： > > > > 35% sounds high to me. Did you actually check the registration > > > > You can always load the the fMRI as an overlay in freeview, try > > tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz > > Also, please include command lines you used > > > > On 11/21/19 10:03 AM, An wrote: > > > > > > External Email - Use Caution > > > > > > Hi there, > > > > > > I want to map the intensities of the fMRI 4D volumes onto its > > surface > > > in order to get the functional values on each vertex in > each frame. > > > > > > I have done the following steps for achieving this: > > > 1. ran recon-all on its anatomical volume. > > > 2. register the fMRI series with the anatomical volume by > using > > > bbregister. > > > 3. assign values from volumes to each surface vertex > through the > > > command mri_vol2surf. > > > > > > I have got a result of mapping the 4D volumes intensities > onto its > > > surfaces but there are 35.5% vertices assigned 0 value in > every > > time > > > frame. > > > > > > I am wondering is the ratio reasonable and how could I > improve the > > > result? I guess resolution would be one of reasons causing the > > high 0 > > > value ratio, my fMRI data is 2mm^3 and anatomical data is > 1mm^3. > > > > > > Many thanks for your help. > > > > > > Best, > > > An > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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
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Hi Prof. Greve,
Thanks for your help. Now I can successfully map the time frames intensities onto the surface without 0 value. The problem is that I used the wrong input data. What I got from others is a preprocessed fMRI data by using other tools and it is a set of points instead of a grayscale image. I got the raw data today and finally it mapped onto surface correctly.
Thanks again for your help!
Best, An
An annaqu1024@gmail.com 于2019年11月21日周四 下午4:35写道：
Hi Prof. Greve,
Thanks for the correction. Here are the results when I ran bbregister with --t2. It's still does not well registered. The log file is attached in this email.
Also, I was just informed that the fMRI 4D series and the MRI are not scanned in the same day. Is it possible to register them in freesurfer.
Many thanks.
Best, An [image: image.png]
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月21日周四 下午3:54写道：
Why are you using --t1? If this is fmri, it should be --t2
On 11/21/19 3:27 PM, An wrote:
External Email - Use CautionThe image in the previous email uses the command tkregisterfv to visualize the registration result after step2 bbregister, where I uncheck the boxes of the surface layers. The full command of my bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat --t1. I attached both the registration result with checking the boxes of the surface layers and my final result mapped onto surface below. The log file is also attached to this email, please take a look at your convenience.
Many thanks.
Best, An
image.png image.png
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月21日周四 下午2:49写道：
It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give thefull
command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI On 11/21/19 1:20 PM, An wrote: > > External Email - Use Caution > > Hi Prof. Greve, > > Thanks for your reply. I do it in the following steps: > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s > subjid -all > 2. register the fMRI series with the anatomical volume by using > bbregister: bbregister --mov fMRI.nii --s subjid --regregister.dat
> 3. assign values from volumes to each surface vertex through the > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz > --srcreg register.dat --hemi lh > > I also attached the registered image after step2. It looks like they > are not perfectly aligned. Is there anyway to improve that andalso
> the final result? > > Many thanks. > > Best, > An > image.png > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> 于2019年11月21日周四 下午12:42写道： > > 35% sounds high to me. Did you actually check the registration > > You can always load the the fMRI as an overlay in freeview,try
> tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz > Also, please include command lines you used > > On 11/21/19 10:03 AM, An wrote: > > > > External Email - Use Caution > > > > Hi there, > > > > I want to map the intensities of the fMRI 4D volumes ontoits
> surface > > in order to get the functional values on each vertex in each frame. > > > > I have done the following steps for achieving this: > > 1. ran recon-all on its anatomical volume. > > 2. register the fMRI series with the anatomical volume by using > > bbregister. > > 3. assign values from volumes to each surface vertex through the > > command mri_vol2surf. > > > > I have got a result of mapping the 4D volumes intensities onto its > > surfaces but there are 35.5% vertices assigned 0 value in every > time > > frame. > > > > I am wondering is the ratio reasonable and how could I improve the > > result? I guess resolution would be one of reasons causingthe
> high 0 > > value ratio, my fMRI data is 2mm^3 and anatomical data is 1mm^3. > > > > Many thanks for your help. > > > > Best, > > An > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Greve, Douglas N.,Ph.D.