If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally
On 11/12/19 8:41 PM, an wrote:
External Email - Use Caution
Many thanks.
I got the 4D fMRI dataset from others and it is not raw data. In order to run mri_vol2surf, I need to calculate the register.dat for the required flag --srcreg so I tried in this way.
FYI, the 4D fMRI dataset should have been registered with its anatomical MR volume by using other tools.
For now I only ran the recon-all on its anatomical MR volume without running the functional stream as I don't have the raw data.
Should I also run the raw fMRI data from scratch by using functional stream? Or if I can run mri_vol2surf independently, which command should I use to get a register.dat file? In addition, the intensity of the 4D fMRI dataset I have is between [-1, 1] and not integers, would this cause any problem?
Best, An
On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
Don't do the 1st step. Why are you registering it to bert? I'm pretty sure bert did not participate in your fmri study When you run mri_vol2surf, it will probably work better with --projfrac 0.5
On 11/11/2019 1:32 PM, An wrote:
External Email - Use Caution
Hi Prof. Greve,
Thanks for your reply and sorry for the confusion.
I have a 4D fMRI dataset with 10 time frames, where the intensity of each voxel is between [-1,1] and not integers. I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I have already run its corresponding anatomical image in freesurfer.
To achieve it, I tried the following steps:
- conform the fmri series by using mri_convert
- register the fmri series with the anatomy image by using
bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat 3. assign values from volumes to each vertex by using mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg register.dat --hemi lh I also tried the -regheader in mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But after step2, the registered volume looks wrong. I am wondering could I use bbregister to register multi-frame fMRI series to a single volume? I also tried to use --regheader to replace the --srcreg file in mri_vol2surf as the output register.dat in step2 is wrong. But the output is still wrong.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月11日周一 下午12:16写道：
When you say it is 4D, what do you mean? That each label has its own frame? On 11/6/19 5:59 PM, 曲岸 wrote: > > External Email - Use Caution > > Hi there, > > I am working with creating a surface parcellation from a volumetric > parcellation and have some questions as follows: > > 1. If the volumetric parcellation is a labeled 4D multi-frame dataset, > could I still use the mris_sample_parc? Or could mri_vol2surf get the > sampled labels for every vertex? > > 2. For the 4D multi-frame dataset and mri_vol2surf output results, > which GUI should I use to visualize it? I tried freeview for 4D > multi-frame dataset but it looks weird. > > 3. Is there any command to separate multi-frame volume to single frame > volumes? > > Many thanks! > > > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Oops sorry for the mistakenly reply. I will pay more attention in the future.
Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that the volume was not registered. After that I tried another 4D volume to do the steps and successfully got the sampled intensity onto the surface.
The difference between the new 4D volume I used and the previous one is that there are two transformation matrices between them. The 4D dataset that I previously used but failed is the volume already registered to its anatomical volume(by using others tools). The new 4D volume that I tried and succeed is the volume not registered.
I have no idea why the 4D volume after the transformation would cause a failed result. Could you please let me know that?
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月13日周三 下午12:20写道：
If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally
On 11/12/19 8:41 PM, an wrote:
External Email - Use CautionMany thanks.
I got the 4D fMRI dataset from others and it is not raw data. In order to run mri_vol2surf, I need to calculate the register.dat for the required flag --srcreg so I tried in this way.
FYI, the 4D fMRI dataset should have been registered with its anatomical MR volume by using other tools.
For now I only ran the recon-all on its anatomical MR volume without running the functional stream as I don't have the raw data.
Should I also run the raw fMRI data from scratch by using functional stream? Or if I can run mri_vol2surf independently, which command should I use to get a register.dat file? In addition, the intensity of the 4D fMRI dataset I have is between [-1, 1] and not integers, would this cause any problem?
Best, An
On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
Don't do the 1st step. Why are you registering it to bert? I'm pretty sure bert did not participate in your fmri study When you run mri_vol2surf, it will probably work better with --projfrac 0.5
On 11/11/2019 1:32 PM, An wrote:
External Email - Use CautionHi Prof. Greve,
Thanks for your reply and sorry for the confusion.
I have a 4D fMRI dataset with 10 time frames, where the intensity of each voxel is between [-1,1] and not integers. I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I have already run its corresponding anatomical image in freesurfer.
To achieve it, I tried the following steps:
- conform the fmri series by using mri_convert
- register the fmri series with the anatomy image by using
bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat 3. assign values from volumes to each vertex by using mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg register.dat --hemi lh I also tried the -regheader in mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But after step2, the registered volume looks wrong. I am wondering could I use bbregister to register multi-frame fMRI series to a single volume? I also tried to use --regheader to replace the --srcreg file in mri_vol2surf as the output register.dat in step2 is wrong. But the output is still wrong.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月11日周一 下午12:16写道：
When you say it is 4D, what do you mean? That each label has its own frame? On 11/6/19 5:59 PM, 曲岸 wrote: > > External Email - Use Caution > > Hi there, > > I am working with creating a surface parcellation from a volumetric > parcellation and have some questions as follows: > > 1. If the volumetric parcellation is a labeled 4D multi-frame dataset, > could I still use the mris_sample_parc? Or could mri_vol2surf get the > sampled labels for every vertex? > > 2. For the 4D multi-frame dataset and mri_vol2surf output results, > which GUI should I use to visualize it? I tried freeview for 4D > multi-frame dataset but it looks weird. > > 3. Is there any command to separate multi-frame volume to single frame > volumes? > > Many thanks! > > > 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
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.
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In addition, in my mri_vol2surf result, there are 35.5% vertices that are assigned 0 in all time frames. Then I checked its previous registration result and found that most parts of the brain are registered but I could also see some parts are not matched in some view. I attached a snapshot below for your reference, where the blue points are fMRI data. In the axial view, there is still a rotation between the functional and the anatomical volumes.
So I am wondering is the ratio of the vertices with 0 values in all time frame in my result reasonable and how could I reduce that? fMRI resolution: 2mm*2mm*2mm / anatomical MRI resolution: 1mm*1mm*1mm
Many thanks.
Best, An
[image: image.png]
An annaqu1024@gmail.com 于2019年11月14日周四 上午10:47写道：
Oops sorry for the mistakenly reply. I will pay more attention in the future.
Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that the volume was not registered. After that I tried another 4D volume to do the steps and successfully got the sampled intensity onto the surface.
The difference between the new 4D volume I used and the previous one is that there are two transformation matrices between them. The 4D dataset that I previously used but failed is the volume already registered to its anatomical volume(by using others tools). The new 4D volume that I tried and succeed is the volume not registered.
I have no idea why the 4D volume after the transformation would cause a failed result. Could you please let me know that?
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月13日周三 下午12:20写道：
If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally
On 11/12/19 8:41 PM, an wrote:
External Email - Use CautionMany thanks.
I got the 4D fMRI dataset from others and it is not raw data. In order to run mri_vol2surf, I need to calculate the register.dat for the required flag --srcreg so I tried in this way.
FYI, the 4D fMRI dataset should have been registered with its anatomical MR volume by using other tools.
For now I only ran the recon-all on its anatomical MR volume without running the functional stream as I don't have the raw data.
Should I also run the raw fMRI data from scratch by using functional stream? Or if I can run mri_vol2surf independently, which command should I use to get a register.dat file? In addition, the intensity of the 4D fMRI dataset I have is between [-1, 1] and not integers, would this cause any problem?
Best, An
On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
Don't do the 1st step. Why are you registering it to bert? I'm pretty sure bert did not participate in your fmri study When you run mri_vol2surf, it will probably work better with --projfrac 0.5
On 11/11/2019 1:32 PM, An wrote:
External Email - Use CautionHi Prof. Greve,
Thanks for your reply and sorry for the confusion.
I have a 4D fMRI dataset with 10 time frames, where the intensity of each voxel is between [-1,1] and not integers. I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I have already run its corresponding anatomical image in freesurfer.
To achieve it, I tried the following steps:
- conform the fmri series by using mri_convert
- register the fmri series with the anatomy image by using
bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat 3. assign values from volumes to each vertex by using mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg register.dat --hemi lh I also tried the -regheader in mri_vol2surf: mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But after step2, the registered volume looks wrong. I am wondering could I use bbregister to register multi-frame fMRI series to a single volume? I also tried to use --regheader to replace the --srcreg file in mri_vol2surf as the output register.dat in step2 is wrong. But the output is still wrong.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月11日周一 下午12:16写道：
When you say it is 4D, what do you mean? That each label has its own frame? On 11/6/19 5:59 PM, 曲岸 wrote: > > External Email - Use Caution > > Hi there, > > I am working with creating a surface parcellation from a volumetric > parcellation and have some questions as follows: > > 1. If the volumetric parcellation is a labeled 4D multi-frame dataset, > could I still use the mris_sample_parc? Or could mri_vol2surf get the > sampled labels for every vertex? > > 2. For the 4D multi-frame dataset and mri_vol2surf output results, > which GUI should I use to visualize it? I tried freeview for 4D > multi-frame dataset but it looks weird. > > 3. Is there any command to separate multi-frame volume to single frame > volumes? > > Many thanks! > > > 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
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.
I don't understand what you are trying to do. I'm very confused by your mentioning of bert. What does bert have to do with any of your data?
On 11/14/19 10:47 AM, An wrote:
External Email - Use Caution
Oops sorry for the mistakenly reply. I will pay more attention in the future.
Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that the volume was not registered. After that I tried another 4D volume to do the steps and successfully got the sampled intensity onto the surface.
The difference between the new 4D volume I used and the previous one is that there are two transformation matrices between them. The 4D dataset that I previously used but failed is the volume already registered to its anatomical volume(by using others tools). The new 4D volume that I tried and succeed is the volume not registered.
I have no idea why the 4D volume after the transformation would cause a failed result. Could you please let me know that?
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月13日周三 下午12:20写道：
If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally On 11/12/19 8:41 PM, an wrote: > > External Email - Use Caution > > Many thanks. > > I got the 4D fMRI dataset from others and it is not raw data. In order > to run mri_vol2surf, I need to calculate the register.dat for the > required flag --srcreg so I tried in this way. > > FYI, the 4D fMRI dataset should have been registered with its > anatomical MR volume by using other tools. > > For now I only ran the recon-all on its anatomical MR volume without > running the functional stream as I don't have the raw data. > > Should I also run the raw fMRI data from scratch by using functional > stream? Or if I can run mri_vol2surf independently, which command > should I use to get a register.dat file? > In addition, the intensity of the 4D fMRI dataset I have is between > [-1, 1] and not integers, would this cause any problem? > > Best, > An > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >> Don't do the 1st step. >> Why are you registering it to bert? I'm pretty sure bert did not >> participate in your fmri study >> When you run mri_vol2surf, it will probably work better with >> --projfrac 0.5 >> >> On 11/11/2019 1:32 PM, An wrote: >>> >>> External Email - Use Caution >>> >>> Hi Prof. Greve, >>> >>> Thanks for your reply and sorry for the confusion. >>> >>> I have a 4D fMRI dataset with 10 time frames, where the intensity of >>> each voxel is between [-1,1] and not integers. I want to map the >>> intensities of the volumes on its corresponding surface in order to >>> get the functional values on each vertex in each frame. I have >>> already run its corresponding anatomical image in freesurfer. >>> >>> To achieve it, I tried the following steps: >>> 1. conform the fmri series by using mri_convert >>> 2. register the fmri series with the anatomy image by using >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat >>> 3. assign values from volumes to each vertex by using mri_vol2surf: >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>> register.dat --hemi lh >>> I also tried the -regheader in mri_vol2surf: mri_vol2surf --src >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>> >>> >>> The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But >>> after step2, the registered volume looks wrong. I am wondering could >>> I use bbregister to register multi-frame fMRI series to a single >>> volume? >>> I also tried to use --regheader to replace the --srcreg file in >>> mri_vol2surf as the output register.dat in step2 is wrong. But the >>> output is still wrong. >>> >>> Many thanks. >>> >>> Best, >>> An >>> >>> 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11日周一 下午12:16写道： >>> >>> When you say it is 4D, what do you mean? That each label has its >>> own frame? >>> >>> On 11/6/19 5:59 PM, 曲岸 wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Hi there, >>> > >>> > I am working with creating a surface parcellation from a >>> volumetric >>> > parcellation and have some questions as follows: >>> > >>> > 1. If the volumetric parcellation is a labeled 4D multi-frame >>> dataset, >>> > could I still use the mris_sample_parc? Or could mri_vol2surf >>> get the >>> > sampled labels for every vertex? >>> > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf output >>> results, >>> > which GUI should I use to visualize it? I tried freeview for 4D >>> > multi-frame dataset but it looks weird. >>> > >>> > 3. Is there any command to separate multi-frame volume to >>> single frame >>> > volumes? >>> > >>> > Many thanks! >>> > >>> > >>> > 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 > 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.
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I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I ran recon-all for the anatomical volume and saved all outputs(mri,labels,surf and etc.) in the bert folder. I use it because I need to specify the required flag -s in bbregister in order to register the functional volume to its anatomical volume.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月18日周一 下午1:31写道：
I don't understand what you are trying to do. I'm very confused by your mentioning of bert. What does bert have to do with any of your data?
On 11/14/19 10:47 AM, An wrote:
External Email - Use CautionOops sorry for the mistakenly reply. I will pay more attention in the future.
Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that the volume was not registered. After that I tried another 4D volume to do the steps and successfully got the sampled intensity onto the surface.
The difference between the new 4D volume I used and the previous one is that there are two transformation matrices between them. The 4D dataset that I previously used but failed is the volume already registered to its anatomical volume(by using others tools). The new 4D volume that I tried and succeed is the volume not registered.
I have no idea why the 4D volume after the transformation would cause a failed result. Could you please let me know that?
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月13日周三 下午12:20写道：
If you have an anatomical MR that you have run through recon-all, then just use that one instead of bert in your steps below ps. Please remember to post to the FS list and not to us personally On 11/12/19 8:41 PM, an wrote: > > External Email - Use Caution > > Many thanks. > > I got the 4D fMRI dataset from others and it is not raw data. In order > to run mri_vol2surf, I need to calculate the register.dat for the > required flag --srcreg so I tried in this way. > > FYI, the 4D fMRI dataset should have been registered with its > anatomical MR volume by using other tools. > > For now I only ran the recon-all on its anatomical MR volume without > running the functional stream as I don't have the raw data. > > Should I also run the raw fMRI data from scratch by using functional > stream? Or if I can run mri_vol2surf independently, which command > should I use to get a register.dat file? > In addition, the intensity of the 4D fMRI dataset I have is between > [-1, 1] and not integers, would this cause any problem? > > Best, > An > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >> Don't do the 1st step. >> Why are you registering it to bert? I'm pretty sure bert did not >> participate in your fmri study >> When you run mri_vol2surf, it will probably work better with >> --projfrac 0.5 >> >> On 11/11/2019 1:32 PM, An wrote: >>> >>> External Email - Use Caution >>> >>> Hi Prof. Greve, >>> >>> Thanks for your reply and sorry for the confusion. >>> >>> I have a 4D fMRI dataset with 10 time frames, where the intensity of >>> each voxel is between [-1,1] and not integers. I want to map the >>> intensities of the volumes on its corresponding surface in order to >>> get the functional values on each vertex in each frame. I have >>> already run its corresponding anatomical image in freesurfer. >>> >>> To achieve it, I tried the following steps: >>> 1. conform the fmri series by using mri_convert >>> 2. register the fmri series with the anatomy image by using >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg register.dat >>> 3. assign values from volumes to each vertex by using mri_vol2surf: >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>> register.dat --hemi lh >>> I also tried the -regheader in mri_vol2surf: mri_vol2surf --src >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>> >>> >>> The /4Dvol.nii /aligns very well with the orig.mgz in freeview. But >>> after step2, the registered volume looks wrong. I am wondering could >>> I use bbregister to register multi-frame fMRI series to a single >>> volume? >>> I also tried to use --regheader to replace the --srcreg file in >>> mri_vol2surf as the output register.dat in step2 is wrong. But the >>> output is still wrong. >>> >>> Many thanks. >>> >>> Best, >>> An >>> >>> 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11日周一 下午12:16写道： >>> >>> When you say it is 4D, what do you mean? That each label has its >>> own frame? >>> >>> On 11/6/19 5:59 PM, 曲岸 wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Hi there, >>> > >>> > I am working with creating a surface parcellation from a >>> volumetric >>> > parcellation and have some questions as follows: >>> > >>> > 1. If the volumetric parcellation is a labeled 4D multi-frame >>> dataset, >>> > could I still use the mris_sample_parc? Or could mri_vol2surf >>> get the >>> > sampled labels for every vertex? >>> > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf output >>> results, >>> > which GUI should I use to visualize it? I tried freeview for 4D >>> > multi-frame dataset but it looks weird. >>> > >>> > 3. Is there any command to separate multi-frame volume to >>> single frame >>> > volumes? >>> > >>> > Many thanks! >>> > >>> > >>> > 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 > 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.
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What was your original recon-all command?
On 11/18/19 1:48 PM, An wrote:
External Email - Use Caution
I want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I ran recon-all for the anatomical volume and saved all outputs(mri,labels,surf and etc.) in the bert folder. I use it because I need to specify the required flag -s in bbregister in order to register the functional volume to its anatomical volume.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月18日周一 下午1:31写道：
I don't understand what you are trying to do. I'm very confused by your mentioning of bert. What does bert have to do with any of your data? On 11/14/19 10:47 AM, An wrote: > > External Email - Use Caution > > Oops sorry for the mistakenly reply. I will pay more attention in the > future. > > Bert is the folder with the anatomical data. I tried the following > steps with the 4D volume but failed. Then I checked the registration > result after bbregister and found that the volume was not registered. > After that I tried another 4D volume to do the steps and successfully > got the sampled intensity onto the surface. > > The difference between the new 4D volume I used and the previous one > is that there are two transformation matrices between them. The 4D > dataset that I previously used but failed is the volume already > registered to its anatomical volume(by using others tools). The new 4D > volume that I tried and succeed is the volume not registered. > > I have no idea why the 4D volume after the transformation would cause > a failed result. Could you please let me know that? > > Many thanks. > > Best, > An > > 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13日周三 下午12:20写道： > > If you have an anatomical MR that you have run through recon-all, > then > just use that one instead of bert in your steps below > ps. Please remember to post to the FS list and not to us personally > > On 11/12/19 8:41 PM, an wrote: > > > > External Email - Use Caution > > > > Many thanks. > > > > I got the 4D fMRI dataset from others and it is not raw data. In > order > > to run mri_vol2surf, I need to calculate the register.dat for the > > required flag --srcreg so I tried in this way. > > > > FYI, the 4D fMRI dataset should have been registered with its > > anatomical MR volume by using other tools. > > > > For now I only ran the recon-all on its anatomical MR volume > without > > running the functional stream as I don't have the raw data. > > > > Should I also run the raw fMRI data from scratch by using > functional > > stream? Or if I can run mri_vol2surf independently, which command > > should I use to get a register.dat file? > > In addition, the intensity of the 4D fMRI dataset I have is between > > [-1, 1] and not integers, would this cause any problem? > > > > Best, > > An > > > > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: > >> Don't do the 1st step. > >> Why are you registering it to bert? I'm pretty sure bert did not > >> participate in your fmri study > >> When you run mri_vol2surf, it will probably work better with > >> --projfrac 0.5 > >> > >> On 11/11/2019 1:32 PM, An wrote: > >>> > >>> External Email - Use Caution > >>> > >>> Hi Prof. Greve, > >>> > >>> Thanks for your reply and sorry for the confusion. > >>> > >>> I have a 4D fMRI dataset with 10 time frames, where the > intensity of > >>> each voxel is between [-1,1] and not integers. I want to map the > >>> intensities of the volumes on its corresponding surface in > order to > >>> get the functional values on each vertex in each frame. I have > >>> already run its corresponding anatomical image in freesurfer. > >>> > >>> To achieve it, I tried the following steps: > >>> 1. conform the fmri series by using mri_convert > >>> 2. register the fmri series with the anatomy image by using > >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg > register.dat > >>> 3. assign values from volumes to each vertex by using > mri_vol2surf: > >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg > >>> register.dat --hemi lh > >>> I also tried the -regheader in mri_vol2surf: mri_vol2surf > --src > >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh > >>> > >>> > >>> The /4Dvol.nii /aligns very well with the orig.mgz in > freeview. But > >>> after step2, the registered volume looks wrong. I am wondering > could > >>> I use bbregister to register multi-frame fMRI series to a single > >>> volume? > >>> I also tried to use --regheader to replace the --srcreg file in > >>> mri_vol2surf as the output register.dat in step2 is wrong. But > the > >>> output is still wrong. > >>> > >>> Many thanks. > >>> > >>> Best, > >>> An > >>> > >>> 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11日周一 下午12:16写道： > >>> > >>> When you say it is 4D, what do you mean? That each label > has its > >>> own frame? > >>> > >>> On 11/6/19 5:59 PM, 曲岸 wrote: > >>> > > >>> > External Email - Use Caution > >>> > > >>> > Hi there, > >>> > > >>> > I am working with creating a surface parcellation from a > >>> volumetric > >>> > parcellation and have some questions as follows: > >>> > > >>> > 1. If the volumetric parcellation is a labeled 4D > multi-frame > >>> dataset, > >>> > could I still use the mris_sample_parc? Or could > mri_vol2surf > >>> get the > >>> > sampled labels for every vertex? > >>> > > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf output > >>> results, > >>> > which GUI should I use to visualize it? I tried freeview > for 4D > >>> > multi-frame dataset but it looks weird. > >>> > > >>> > 3. Is there any command to separate multi-frame volume to > >>> single frame > >>> > volumes? > >>> > > >>> > Many thanks! > >>> > > >>> > > >>> > 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 > > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <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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External Email - Use Caution
Here is my recon-all command line:
recon-all -i ana_Vol.nii -s bert -all
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月18日周一 下午2:33写道：
What was your original recon-all command?
On 11/18/19 1:48 PM, An wrote:
External Email - Use CautionI want to map the intensities of the volumes on its corresponding surface in order to get the functional values on each vertex in each frame. I ran recon-all for the anatomical volume and saved all outputs(mri,labels,surf and etc.) in the bert folder. I use it because I need to specify the required flag -s in bbregister in order to register the functional volume to its anatomical volume.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月18日周一 下午1:31写道：
I don't understand what you are trying to do. I'm very confused by your mentioning of bert. What does bert have to do with any of your data? On 11/14/19 10:47 AM, An wrote: > > External Email - Use Caution > > Oops sorry for the mistakenly reply. I will pay more attention in the > future. > > Bert is the folder with the anatomical data. I tried the following > steps with the 4D volume but failed. Then I checked the registration > result after bbregister and found that the volume was not registered. > After that I tried another 4D volume to do the steps and successfully > got the sampled intensity onto the surface. > > The difference between the new 4D volume I used and the previous one > is that there are two transformation matrices between them. The 4D > dataset that I previously used but failed is the volume already > registered to its anatomical volume(by using others tools). The new 4D > volume that I tried and succeed is the volume not registered. > > I have no idea why the 4D volume after the transformation would cause > a failed result. Could you please let me know that? > > Many thanks. > > Best, > An > > 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13日周三 下午12:20写道： > > If you have an anatomical MR that you have run through recon-all, > then > just use that one instead of bert in your steps below > ps. Please remember to post to the FS list and not to us personally > > On 11/12/19 8:41 PM, an wrote: > > > > External Email - Use Caution > > > > Many thanks. > > > > I got the 4D fMRI dataset from others and it is not raw data. In > order > > to run mri_vol2surf, I need to calculate the register.dat for the > > required flag --srcreg so I tried in this way. > > > > FYI, the 4D fMRI dataset should have been registered with its > > anatomical MR volume by using other tools. > > > > For now I only ran the recon-all on its anatomical MR volume > without > > running the functional stream as I don't have the raw data. > > > > Should I also run the raw fMRI data from scratch by using > functional > > stream? Or if I can run mri_vol2surf independently, which command > > should I use to get a register.dat file? > > In addition, the intensity of the 4D fMRI dataset I have is between > > [-1, 1] and not integers, would this cause any problem? > > > > Best, > > An > > > > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: > >> Don't do the 1st step. > >> Why are you registering it to bert? I'm pretty sure bert did not > >> participate in your fmri study > >> When you run mri_vol2surf, it will probably work better with > >> --projfrac 0.5 > >> > >> On 11/11/2019 1:32 PM, An wrote: > >>> > >>> External Email - Use Caution > >>> > >>> Hi Prof. Greve, > >>> > >>> Thanks for your reply and sorry for the confusion. > >>> > >>> I have a 4D fMRI dataset with 10 time frames, where the > intensity of > >>> each voxel is between [-1,1] and not integers. I want to map the > >>> intensities of the volumes on its corresponding surface in > order to > >>> get the functional values on each vertex in each frame. I have > >>> already run its corresponding anatomical image in freesurfer. > >>> > >>> To achieve it, I tried the following steps: > >>> 1. conform the fmri series by using mri_convert > >>> 2. register the fmri series with the anatomy image by using > >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg > register.dat > >>> 3. assign values from volumes to each vertex by using > mri_vol2surf: > >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg > >>> register.dat --hemi lh > >>> I also tried the -regheader in mri_vol2surf: mri_vol2surf > --src > >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh > >>> > >>> > >>> The /4Dvol.nii /aligns very well with the orig.mgz in > freeview. But > >>> after step2, the registered volume looks wrong. I am wondering > could > >>> I use bbregister to register multi-frame fMRI series to a single > >>> volume? > >>> I also tried to use --regheader to replace the --srcreg file in > >>> mri_vol2surf as the output register.dat in step2 is wrong. But > the > >>> output is still wrong. > >>> > >>> Many thanks. > >>> > >>> Best, > >>> An > >>> > >>> 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11日周一 下午12:16写道： > >>> > >>> When you say it is 4D, what do you mean? That eachlabel
> has its > >>> own frame? > >>> > >>> On 11/6/19 5:59 PM, 曲岸 wrote: > >>> > > >>> > External Email - Use Caution > >>> > > >>> > Hi there, > >>> > > >>> > I am working with creating a surface parcellation from a > >>> volumetric > >>> > parcellation and have some questions as follows: > >>> > > >>> > 1. If the volumetric parcellation is a labeled 4D > multi-frame > >>> dataset, > >>> > could I still use the mris_sample_parc? Or could > mri_vol2surf > >>> get the > >>> > sampled labels for every vertex? > >>> > > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf output > >>> results, > >>> > which GUI should I use to visualize it? I tried freeview > for 4D > >>> > multi-frame dataset but it looks weird. > >>> > > >>> > 3. Is there any command to separate multi-frame volume to > >>> single frame > >>> > volumes? > >>> > > >>> > Many thanks! > >>> > > >>> > > >>> > 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
> > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <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>
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why did you call it bert? It just makes things confusing
On 11/18/19 2:53 PM, An wrote:
External Email - Use Caution
Here is my recon-all command line: recon-all -i ana_Vol.nii -s bert -all Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月18日周一 下午2:33写道：
What was your original recon-all command? On 11/18/19 1:48 PM, An wrote: > > External Email - Use Caution > > I want to map the intensities of the volumes on its corresponding > surface in order to get the functional values on each vertex in each > frame. I ran recon-all for the anatomical volume and saved all > outputs(mri,labels,surf and etc.) in the bert folder. I use it because > I need to specify the required flag -s in bbregister in order to > register the functional volume to its anatomical volume. > > Many thanks. > > Best, > An > > 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18日周一 下午1:31写道： > > I don't understand what you are trying to do. I'm very confused by > your > mentioning of bert. What does bert have to do with any of your data? > > On 11/14/19 10:47 AM, An wrote: > > > > External Email - Use Caution > > > > Oops sorry for the mistakenly reply. I will pay more attention > in the > > future. > > > > Bert is the folder with the anatomical data. I tried the following > > steps with the 4D volume but failed. Then I checked the > registration > > result after bbregister and found that the volume was not > registered. > > After that I tried another 4D volume to do the steps and > successfully > > got the sampled intensity onto the surface. > > > > The difference between the new 4D volume I used and the previous > one > > is that there are two transformation matrices between them. The 4D > > dataset that I previously used but failed is the volume already > > registered to its anatomical volume(by using others tools). The > new 4D > > volume that I tried and succeed is the volume not registered. > > > > I have no idea why the 4D volume after the transformation would > cause > > a failed result. Could you please let me know that? > > > > Many thanks. > > > > Best, > > An > > > > 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13日周三 下午12:20写道： > > > > If you have an anatomical MR that you have run through > recon-all, > > then > > just use that one instead of bert in your steps below > > ps. Please remember to post to the FS list and not to us > personally > > > > On 11/12/19 8:41 PM, an wrote: > > > > > > External Email - Use Caution > > > > > > Many thanks. > > > > > > I got the 4D fMRI dataset from others and it is not raw > data. In > > order > > > to run mri_vol2surf, I need to calculate the register.dat > for the > > > required flag --srcreg so I tried in this way. > > > > > > FYI, the 4D fMRI dataset should have been registered with its > > > anatomical MR volume by using other tools. > > > > > > For now I only ran the recon-all on its anatomical MR volume > > without > > > running the functional stream as I don't have the raw data. > > > > > > Should I also run the raw fMRI data from scratch by using > > functional > > > stream? Or if I can run mri_vol2surf independently, which > command > > > should I use to get a register.dat file? > > > In addition, the intensity of the 4D fMRI dataset I have > is between > > > [-1, 1] and not integers, would this cause any problem? > > > > > > Best, > > > An > > > > > > > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: > > >> Don't do the 1st step. > > >> Why are you registering it to bert? I'm pretty sure bert > did not > > >> participate in your fmri study > > >> When you run mri_vol2surf, it will probably work better with > > >> --projfrac 0.5 > > >> > > >> On 11/11/2019 1:32 PM, An wrote: > > >>> > > >>> External Email - Use Caution > > >>> > > >>> Hi Prof. Greve, > > >>> > > >>> Thanks for your reply and sorry for the confusion. > > >>> > > >>> I have a 4D fMRI dataset with 10 time frames, where the > > intensity of > > >>> each voxel is between [-1,1] and not integers. I want to > map the > > >>> intensities of the volumes on its corresponding surface in > > order to > > >>> get the functional values on each vertex in each frame. > I have > > >>> already run its corresponding anatomical image in > freesurfer. > > >>> > > >>> To achieve it, I tried the following steps: > > >>> 1. conform the fmri series by using mri_convert > > >>> 2. register the fmri series with the anatomy image by using > > >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg > > register.dat > > >>> 3. assign values from volumes to each vertex by using > > mri_vol2surf: > > >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg > > >>> register.dat --hemi lh > > >>> I also tried the -regheader in mri_vol2surf: > mri_vol2surf > > --src > > >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh > > >>> > > >>> > > >>> The /4Dvol.nii /aligns very well with the orig.mgz in > > freeview. But > > >>> after step2, the registered volume looks wrong. I am > wondering > > could > > >>> I use bbregister to register multi-frame fMRI series to > a single > > >>> volume? > > >>> I also tried to use --regheader to replace the --srcreg > file in > > >>> mri_vol2surf as the output register.dat in step2 is > wrong. But > > the > > >>> output is still wrong. > > >>> > > >>> Many thanks. > > >>> > > >>> Best, > > >>> An > > >>> > > >>> 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>>> > > >>> <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 <mailto:DGREVE@mgh.harvard.edu>>>>> 于2019年11月11日周一 > 下午12:16写道： > > >>> > > >>> When you say it is 4D, what do you mean? That each label > > has its > > >>> own frame? > > >>> > > >>> On 11/6/19 5:59 PM, 曲岸 wrote: > > >>> > > > >>> > External Email - Use Caution > > >>> > > > >>> > Hi there, > > >>> > > > >>> > I am working with creating a surface parcellation > from a > > >>> volumetric > > >>> > parcellation and have some questions as follows: > > >>> > > > >>> > 1. If the volumetric parcellation is a labeled 4D > > multi-frame > > >>> dataset, > > >>> > could I still use the mris_sample_parc? Or could > > mri_vol2surf > > >>> get the > > >>> > sampled labels for every vertex? > > >>> > > > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf > output > > >>> results, > > >>> > which GUI should I use to visualize it? I tried > freeview > > for 4D > > >>> > multi-frame dataset but it looks weird. > > >>> > > > >>> > 3. Is there any command to separate multi-frame > volume to > > >>> single frame > > >>> > volumes? > > >>> > > > >>> > Many thanks! > > >>> > > > >>> > > > >>> > 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>>> > > >>> <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 <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>>> > > >>> <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 <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>> > > <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 > > > > > > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <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
External Email - Use Caution
Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the freesurfer download and install webpage to install the software and then ran the recon-all command. I will try to avoid this kind of issues in the future.
Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月18日周一 下午4:47写道：
why did you call it bert? It just makes things confusing
On 11/18/19 2:53 PM, An wrote:
External Email - Use CautionHere is my recon-all command line: recon-all -i ana_Vol.nii -s bert -all Many thanks.
Best, An
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> 于2019年11月18日周一 下午2:33写道：
What was your original recon-all command? On 11/18/19 1:48 PM, An wrote: > > External Email - Use Caution > > I want to map the intensities of the volumes on its corresponding > surface in order to get the functional values on each vertex in each > frame. I ran recon-all for the anatomical volume and saved all > outputs(mri,labels,surf and etc.) in the bert folder. I use it because > I need to specify the required flag -s in bbregister in order to > register the functional volume to its anatomical volume. > > Many thanks. > > Best, > An > > 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18日周一 下午1:31写道： > > I don't understand what you are trying to do. I'm very confused by > your > mentioning of bert. What does bert have to do with any of your data? > > On 11/14/19 10:47 AM, An wrote: > > > > External Email - Use Caution > > > > Oops sorry for the mistakenly reply. I will pay moreattention
> in the > > future. > > > > Bert is the folder with the anatomical data. I tried the following > > steps with the 4D volume but failed. Then I checked the > registration > > result after bbregister and found that the volume was not > registered. > > After that I tried another 4D volume to do the steps and > successfully > > got the sampled intensity onto the surface. > > > > The difference between the new 4D volume I used and the previous > one > > is that there are two transformation matrices between them. The 4D > > dataset that I previously used but failed is the volume already > > registered to its anatomical volume(by using others tools). The > new 4D > > volume that I tried and succeed is the volume not registered. > > > > I have no idea why the 4D volume after the transformation would > cause > > a failed result. Could you please let me know that? > > > > Many thanks. > > > > Best, > > An > > > > 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13日周三 下午12:20写道： > > > > If you have an anatomical MR that you have run through > recon-all, > > then > > just use that one instead of bert in your steps below > > ps. Please remember to post to the FS list and not to us > personally > > > > On 11/12/19 8:41 PM, an wrote: > > > > > > External Email - Use Caution > > > > > > Many thanks. > > > > > > I got the 4D fMRI dataset from others and it is not raw > data. In > > order > > > to run mri_vol2surf, I need to calculate the register.dat > for the > > > required flag --srcreg so I tried in this way. > > > > > > FYI, the 4D fMRI dataset should have been registered with its > > > anatomical MR volume by using other tools. > > > > > > For now I only ran the recon-all on its anatomical MR volume > > without > > > running the functional stream as I don't have the raw data. > > > > > > Should I also run the raw fMRI data from scratch by using > > functional > > > stream? Or if I can run mri_vol2surf independently, which > command > > > should I use to get a register.dat file? > > > In addition, the intensity of the 4D fMRI dataset Ihave
> is between > > > [-1, 1] and not integers, would this cause any problem? > > > > > > Best, > > > An > > > > > > > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: > > >> Don't do the 1st step. > > >> Why are you registering it to bert? I'm pretty sure bert > did not > > >> participate in your fmri study > > >> When you run mri_vol2surf, it will probably work better with > > >> --projfrac 0.5 > > >> > > >> On 11/11/2019 1:32 PM, An wrote: > > >>> > > >>> External Email - Use Caution > > >>> > > >>> Hi Prof. Greve, > > >>> > > >>> Thanks for your reply and sorry for the confusion. > > >>> > > >>> I have a 4D fMRI dataset with 10 time frames, where the > > intensity of > > >>> each voxel is between [-1,1] and not integers. I want to > map the > > >>> intensities of the volumes on its corresponding surface in > > order to > > >>> get the functional values on each vertex in each frame. > I have > > >>> already run its corresponding anatomical image in > freesurfer. > > >>> > > >>> To achieve it, I tried the following steps: > > >>> 1. conform the fmri series by using mri_convert > > >>> 2. register the fmri series with the anatomy image by using > > >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg > > register.dat > > >>> 3. assign values from volumes to each vertex by using > > mri_vol2surf: > > >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg > > >>> register.dat --hemi lh > > >>> I also tried the -regheader in mri_vol2surf: > mri_vol2surf > > --src > > >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh > > >>> > > >>> > > >>> The /4Dvol.nii /aligns very well with the orig.mgz in > > freeview. But > > >>> after step2, the registered volume looks wrong. I am > wondering > > could > > >>> I use bbregister to register multi-frame fMRI series to > a single > > >>> volume? > > >>> I also tried to use --regheader to replace the --srcreg > file in > > >>> mri_vol2surf as the output register.dat in step2 is > wrong. But > > the > > >>> output is still wrong. > > >>> > > >>> Many thanks. > > >>> > > >>> Best, > > >>> An > > >>> > > >>> 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>>> > > >>> <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 <mailto:DGREVE@mgh.harvard.edu>>>>> 于2019年11月11日周一 > 下午12:16写道： > > >>> > > >>> When you say it is 4D, what do you mean? That each label > > has its > > >>> own frame? > > >>> > > >>> On 11/6/19 5:59 PM, 曲岸 wrote: > > >>> > > > >>> > External Email - Use Caution > > >>> > > > >>> > Hi there, > > >>> > > > >>> > I am working with creating a surface parcellation > from a > > >>> volumetric > > >>> > parcellation and have some questions asfollows:
> > >>> > > > >>> > 1. If the volumetric parcellation is a labeled 4D > > multi-frame > > >>> dataset, > > >>> > could I still use the mris_sample_parc? Orcould
> > mri_vol2surf > > >>> get the > > >>> > sampled labels for every vertex? > > >>> > > > >>> > 2. For the 4D multi-frame dataset and mri_vol2surf > output > > >>> results, > > >>> > which GUI should I use to visualize it? I tried > freeview > > for 4D > > >>> > multi-frame dataset but it looks weird. > > >>> > > > >>> > 3. Is there any command to separate multi-frame > volume to > > >>> single frame > > >>> > volumes? > > >>> > > > >>> > Many thanks! > > >>> > > > >>> > > > >>> > 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>>> > > >>> <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 <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>>> > > >>> <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 <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>> > > <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 > > > > > > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <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>
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it's not delicate - it's just confusing for us when you use it as it refers to a specific dataset
cheers Bruce On Mon, 18 Nov 2019, An wrote:
External Email - Use Caution
Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the freesurfer download and install webpage to install the software and then ran the recon-all command. I will try to avoid this kind of issues in the future. Many thanks.
Best, An
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年11月18日周一 下午4:47写道： why did you call it bert? It just makes things confusing
On 11/18/19 2:53 PM, An wrote: > > External Email - Use Caution > > Here is my recon-all command line: > recon-all -i ana_Vol.nii -s bert -all > Many thanks. > > Best, > An > > > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu > <mailto:DGREVE@mgh.harvard.edu>> 于2019年11月18日周一 下午2:33写道： > > What was your original recon-all command? > > On 11/18/19 1:48 PM, An wrote: > > > > External Email - Use Caution > > > > I want to map the intensities of the volumes on its corresponding > > surface in order to get the functional values on each vertex in > each > > frame. I ran recon-all for the anatomical volume and saved all > > outputs(mri,labels,surf and etc.) in the bert folder. I use it > because > > I need to specify the required flag -s in bbregister in order to > > register the functional volume to its anatomical volume. > > > > Many thanks. > > > > Best, > > An > > > > 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18日周一 下午1:31写道： > > > > I don't understand what you are trying to do. I'm very > confused by > > your > > mentioning of bert. What does bert have to do with any of > your data? > > > > On 11/14/19 10:47 AM, An wrote: > > > > > > External Email - Use Caution > > > > > > Oops sorry for the mistakenly reply. I will pay more attention > > in the > > > future. > > > > > > Bert is the folder with the anatomical data. I tried the > following > > > steps with the 4D volume but failed. Then I checked the > > registration > > > result after bbregister and found that the volume was not > > registered. > > > After that I tried another 4D volume to do the steps and > > successfully > > > got the sampled intensity onto the surface. > > > > > > The difference between the new 4D volume I used and the > previous > > one > > > is that there are two transformation matrices between > them. The 4D > > > dataset that I previously used but failed is the volume > already > > > registered to its anatomical volume(by using others > tools). The > > new 4D > > > volume that I tried and succeed is the volume not registered. > > > > > > I have no idea why the 4D volume after the transformation > would > > cause > > > a failed result. Could you please let me know that? > > > > > > Many thanks. > > > > > > Best, > > > An > > > > > > 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13日周三 下午12:20写道： > > > > > > If you have an anatomical MR that you have run through > > recon-all, > > > then > > > just use that one instead of bert in your steps below > > > ps. Please remember to post to the FS list and not to us > > personally > > > > > > On 11/12/19 8:41 PM, an wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Many thanks. > > > > > > > > I got the 4D fMRI dataset from others and it is not raw > > data. In > > > order > > > > to run mri_vol2surf, I need to calculate the > register.dat > > for the > > > > required flag --srcreg so I tried in this way. > > > > > > > > FYI, the 4D fMRI dataset should have been registered > with its > > > > anatomical MR volume by using other tools. > > > > > > > > For now I only ran the recon-all on its anatomical > MR volume > > > without > > > > running the functional stream as I don't have the > raw data. > > > > > > > > Should I also run the raw fMRI data from scratch by > using > > > functional > > > > stream? Or if I can run mri_vol2surf independently, > which > > command > > > > should I use to get a register.dat file? > > > > In addition, the intensity of the 4D fMRI dataset I have > > is between > > > > [-1, 1] and not integers, would this cause any problem? > > > > > > > > Best, > > > > An > > > > > > > > > > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: > > > >> Don't do the 1st step. > > > >> Why are you registering it to bert? I'm pretty sure > bert > > did not > > > >> participate in your fmri study > > > >> When you run mri_vol2surf, it will probably work > better with > > > >> --projfrac 0.5 > > > >> > > > >> On 11/11/2019 1:32 PM, An wrote: > > > >>> > > > >>> External Email - Use Caution > > > >>> > > > >>> Hi Prof. Greve, > > > >>> > > > >>> Thanks for your reply and sorry for the confusion. > > > >>> > > > >>> I have a 4D fMRI dataset with 10 time frames, > where the > > > intensity of > > > >>> each voxel is between [-1,1] and not integers. I > want to > > map the > > > >>> intensities of the volumes on its corresponding > surface in > > > order to > > > >>> get the functional values on each vertex in each > frame. > > I have > > > >>> already run its corresponding anatomical image in > > freesurfer. > > > >>> > > > >>> To achieve it, I tried the following steps: > > > >>> 1. conform the fmri series by using mri_convert > > > >>> 2. register the fmri series with the anatomy image > by using > > > >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert > --reg > > > register.dat > > > >>> 3. assign values from volumes to each vertex by using > > > mri_vol2surf: > > > >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ > --srcreg > > > >>> register.dat --hemi lh > > > >>> I also tried the -regheader in mri_vol2surf: > > mri_vol2surf > > > --src > > > >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert > --hemi lh > > > >>> > > > >>> > > > >>> The /4Dvol.nii /aligns very well with the orig.mgz in > > > freeview. But > > > >>> after step2, the registered volume looks wrong. I am > > wondering > > > could > > > >>> I use bbregister to register multi-frame fMRI > series to > > a single > > > >>> volume? > > > >>> I also tried to use --regheader to replace the > --srcreg > > file in > > > >>> mri_vol2surf as the output register.dat in step2 is > > wrong. But > > > the > > > >>> output is still wrong. > > > >>> > > > >>> Many thanks. > > > >>> > > > >>> Best, > > > >>> An > > > >>> > > > >>> 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>>> > > > >>> <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 > <mailto:DGREVE@mgh.harvard.edu>>>>> 于2019年11月11日周一 > > 下午12:16写道： > > > >>> > > > >>> When you say it is 4D, what do you mean? That > each label > > > has its > > > >>> own frame? > > > >>> > > > >>> On 11/6/19 5:59 PM, 曲岸 wrote: > > > >>> > > > > >>> > External Email - Use Caution > > > >>> > > > > >>> > Hi there, > > > >>> > > > > >>> > I am working with creating a surface > parcellation > > from a > > > >>> volumetric > > > >>> > parcellation and have some questions as follows: > > > >>> > > > > >>> > 1. If the volumetric parcellation is a > labeled 4D > > > multi-frame > > > >>> dataset, > > > >>> > could I still use the mris_sample_parc? Or could > > > mri_vol2surf > > > >>> get the > > > >>> > sampled labels for every vertex? > > > >>> > > > > >>> > 2. For the 4D multi-frame dataset and > mri_vol2surf > > output > > > >>> results, > > > >>> > which GUI should I use to visualize it? I tried > > freeview > > > for 4D > > > >>> > multi-frame dataset but it looks weird. > > > >>> > > > > >>> > 3. Is there any command to separate multi-frame > > volume to > > > >>> single frame > > > >>> > volumes? > > > >>> > > > > >>> > Many thanks! > > > >>> > > > > >>> > > > > >>> > 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>>> > > > >>> <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 > <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>>> > > > >>> <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 > <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>> > > > <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 > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > sent to > > > you in error > > > but does not contain patient information, please > contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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An -
Bruce Fischl -
Greve, Douglas N.,Ph.D.