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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
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