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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
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