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. <dgr...@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. <dgr...@mgh.harvard.edu > >>> <mailto:dgr...@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. 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