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. <dgr...@mgh.harvard.edu > <mailto:dgr...@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. <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu <mailto: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> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > > >>> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> > > <mailto: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> > > <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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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