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