You can try following this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_...
Eg, run tkregisterfv --s subject --mov template.nii.gz --regheader --reg reg.manual.lta Adjust the registration so that it is relatively close (does not need to be exact) Then run bbregister --mov template.nii.gz --init-reg reg.manual.lta --reg register.dof6.lta --t2
On 9/21/2020 10:55 AM, Wenzhen Zhao wrote:
External Email - Use Caution
Dear Douglas,
Yes, it happens with almost every subject I have (n=53). Is there a way to apply the method to all the participants? If you could instruct me on initializing by hand, I can manually do them on all subjects.
Thank you for your help!
Best, Wenzhen On Mon, Sep 21, 2020 at 10:48 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Does this happen on a lot of your subjects? I'm not entire sure why it is happening to this one, but one reason may be that there is more torso (eg, shoulders) than the usual scan. I was able to get it working if I initialized it by hand. This would be ok for one subject, but you would not have to do so with many subjects. On 9/18/2020 3:58 PM, Wenzhen Zhao wrote:External Email - Use Caution Dear Douglas, I uploaded the file and the file name is wenzhen.tar.gz. the file has freesurfer_results and template.nii.gz. Thank you for looking into the problem. Please let me know if you need anything. Best, WenzhenOn Sep 18, 2020, at 12:40 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: I can't figure out what is going on unless I have the data. Can you upload it? All I need is the subject's dir (output of recon-all) and the template.nii.gz. You can follow the instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu <http://surfer.nmr.mgh.harvard.edu> It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 9/18/2020 12:15 PM, Wenzhen Zhao wrote:External Email - Use Caution Dear Douglas, Yes, they do look properly oriented to me.one thing I noticed is that when I switch over coronal view, sagittal view, and axial view, brains seem to shift back and forth in horizontal direction. If you see the picture below, brains are not in the same spot. I am not sure if this is an issue. Best, Wenzhen <Screen Shot 2020-09-18 at 12.04.54 PM.png>On Sep 18, 2020, at 10:47 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: Is the fmri scan properly oriented? Eg, run freeview template.nii.gz and see of it is oriented correctly in the FV window On 9/15/20 2:57 PM, Wenzhen Zhao wrote:External Email - Use CautionDear Douglas, I am using freesurfer 6. I used following command to register fMRI data to anatomical scan. $ bbregister --mov sess01/rest/001/template.nii.gz --t2 --s subject --lta register.dof6.lta I used following command to visualize the output; red: functional scan; overlaid on orig.mgz structural scan. $ tkregisterfv --mov sess01/rest/001/template.nii.gz --reg register.dof6.lta --surfs It seems like two are not aligning well. Is there any step that I should take to improve? Again, thank you so much for helping. Best, Wenzhen <Screen Shot 2020-09-15 at 2.51.32 PM.png>> > > On Sep 15, 2020, at 1:47 > > PM, Douglas N. Greve <dgreve@mgh.harvard.edu > mailto:dgreve@mgh.harvard.edu> > > wrote: > > > > > > > > What version of FS > > are you using? Try using > > bbregister without an init option. > > Also make sure you are specifying > > --t2 > > > And send your full command lines > > next time > > > > > > On > > 9/15/2020 1:44 PM, Wenzhen Zhao > > wrote: > > > > >> >> >> External >> >> Email - Use Caution >> >> >> >> Dear Douglas, >> >> >> >> >> >> >> Do you have any >> >> recommendation on which >> >> registration method to use? If >> >> I use default or init-spm, I >> >> would not get a correct >> >> orientation. Below is the >> >> images I got using the >> >> following command: >> >> >> >> >> >> >> >> >> >> freeview -v >> >> $SUBJECTS_DIR/subject/mri/orig.mgz:visible=0 >> >> sess01/rest/001/template.nii.gz:reg=sess01/rest/register.dof6.lta >> -f >> >> $SUBJECTS_DIR/subject/surf/lh.white >> >> $SUBJECTS_DIR/subject/surf/rh.white -viewport cor >> -transform-volume >> >> >> >> >> >> >> >> >> >> >> >> >> Thanks, >> >> >> Wenzhen >> >> >> <Screen Shot >> >> 2020-09-15 at 1.42.34 >> >> PM.png> >> >> >>> >>> >>> On Sep 15, >>> >>> 2020, at 12:59 PM, >>> >>> Douglas N. Greve <dgreve@mgh.harvard.edu >>> mailto:dgreve@mgh.harvard.edu> >>> >>> wrote: >>> >>> >>> >>> >>> >>> >>> >>> Both do >>> >>> both ways. I would >>> >>> recommend not using >>> >>> the --init-rr option >>> >>> for BOLD images >>> >>> >>> >>> >>> >>> On >>> >>> 9/15/2020 11:42 AM, >>> >>> Wenzhen Zhao wrote: >>> >>> >>> >>> >>>> >>>> >>>> External >>>> >>>> Email - Use >>>> >>>> Caution >>>> >>>> >>>> >>>> Dear Douglas, >>>> >>>> >>>> >>>> >>>> >>>> >>>> Thank >>>> >>>> you for your quick >>>> >>>> response. I just >>>> >>>> have one more >>>> >>>> question. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Does >>>> >>>> the “both-way” >>>> >>>> transformation >>>> >>>> only done through >>>> >>>> mri_coreg command >>>> >>>> that is embedded >>>> >>>> in preproc-sess >>>> >>>> command? Or does >>>> >>>> “bbregister >>>> >>>> —init-rr “ rigid >>>> >>>> transformation >>>> >>>> also does both-way >>>> >>>> transformation? >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Best, >>>> >>>> >>>> Wenzhen >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> >>>>> >>>>> On >>>>> >>>>> Sep 15, 2020, >>>>> >>>>> at 11:34 AM, >>>>> >>>>> Douglas N. >>>>> >>>>> Greve <dgreve@mgh.harvard.edu >>>>> mailto:dgreve@mgh.harvard.edu> >>>>> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On >>>>> >>>>> 9/15/2020 >>>>> >>>>> 11:26 AM, >>>>> >>>>> Wenzhen Zhao >>>>> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> External Email - Use >>>>>> >>>>>> Caution >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Dear >>>>>> >>>>>> freesurfer >>>>>> >>>>>> developers, >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> I’m >>>>>> >>>>>> attempting to >>>>>> >>>>>> analyze my >>>>>> >>>>>> resting -state >>>>>> >>>>>> fMRI data, and >>>>>> >>>>>> I followed >>>>>> >>>>>> procedures on >>>>>> >>>>>> your >>>>>> >>>>>> functional >>>>>> >>>>>> connectivity >>>>>> >>>>>> page. When I >>>>>> >>>>>> tried to run >>>>>> >>>>>> preprocessing >>>>>> >>>>>> with my data, >>>>>> >>>>>> but it turns >>>>>> >>>>>> out that >>>>>> >>>>>> default >>>>>> >>>>>> mri_coreg did >>>>>> >>>>>> not register >>>>>> >>>>>> my fMRI >>>>>> >>>>>> template >>>>>> >>>>>> volume onto >>>>>> >>>>>> anatomical >>>>>> >>>>>> scan well. So, >>>>>> >>>>>> I went on to >>>>>> >>>>>> register fMRI >>>>>> >>>>>> to anatomical >>>>>> >>>>>> space on my >>>>>> >>>>>> own using >>>>>> >>>>>> bbregister >>>>>> >>>>>> with (init-rr >>>>>> >>>>>> method - rigid >>>>>> >>>>>> transformation). I re-ran preprocessing without >>>>>> registration (-noreg) to >>>>>> >>>>>> correct motion >>>>>> >>>>>> and >>>>>> >>>>>> slice-timing. >>>>>> >>>>>> My commands >>>>>> >>>>>> looked like >>>>>> >>>>>> below: >>>>>> >>>>>> >>>>>> #bbregister >>>>>> >>>>>> —mov >>>>>> >>>>>> fMRI_template_volume >>>>>> >>>>>> —bold —s >>>>>> >>>>>> subject >>>>>> >>>>>> —init-rr —lta >>>>>> >>>>>> functional2anatomical.lta >>>>>> >>>>>> >>>>>> #preproc-sess >>>>>> >>>>>> -s sess01 -fsd >>>>>> >>>>>> rest -stc >>>>>> >>>>>> siemens -noreg >>>>>> >>>>>> -surface >>>>>> >>>>>> fsaverage lhrh >>>>>> >>>>>> -surf-fwhm 5 >>>>>> >>>>>> -mni305-2mm >>>>>> >>>>>> -vol-fwhm 0 >>>>>> >>>>>> -per-run >>>>>> >>>>>> -force >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Then, >>>>>> >>>>>> I configured >>>>>> >>>>>> seeds (ex. >>>>>> >>>>>> Hippocampus), >>>>>> >>>>>> and ran >>>>>> >>>>>> following >>>>>> >>>>>> commands: >>>>>> >>>>>> >>>>>> #fcseed-config >>>>>> >>>>>> -segid 17 >>>>>> >>>>>> -fcname >>>>>> >>>>>> left_hippocampus.dat >>>>>> >>>>>> -fsd rest >>>>>> >>>>>> -mean -cfg >>>>>> >>>>>> left_hippocampus.config >>>>>> >>>>>> >>>>>> #fcseed-sess >>>>>> >>>>>> -s sess01 -cfg >>>>>> >>>>>> left_hippocampus.config >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> It >>>>>> >>>>>> did run >>>>>> >>>>>> smoothly, but >>>>>> >>>>>> what I noticed >>>>>> >>>>>> from >>>>>> >>>>>> fcseed-sess >>>>>> >>>>>> script was it >>>>>> >>>>>> was >>>>>> >>>>>> transforming >>>>>> >>>>>> anatomical >>>>>> >>>>>> aseg mask into >>>>>> >>>>>> functional >>>>>> >>>>>> space. I am >>>>>> >>>>>> confused on >>>>>> >>>>>> this part, >>>>>> >>>>>> because during >>>>>> >>>>>> processing >>>>>> >>>>>> step, we only >>>>>> >>>>>> make >>>>>> >>>>>> registration >>>>>> >>>>>> file for >>>>>> >>>>>> transformation >>>>>> >>>>>> from >>>>>> >>>>>> functional >>>>>> >>>>>> space to >>>>>> >>>>>> anatomical >>>>>> >>>>>> space, but >>>>>> >>>>>> fcseed-sess >>>>>> >>>>>> command needs >>>>>> >>>>>> registration >>>>>> >>>>>> file that >>>>>> >>>>>> moves >>>>>> >>>>>> anatomical >>>>>> >>>>>> scan to >>>>>> >>>>>> functional >>>>>> >>>>>> scan. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> Yes, it just >>>>> >>>>> inverts the >>>>> >>>>> transform to >>>>> >>>>> go in the >>>>> >>>>> opposite >>>>> >>>>> direction >>>>> >>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> # Convert segmentation to native functional space (##from fcseed-sess script##) >>>>>> >>>>>> >>>>>> >>>>>> set cmd = (mri_label2vol --seg $seganat \ >>>>>> >>>>>> >>>>>> >>>>>> --reg $reg --temp $template --fillthresh $FillThresh \ >>>>>> >>>>>> >>>>>> >>>>>> --o $seg --pvf $pvf); >>>>>> >>>>>> >>>>>> >>>>>> echo $cmd | tee -a $LLF >>>>>> >>>>>> >>>>>> >>>>>> Then, Later, during mkanalysis-sess step, the command seems to use functional 2 anatomical transformation. Could you please clarify which registration file it uses to process each step that I talked about above? Do I also need to make anatomical to functional transformation registration? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> No, once it >>>>> >>>>> has a >>>>> >>>>> transformation >>>>> >>>>> in one >>>>> >>>>> direction, it >>>>> >>>>> has it in both >>>>> >>>>> directions >>>>> >>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> I deeply appreciate your help. >>>>>> >>>>>> >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Wenzhen >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> >>>>>> 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 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 > mailto:Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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