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:
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Dear 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
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:
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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:
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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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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