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Dear Douglas,On Sep 18, 2020, at 12:40 PM, Douglas N. Greve <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 $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.
On 9/18/2020 12:15 PM, Wenzhen Zhao wrote:
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Dear Douglas,
Yes, they do look properly oriented to me.one thing I noticed is that when I switch over coronal view, sagittal view, and axial view, brains seem to shift back and forth in horizontal direction. If you see the picture below, brains are not in the same spot. I am not sure if this is an issue.
Best,Wenzhen<Screen Shot 2020-09-18 at 12.04.54 PM.png>
On Sep 18, 2020, at 10:47 AM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:
Is the fmri scan properly oriented? Eg, run freeview template.nii.gz and see of it is oriented correctly in the FV window
On 9/15/20 2:57 PM, Wenzhen Zhao wrote:
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_______________________________________________Dear Douglas,
I am using freesurfer 6. I used following command to register fMRI data to anatomical scan.$ 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
<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> 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> 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> wrote:
_______________________________________________
On 9/15/2020 11:26 AM, Wenzhen Zhao wrote:
Yes, it just inverts the transform to go in the opposite directionExternal 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.
No, once it has a transformation in one direction, it has it in both directions# 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 $LLFThen, 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?
I deeply appreciate your help.Sincerely,Wenzhen
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