External Email - Use Caution
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,
Wenzhen
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:
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>
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 Caution
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>
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>
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
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
_______________________________________________
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
_______________________________________________
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
_______________________________________________
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
_______________________________________________
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
_______________________________________________
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer