You will need to either get the ROIs into the anatomical space or compute a new
registration to the space of the ROIs from the functional template
On 2/22/19 3:43 PM, Francesca Strappini wrote:
External Email - Use Caution
Thanks!
The vox2ras matrices are not same.
This is one region:
francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info
sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
type: nii
dimensions: 64 x 64 x 50
voxel sizes: 3.000000, 3.000000, 3.000000
type: FLOAT (3)
fov: 192.000
dof: 0
xstart: -96.0, xend: 96.0
ystart: -96.0, yend: 96.0
zstart: -75.0, zend: 75.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r = -2.2923
: x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a = 19.4768
: x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s = 25.1269
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-2.9964 0.0704 0.1281 88.1380
0.0373 2.9106 -0.7261 -56.7017
0.1414 0.7237 2.9080 -75.2534
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -27
ras to voxel transform:
-0.3329 0.0041 0.0157 30.7614
0.0078 0.3234 0.0804 23.6988
0.0142 -0.0807 0.3231 18.4853
-0.0000 -0.0000 -0.0000 1.0000
Orig:
francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -2.3092
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 26.4827
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 19.0338
talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 125.6908
0.0000 0.0000 1.0000 -101.5173
0.0000 -1.0000 0.0000 147.0338
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 125.6908
-0.0000 0.0000 -1.0000 147.0338
-0.0000 1.0000 0.0000 101.5173
-0.0000 -0.0000 -0.0000 1.0000
This is the raw T1 to which the regions are registered:
Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz
type: nii
dimensions: 256 x 256 x 192
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -96.0, zend: 96.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r = -2.3092
: x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a = 26.4827
: x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s = 19.0338
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0069 -0.0360 -0.9993 99.1125
-0.9823 0.1874 -0.0000 128.2306
-0.1873 -0.9816 0.0366 165.1330
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0069 -0.9823 -0.1873 157.5619
-0.0360 0.1874 -0.9816 141.6386
-0.9993 0.0000 0.0366 92.9949
-0.0000 -0.0000 -0.0000 1.0000
Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the
conformed anatomical space? Use mri_info can compare the output (particularly
the vox2ras matrix) against orig.mgz. If they are the same, you can try adding
--invertmtx to the mri_label2vol command line.
On 2/22/19 2:24 PM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot, Doug!
I run the preprocessing:
preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
And the runs look well registered.
Then I run mri_label2vol:
mri_label2vol --seg
/home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
--reg register.dof6.lta --temp template.nii.gz --o
sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
The region is in the correct space but completely misaligned. The misalignment
is even bigger than the unregistered region. Maybe I'm not running the function
correctly.
This set of regions are in the same space of the functional data but registered
to the raw T1.
Best
Francesca
Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> ha scritto:
There should be a registration file called register.dof6.lta. Use that with
mri_label2vol passing your segmentation in with --seg. Run with --help to get
more info
On 2/21/19 11:54 AM, Francesca Strappini wrote:
External Email - Use Caution
Thanks a lot!
Running preproc-sess with the --per-session flag is exactly was I was looking
for!
Now that my functional runs are correctly registered to a reference image (so,
to each other) I need to register them to a dataset of ROIs that were created
outside freesurfer. These regions are in volume space and have the same
resolution and box size of the functional runs. They are registered to the T1
that was used for the reconstruction of the surface. I've tried different
functions for the registration but nothing really worked. I suppose I need a
registration matrix that relates these regions to the reference image I used
during the preprocessing and to apply this to each region. What's the best
procedure?
Best
Francesca
Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> ha scritto:
Yes, if you run it with the --targ as orig.mgz for the given subject,
then it will sample each run into the anatomical space (this can create
enourmous data data files!). Alternatively, you can run preproc-sess
with the --per-session flag and it will align all the runs to a single
template but otherwise keep everything in the functional space
On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> I'll try to find some visual way to show what I mean, but it's really
> something mild and probably negligible.
> Do you know if is it possible with mri_vol2vol to give to all the runs
> that belong to the same subject the same system coordinates? So that
> each voxel across runs will have the same coordinates. I noticed that
> the transformation matrix is written in the header but it's not really
> applied to the data. Thank you!
>
>
> Best
> Francesca
>
>
> On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
> <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>> wrote:
>
> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>> ha
> > scritto:
> > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> weighted? If so,
> > you should use --t2 instead of --t1 in bbregister
> >
> > On 2/14/19 2:18 PM, Francesca Strappini wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Doug,
> > >
> > > Could you advise me about how to correctly run mri_vol2vol?
> > > The functional data did not get perfectly registered to
> the anatomy so
> > > I'm afraid I'm not running it correctly.
> > >
> > > Thanks!
> > >
> > >
> > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> > > <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>>>
> ha
> > > scritto:
> > >
> > > Hi Francesca
> > >
> > > sorry, I defer to Doug on the details of mri_vol2vol.
> > >
> > > cheers
> > > Bruce
> > >
> > > On Tue, 12 Feb 2019,
> > > Francesca Strappini wrote:
> > >
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Thank you for the reply!
> > > > I run:
> > > > mri_vol2vol --reg register.dat --mov
> func_data.nii.gz --targ
> > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> > > func_data_registered2T1.nii.gz --no-resample
> > > >
> > > > Then I checked the registration and it seems that
> the original
> > > run is better aligned to the T1 than
> > > > the registered one. Maybe am I not running
> mri_vol2vol correctly?
> > > >
> > > > Thanks!
> > > > Best
> > > >
> > > >
> > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> > >
> <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>>>
> > > ha scritto:
> > > > Hi Francesca
> > > >
> > > > check out the --no-resample option in
> mri_vol2vol. It just
> > > changes the
> > > > header, so I think should do what you want.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Tue, 12 Feb 2019, Francesca Strappini wrote:
> > > >
> > > > >
> > > > > External Email - Use Caution
> > > > >
> > > > > Dear Freesurfer's experts,
> > > > >
> > > > > I would like to register some functional
> data to the T1,
> > > that were collected in
> > > > separate days.
> > > > > I used bbregister:
> > > > >
> > > > > bbregister --s sub3 --mov func_data.nii.gz
> - --reg
> > > register.dat --init-coreg --t1
> > > > >
> > > > > Now, I would like to resample the data
> based on the
> > > register.dat without upsampling
> > > > and keeping the
> > > > > same FoV (3x3x3 mm; 64 64 50). Is it doable?
> > > > >
> > > > > Thanks!
> > > > > Best
> > > > >
> > > > >
> > > > > --
> > > > > Francesca Strappini, Ph.D.
> > > > > Neurobiology Department
> > > > > Weizmann Institute of Science
> > > > > 234 Herzl Street, Rehovot 7610001 Israel
> > > > > Tel.: +972 58 444 2584
> > > > > E-mail:
> francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>
> > >
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>>
> > > > >
> > > > >_______________________________________________
> > > > 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
> > > >
> > > >
> > > >
> > > > --
> > > > Francesca Strappini, Ph.D.
> > > > Neurobiology Department
> > > > Weizmann Institute of Science
> > > > 234 Herzl Street, Rehovot 7610001 Israel
> > > > Tel.: +972 58 444 2584
> > > > E-mail:
> francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>
> > >
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>>
> > > >
> > > >_______________________________________________
> > > 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
> > >
> > >
> > >
> > > --
> > > Francesca Strappini, Ph.D.
> > > Neurobiology Department
> > > Weizmann Institute of Science
> > > 234 Herzl Street, Rehovot 7610001 Israel
> > > Tel.: +972 58 444 2584
> > > E-mail:
> francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>
> > >
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>>
> > >
> > > _______________________________________________
> > > 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
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail:
> francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
>
> <mailto:francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>>
> >
> >_______________________________________________
> 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
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail:
francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
_______________________________________________
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
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail:
francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
_______________________________________________
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
--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail:
francesca.strapp...@weizmann.ac.il<mailto:francesca.strapp...@weizmann.ac.il>
_______________________________________________
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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
