External Email - Use Caution Hi Doug,
Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks! Best Francesca On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrapp...@gmail.com> wrote: > What is the best procedure? I really have no idea, I've been tried so many > things but nothing worked... > > Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> ha scritto: > >> 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> 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> 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> 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>> >>>>> 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>> 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>>> 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>>> >>>>> > > > 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>> >>>>> > > > > > >>>>> > > > > >_______________________________________________ >>>>> > > > > 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 >>>>> > > > >>>>> > > > >>>>> > > > >>>>> > > > -- >>>>> > > > 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> >>>>> > > > >>>>> 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 >>>>> > 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 >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing >>>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >>> >>> >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> >> >> >> -- >> 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 >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > > -- > 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 >
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