[Freesurfer] tkmeditParcColorsCMA
Dear Freesurfer, Is it possible to obtain a label image with tkmeditParcColorsCMA regions, similar to aseg+aparc.mgz or aparc.a2009s+aseg.mgz ? If so how should I proceed ? Thank you in advance. Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] problem with createMorph
Dear freesurfer experts, when running the createMorph function an error of shared libraries occur. createMorph: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory I searched for such shared library and although I have a different version I do not have this specific. /usr/lib/libboost_program_options-mt.so /usr/lib/libboost_program_options.so.1.49.0_orig /usr/lib/libboost_program_options-mt.a /usr/lib/libboost_program_options.so /usr/lib/libboost_program_options.so.1.49.0 /usr/lib/libboost_program_options.a Updating the libboost did not worked and I couldn’t find any useful suggestion on the web. I am running freesurfer under Ubuntu 13.04 I would appreciate any suggestion. Cheers, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problem with createMorph
Hi Lilla, Thank you for your reply. I have boost installed, yet it is not the version required (v. 1.49). Although, even after installing an older version such as the 1.41 it is not straightforward to use this libboost with freesurfer. The doc from libboost is not easy to understand and even if done correctly you will not be able to use this installation as there is no libboost_program_options.so.5. Nevertheless, I got it to work so here goes the solution that worked for me. >Download libboost v. 1.41 and untar >cd libboost_folder >mkdir libraries >./bootstrap.sh --prefix=./libraries >./bjam install >cd libraries/lib > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5 >export LD_LIBRARY_PATH=.../boost_temp/boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH Cheers, Andre Santos Ribeiro On Wed, Nov 27, 2013 at 5:19 PM, Lilla Zollei wrote: > > Hi Andre, > > I posted the below on Monday on the list: > > The boost library is installed by default on CentOS platforms. If a user > gets the libboost error then they are using a different platform which > doesn't have boost installed by default. On RedHat systems libboost can be > installed by typing the follwing command: > $>yum install boost-devel" > > The version of libboost that we use for our latest release is 1.41. > > I hope that helps, > > --Lilla > > > On Wed, 27 Nov 2013, André Ribeiro wrote: > > Dear freesurfer experts, >> >> when running the createMorph function an error of shared libraries occur. >> >> createMorph: error while loading shared libraries: >> libboost_program_options.so.5: cannot open shared object file: No such file >> or directory >> >> I searched for such shared library and although I have a different >> version I do not have this specific. >> >> /usr/lib/libboost_program_options-mt.so >> /usr/lib/libboost_program_options.so.1.49.0_orig >> /usr/lib/libboost_program_options-mt.a >> /usr/lib/libboost_program_options.so >> /usr/lib/libboost_program_options.so.1.49.0 >> /usr/lib/libboost_program_options.a >> >> Updating the libboost did not worked and I couldn’t find any useful >> suggestion on the web. >> >> I am running freesurfer under Ubuntu 13.04 I would appreciate any >> suggestion. >> >> Cheers, >> Andre Santos Ribeiro >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Which boost version is used in CVS, mris_resample
Hi Martin, In November 27 I posted a similar question, which later I found a solution. See if it works for you. Hi Lilla, > Thank you for your reply. I have boost installed, yet it is not the > version required (v. 1.49). Although, even after installing an older > version such as the 1.41 it is not straightforward to use this libboost > with freesurfer. The doc from libboost is not easy to understand and even > if done correctly you will not be able to use this installation as there is > no libboost_program_options.so.5. Nevertheless, I got it to work so here > goes the solution that worked for me. > >Download libboost v. 1.41 and untar > >cd libboost_folder > >mkdir libraries > >./bootstrap.sh --prefix=./libraries > >./bjam install > >cd libraries/lib > > ln -s libboost_program_options.so.1.41.0 libboost_program_options.so.5 > >export LD_LIBRARY_PATH=.../boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH > Cheers, > Andre Santos Ribeiro regards, Andre Santos Ribeiro On Mon, Dec 2, 2013 at 9:57 PM, Martin Kavec wrote: > Hi Zeke, > > Thanks a lot for explanation. I think I will install centOS into a virtual > machine for quick solution. I only need it to run CVS. > > Thanks and best regards, > > Martin > > Sent from my iPad > > > On 2.12.2013, at 22:50, Z K wrote: > > > > Martin, > > > > Upx (http://upx.sourceforge.net) is an executable packaging utility we > run on all our binaries before shipping to reduce their overall size. One > consequence of upx is that it changes the way the "file" and "ld" commands > process the binaries. In this case it makes the "file" command say they are > statically linked when infact it is dynamically linked. You can view this > for yourself by running upx in reverse (upx -d mris_resample) and indeed > you will see that it says dynamically linked. > > > > libboost1.41 is what comes by default on our centOS6_x86_64 platforms > and it is what freesurfer builds against. All I can suggest is that you > install the same version, or one very close to it. > > > > -Zeke > > > > > > > >> On 12/02/2013 02:50 PM, Martin Kavec wrote: > >> Hi Zeke, > >> > >> Thanks for response. Well it was the first thing for me to try to > compile boost on gentoo, which went fine. However the libraries were not > compatible. Gentoo has 1.52 version, while the one needed is about 4 years > old. > >> > >> When I do "ldd mris_resample" I get "not a dynamic executable" and when > I do "file mris_resample" I get that it is a statically linked executable, > stripped. I think something could have happened with when stripping the > executable. I get the same output from file mris_rescale, but mris_rescale > runs fine. > >> > >> I am using Freesurfer-5.3.0 for Centos6 x86_64. > >> > >> Thanks, > >> > >> Martin > >> > >> Sent from my iPad > >> > >>> On 2.12.2013, at 17:33, Z K wrote: > >>> > >>> Martin, > >>> > >>> libboost is not a static library, it is a shared library. It comes by > >>> default on centOS platforms and freesurfer compiles against it during > >>> the the build process. Typing 'ldd mris_resample' and examining the > >>> output confirms this: > >>> > >>> $>ldd mris_resample > >>> linux-vdso.so.1 => (0x7fffd2773000) > >>> libboost_program_options.so.5 => > >>> /usr/lib64/libboost_program_options.so.5 (0x7fe2e588d000) > >>> etc... > >>> > >>> Also, many of the freesurfer binaries do require the libboost library. > >>> > >>> Freesurfer works on most linux distribution, but we specifically build > >>> on and support centOS platforms. We do not have Gentoo linux machines > to > >>> try and replicate your error but I am confident that if you get the > >>> libboost libraries on your machine, the program will work properly. > >>> > >>> -Zeke > >>> > >>> > >>> > >>> > On 11/28/2013 05:09 PM, Martin Kavec wrote: > Hi Lilla, > > thanks for coming back. Unfortunately I was not able to compile > appropriate boost for my operating system Gentoo linux. Nevertheless I > do not understand why mris_resample misses the library if it should be > statically linked. Other binaries do not need it. Could you please > check > if mris_resample in 64-bit linux version of CentOS is correct? > > Otherwise I cannot run cvs. > > Thanks a lot, > > Martin > > > On Mon, Nov 25, 2013 at 5:32 PM, Lilla Zollei > mailto:lzol...@nmr.mgh.harvard.edu>> > wrote: > > > This is a bit delayed response (my apologies) to an earlier > question to > the list: > > The boost library is installed by default on CentOS platforms. If > a user > gets the libboost error then they are using a different platform > which > doesn't have boost installed by default. On RedHat systems libboost > can be > installed by typing the follwing command: > $>yum install boost-devel" > > The version of libboost that we use for our latest release is 1.41. > > Lilla >
[Freesurfer] Jacobian mri_cvs_register
Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Jacobian mri_cvs_register
Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei wrote: > > Hi Andre > > You can run: > > mri_jacobian -tm3d <3d morph> > > --Lilla > > > On Thu, 10 Jul 2014, André Ribeiro wrote: > > Dear Freesurfer Community, >> >> How can I obtain the Jacobian of the deformation field estimated through >> mri_cvs_register for further use like VBM analysis? >> >> >> Regards, >> Andre Santos Ribeiro >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Jacobian mri_cvs_register
I got an error using the mri_jacobina. The function returns: The input morph originated from a tm3d (mri_cvs_register file). GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d The command is provided below: mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro wrote: > Thank you! Didn't realized that function existed. > > Regards, > Andre Santos Ribeiro > > On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei > wrote: > >> >> Hi Andre >> >> You can run: >> >> mri_jacobian -tm3d <3d morph> >> >> --Lilla >> >> >> On Thu, 10 Jul 2014, André Ribeiro wrote: >> >> Dear Freesurfer Community, >>> >>> How can I obtain the Jacobian of the deformation field estimated through >>> mri_cvs_register for further use like VBM analysis? >>> >>> >>> Regards, >>> Andre Santos Ribeiro >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Jacobian mri_cvs_register
Thank you for the explanation but in that case there are two things that seems odd. First, in the mri_cvs_register I kept all the files and therefore the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" file was not removed. If I try to replicate this file through the "createMorph --out fullCVSmorph.tm3d --template template.mgz --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph el_reg_toTEMPLATE.tm3d" the file produced is different from the one previously created by the program (and gives far worse registration results when used with the "applyMorph"). Is something wrong here? Second, even if the two files gave the same results wouldn’t this fullCVSmorph.tm3d (otherwise called combined_toIBSR_02_elreg_afteraseg-norm.tm3d) have both information from *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, and therefore the Jacobian applied solely to the nlalign-afteraseg-norm.m3z would not match. Lastly, am I right assuming the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" is the last registration (and most accurate) performed by mri_cvs_register? Regards, Andre Santos Ribeiro On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei wrote: > > Hi, You should use the final m3z file. The -tm3d flag just indicates that > the file was created by mri_cvs_register. > Lilla > > > On Fri, 11 Jul 2014, André Ribeiro wrote: > > I got an error using the mri_jacobina. >> The function returns: >> >> The input morph originated from a tm3d (mri_cvs_register file). >> GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): >> invalid version # 0.000 >> >> mri_jacobian: could not read input morph /home/afs13/Documents/data/ >> test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d >> >> >> The command is provided below: >> mri_jacobian -tm3d /home/afs13/Documents/data/ >> test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d >> /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz >> /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz >> >> Regards, >> Andre Santos Ribeiro >> PhD Student, Imperial College London >> >> >> >> On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro >> wrote: >> Thank you! Didn't realized that function existed. >> >> Regards, >> Andre Santos Ribeiro >> >> On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei < >> lzol...@nmr.mgh.harvard.edu> wrote: >> >> Hi Andre >> >> You can run: >> >> mri_jacobian -tm3d <3d morph> >> >> --Lilla >> >> On Thu, 10 Jul 2014, André Ribeiro wrote: >> >> Dear Freesurfer Community, >> >> How can I obtain the Jacobian of the deformation field >> estimated through mri_cvs_register for further use like VBM analysis? >> >> >> Regards, >> Andre Santos Ribeiro >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Jacobian mri_cvs_register
Hi, Ok so most of my problems are now fixed, but there is still one problem regarding the Jacobian. So first of all my images were normalized as follows: createMorph --out fullCVSmorph.tm3d --template f2/mri/brain.mgz --subject f1/mri/brain.mgz --in gcam combined_tof2_elreg_afteraseg-norm.m3z applyMorph --template f2/mri/brain.mgz --transform fullCVSmorph.tm3d vol f1/mri/brain.mgz reg_f1_brain.nii.gz trilinear then for the Jacobian: mri_jacobian -tm3d combined_tof2_elreg_afteraseg-norm.m3z f1_brain.nii.gz jacobian.nii.gz Now if I visualize both the reg_f1_brain.nii.gz and jacobian.nii.gz they do not seem to match voxel-wise, and therefore cannot be applied for VBM. Both the jacobian and the registered t1 brain image use the same transform and therefore should be aligned. Am I making some mistake here? Sorry for this question in advance. Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei wrote: > > Hi, > > > First, in the mri_cvs_register I kept all the files and therefore the >> "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" file was not removed. If >> I try to replicate this file through the >> "createMorph --out fullCVSmorph.tm3d --template template.mgz --subject >> movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph >> el_reg_toTEMPLATE.tm3d" the file produced is different from the one >> previously created by the program (and gives far worse registration results >> when used with the "applyMorph"). Is >> something wrong here? >> > > No, there is nothing wrong. In the above command you are just not > composing the right files. I assume that you have run the default > mri_cvs_register command. In that case there are two non-linear > registration steps one aided by aseg info and one by intensities. In the > above you are skipping the morph created by the former so that is why you > are not getting the same combined output. Instead of "morph > el_reg_toTEMPLATE.tm3d" you would need to use "morph combined*aseg.tm3d" > > > Second, even if the two files gave the same results wouldn’t this >> fullCVSmorph.tm3d (otherwise called >> combined_toIBSR_02_elreg_afteraseg-norm.tm3d) >> have both information from *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, >> and therefore the Jacobian applied solely to the nlalign-afteraseg-norm.m3z >> would not >> match. >> > > It is correct. The jacobians of fullCVSmorph.tm3d and > nlalign-afteraseg-norm.m3z will not match. I am a bit confused about whey > you think they should. > > > Lastly, am I right assuming the > "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" >> is the last registration (and most accurate) performed by mri_cvs_register? >> > > Yes. In the most current FS version though we use the m3z files as we are > trying to phase out the tm3d format. > > Lilla > > > On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei < >> lzol...@nmr.mgh.harvard.edu> wrote: >> >> Hi, You should use the final m3z file. The -tm3d flag just >> indicates that the file was created by mri_cvs_register. >> Lilla >> >> On Fri, 11 Jul 2014, André Ribeiro wrote: >> >> I got an error using the mri_jacobina. >> The function returns: >> >> The input morph originated from a tm3d (mri_cvs_register >> file). >> GCAMread(/home/afs13/Documents/data/test_ >> freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # >> 0.000 >> >> mri_jacobian: could not read input morph >> /home/afs13/Documents/data/test_freesurfer_reg/combined_ >> toIBSR_02_elreg_aseg.tm3d >> >> >> The command is provided below: >> mri_jacobian -tm3d /home/afs13/Documents/data/ >> test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d >> /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz >> /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz >> >> Regards, >> Andre Santos Ribeiro >> PhD Student, Imperial College London >> >> >> >> On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro < >> af...@imperial.ac.uk> wrote: >> Thank you! Didn't realized that function existed. >> >> Regards, >> Andre Santos Ribeiro >> >> On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei < >> lzol...@nmr.mgh.harvard.edu> wrote: >> >> Hi Andre >> >> You can r
Re: [Freesurfer] Fwd: Jacobian mri_cvs_register
Hi Lilla, Thank you for your response. I would argue that they seem to be aligned, yet they are not. If you look at the cerebellum the Jacobian is shifted in respect to the brain_IBSR_01.mgz. Further, there must be a jacobian for each voxel of the brain_IBSR_01.mgz (at least inside the brain mask), which does not happen (the box is smaller than the brain). Though, I will not discuss this point again. Just as final note, if anyone want to retrieve the deformation field, a simple way is to virtually create a 4d image that encode the position of each voxel (3 x 3d images), deform this images using the applyMorph, and subtract the initial virtual 4d image. The Jacobian matrix can also be calculated through this fields. Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Wed, Aug 6, 2014 at 3:35 PM, Lilla Zollei wrote: > > Hi Andre, > > The jacobian field is computed in the coordinate space of the moving > volume so if you overlay it with brain_IBSR_01.mgz, you will see that they > match. > > We currently do not have an executbale in 5.3 that writes out the m3z > transforms in nifti format. > > > Lilla > > On Tue, 5 Aug 2014, André Ribeiro wrote: > > Hi, >> >> The Freesurfer that I am using is: freesurfer-Linux-centos6_x86_ >> 64-stable-pub-v5.3.0. >> >> The source, target, registered, Jacobian images and deformation field are >> provided in attachment. >> >> I mean with voxel-wise that by visualizing both (overlayed) there is a >> shift between the Jacobian and the registered image. I used the same image >> as target so I would suspect that it is not a header problem (though did >> not used a different viewer). Additionally, by looking at the Jacobian (and >> assuming this is >> correct) the algorithm seems to relaxed allowing really high and low >> jacobians. >> >> Further, how can I obtain the deformation fields in a nifti format? >> >> >> >> [icon_10_generic_list.png] combined_toIBSR_02_elreg_afteraseg-norm.m3z >> >> [icon_10_generic_list.png] brain_IBSR_02.mgz >> >> [icon_10_generic_list.png] brain_IBSR_01.mgz >> >> [icon_10_generic_list.png] reg_IBSR_01_2_IBSR_02_brain.nii.gz >> >> [icon_10_generic_list.png] jacobian.nii.gz >> >> >> >> Regards, >> Andre Santos Ribeiro >> PhD Student, Imperial College London >> >> >> >> On Tue, Aug 5, 2014 at 4:24 PM, Lilla Zollei >> wrote: >> >> Hi Andre, >> >> What do you mean by they "do not seem to match voxel-wise"? Are >> they of different size or are they not in a corresponding space? >> >> Which version of FreeSurfer are you using? >> >> Could you send the volumes over? I don't see anything wrong with >> the commands so I would like ot take a look at the files. >> >> Lilla >> >> On Tue, 5 Aug 2014, André Ribeiro wrote: >> >> Hi, >> >> Ok so most of my problems are now fixed, but there is still >> one problem regarding the Jacobian. >> >> So first of all my images were normalized as follows: >> createMorph --out fullCVSmorph.tm3d --template >> f2/mri/brain.mgz --subject f1/mri/brain.mgz --in gcam >> combined_tof2_elreg_afteraseg-norm.m3z >> applyMorph --template f2/mri/brain.mgz --transform >> fullCVSmorph.tm3d vol f1/mri/brain.mgz reg_f1_brain.nii.gz trilinear >> >> then for the Jacobian: >> mri_jacobian -tm3d combined_tof2_elreg_afteraseg-norm.m3z >> f1_brain.nii.gz jacobian.nii.gz >> >> Now if I visualize both the reg_f1_brain.nii.gz and >> jacobian.nii.gz they do not seem to match voxel-wise, and therefore cannot >> be applied for VBM. Both the jacobian and the registered t1 brain image use >> the same transform and therefore should be aligned. Am I making some >> mistake here? >> >> Sorry for this question in advance. >> >> Regards, >> Andre Santos Ribeiro >> PhD Student, Imperial College London >> >> >> >> On Fri, Jul 11, 2014 at 4:11 PM, Lilla Zollei < >> lzol...@nmr.mgh.harvard.edu> wrote: >> >> Hi, >> >> First, in the mri_cvs_register I kept all the >> files and therefore the "combined_toIBSR_02_elreg_afteraseg-norm.tm3d" >> file was not removed. If I try to replicate this file through the >> "createMorph --out fullCVSmorph.tm3d
