Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Re: [Freesurfer] recon-all strip skull and neck by brain volume mask
by Rujing Zha 03 Dec '13

03 Dec '13

Dear Louis, Thanks for your helpful suggestions. I will try. All the best. 2013-12-04 Rujing Zha 发件人：Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> 发送时间：2013-12-03 23:13 主题：Re: Re: [Freesurfer] recon-all strip skull and neck by brain volume mask 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing, If portions of gray matter have been removed, then that will need to be corrected. You can definitely remove skull/dura manually from the brainmask.mgz volume (see link below), but that can be time-consuming and may not be necessary. It's hard to know for sure if a brainmask.mgz is bad until you have generated the surfaces or have some experience with similar cases processed with Freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Tue, 3 Dec 2013, Rujing Zha wrote: > Dear Louis, > Thanks for your helpful prompt in advance. > I see. In my case, there is a not properly stripping, there is a not > properly gray matter(there are a some skull considered as gray matter). Did > you mean I can draw the segmentation without considering the skull > stripping? And a bad brainmask.mgz will not influence the GM thickness > analysis? > Thanks in advance. > All the best. > > 2013-12-03 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-03 03:58 > 主题：Re: [Freesurfer] recon-all strip skull and neck by brain volume mask > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > Hi Rujing, > Even if there is some skull/dura left after the skullstrip step in > recon-all, it still may not negatively impact the surfaces. It might be > worth running the remaining recon-all steps to see how the surfaces turn > out. > > If you want to swap-in a better skullstripped volume into the recon-all > stream then you just need to replace the brainmask.mgz and continue with > autorecon2 and autorecon3. > > Keep in mind that the new brainmask.mgz volume still needs to be in the > conformed anatomical space, so use the T1.mgz or brainmask.mgz to create > the improved skullstrip volume which will replace the existing > brainmask.mgz. > > -Louis > > On Mon, 2 Dec 2013, Rujing Zha wrote: > > > Dear all, > > Part of subjects 3d images cannot be stripped skull and neck properly in ?? ?> recon-all default. I have got the brain volume mask, how I can using the ?? ?> existing proper mask to help strip skull in recon-all and next workflow? ?? ?> Thanks.Any reply will be appreciated. > > All the best. > > > > 2013-12-02 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

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Re: [Freesurfer] Which boost version is used in CVS, mris_resample
by Martin Kavec 03 Dec '13

03 Dec '13

Hi Andre, fantastic advice! You made my day! I followed instructions and so far so good, cvs is running. Thanks a lot, Martin On Tue, Dec 3, 2013 at 12:09 AM, André Ribeiro <andrefsr(a)gmail.com> wrote: > 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 <martin.kavec(a)gmail.com>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 <zkaufman(a)nmr.mgh.harvard.edu> 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 <zkaufman(a)nmr.mgh.harvard.edu> 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 => (0x00007fffd2773000) >> >>> libboost_program_options.so.5 => >> >>> /usr/lib64/libboost_program_options.so.5 (0x00007fe2e588d000) >> >>> 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 >> >>>> <lzollei(a)nmr.mgh.harvard.edu <mailto:lzollei@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 >> >>>> >> >>>> --------------------------------------------- >> >>>> Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800 >> >>>> >> >>>> Hi guys, >> >>>> >> >>>> When running mri_cvs_register on linux (5.3.0), I get into >> problem with >> >>>> mris_resample, which cannot find libboost_programs_options.so.5. I >> >>>> installed >> >>>> the latest version of boost-1.52.0 for my system, but there are >> >>>> unresolved >> >>>> symbols. >> >>>> >> >>>> Which version is suitable for mris_resample? >> >>>> >> >>>> Thanks, >> >>>> >> >>>> Martin >> >>>> >> >>>> Sent from my iPad >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto: >> Freesurfer(a)nmr.mgh.harvard.edu> >> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto: >> Freesurfer(a)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(a)nmr.mgh.harvard.edu >> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer(a)nmr.mgh.harvard.edu >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >

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Re: [Freesurfer] Which boost version is used in CVS, mris_resample
by Z K 03 Dec '13

03 Dec '13

Thank you Andre for this information. -Zeke On 12/02/2013 06:12 PM, André Ribeiro wrote: > 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 <martin.kavec(a)gmail.com > <mailto:martin.kavec@gmail.com>> 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 <zkaufman(a)nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu>> 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 <zkaufman(a)nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu>> 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 => (0x00007fffd2773000) > >>> libboost_program_options.so.5 => > >>> /usr/lib64/libboost_program_options.so.5 (0x00007fe2e588d000) > >>> 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 > >>>> <lzollei(a)nmr.mgh.harvard.edu > <mailto:lzollei@nmr.mgh.harvard.edu> > <mailto:lzollei@nmr.mgh.harvard.edu > <mailto:lzollei@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 > >>>> > >>>> --------------------------------------------- > >>>> Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800 > >>>> > >>>> Hi guys, > >>>> > >>>> When running mri_cvs_register on linux (5.3.0), I get into > problem with > >>>> mris_resample, which cannot find > libboost_programs_options.so.5. I > >>>> installed > >>>> the latest version of boost-1.52.0 for my system, but there are > >>>> unresolved > >>>> symbols. > >>>> > >>>> Which version is suitable for mris_resample? > >>>> > >>>> Thanks, > >>>> > >>>> Martin > >>>> > >>>> Sent from my iPad > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)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(a)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 > >>>> > >>>> > >>>> 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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Units of coordinates in freeview
by pfotiad＠nmr.mgh.harvard.edu 03 Dec '13

03 Dec '13

Great, thanks Bruce! Panos > yes, they should be > On Tue, 3 Dec 2013, pfotiad(a)nmr.mgh.harvard.edu wrote: > >> Hi Bruce, >> >> Yes, I have already resampled my images into 1mm isometric voxel size, >> so >> all of the three reported coordinates must be in mm right? >> >> Thanks, >> Panos >> >>> the RAS and TkRegRAS are mm, the voxel coords are not (unless your >>> acquisition is 1mm isotropic) >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 3 Dec 2013, pfotiad(a)nmr.mgh.harvard.edu wrote: >>> >>>> Hi FS experts, >>>> >>>> When I open a file with freeview, are the coordinates reported in the >>>> third row under Cursor (right under RAS and TkReg RAS) in mm? >>>> >>>> Thank you for your time, >>>> Panos >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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Units of coordinates in freeview
by pfotiad＠nmr.mgh.harvard.edu 03 Dec '13

03 Dec '13

Hi FS experts, When I open a file with freeview, are the coordinates reported in the third row under Cursor (right under RAS and TkReg RAS) in mm? Thank you for your time, Panos

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area of a fsaverage label
by Yolanda Vives 03 Dec '13

03 Dec '13

Dear FreeSurfer experts, I would like to know the area of some manually drawn labels, obtained with QDEC over fsaverage. I have used the following scripts, but I had errors in both of them. - label_area. It doesn't work because it requires surf/lh.smoothwm, which is not present in fsaverage. - mris_anatomical_stats. It doesn't work because it requires mri/wm.mgz, which is also not present in fsaverage. How could I obtain this information? Thank you in advance for your help, Yolanda

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mri_surf2vol in fsaverage space
by Govindarajan, Koushik Athreya 03 Dec '13

03 Dec '13

Dear Freesurfers, I am trying to export the cortical thickness maps in nifti format using the mri_surf2vol command. Is it possible to get these output files in the fsaverage space (1x1x1 mm3) instead of the native space. Thanks Koushik

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Re: [Freesurfer] view inflated surfer by tksurfer
by Bruce Fischl 03 Dec '13

03 Dec '13

I meant "mris_info" not "mri_info". What is your hardware environment? Are you connecting over ssh or something? I guess the simplest thing to try is clicking the "redraw" key in tksurfer after it comes up On Tue, 3 Dec 2013, Rujing Zha wrote: > Dear Bruce, > Thanks for your help. > The size is about 4MB. I am so sorry about poor understanding what you said > "mri_info", but I attach the command line message in the attachment. I can > see that in freeview. > Thanks. > All the best. > > 2013-12-03 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-03 21:26 > 主题：Re: [Freesurfer] view inflated surfer by tksurfer > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > what is the size of the file? What does mris_info tell you about it? Can > you view it in freeview with > > freeview -f $SUBJECTS_DIR/$subject/surf/rh.inflated > > then change to 3D viewing? > > On Tue, 3 Dec > 2013, Rujing Zha wrote: > > > Dear all, > > After recon-all, I want to view the inflated volume by > > > > tksurfer subject rh inflated > > , but there is nothing in Display Window. I checked the file does exist i > n > > the surf directory. That is why? > > Thanks. > > All the best. > > > > 2013-12-03 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

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Re: [Freesurfer] view inflated surfer by tksurfer
by Bruce Fischl 03 Dec '13

03 Dec '13

what is the size of the file? What does mris_info tell you about it? Can you view it in freeview with freeview -f $SUBJECTS_DIR/$subject/surf/rh.inflated then change to 3D viewing? On Tue, 3 Dec 2013, Rujing Zha wrote: > Dear all, > After recon-all, I want to view the inflated volume by > > tksurfer subject rh inflated > , but there is nothing in Display Window. I checked the file does exist in > the surf directory. That is why? > Thanks. > All the best. > > 2013-12-03 > > ____________________________________________________________________________ > Rujing Zha > >

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Re: [Freesurfer] delete skull part in GM by tkmedit
by Rujing Zha 03 Dec '13

03 Dec '13

Dear Gabriel, I read the PialEdits_tktools, but I want to know whether it will determine surrounding voxels belonging to skull regions based on the voxels I have signed by brush? If it does, that is what I need. Thanks. All the best. 2013-12-03 Rujing Zha 发件人：Gabriel Gonzalez Escamilla <ggonesc(a)upo.es> 发送时间：2013-12-03 20:17 主题：Re: [Freesurfer] delete skull part in GM by tkmedit 收件人："Rujing Zha"<charujing123(a)163.com> 抄送： Rujing, Have you tryed the tutorial? http://freesurfer.net/fswiki/FsTutorial/PialEdits_tktools You just need to edit the brain mask and then run again some parts of the recon-all Bests, Gabriel ----- Mensaje original ----- De: Rujing Zha <charujing123(a)163.com> Fecha: Martes, 3 de Diciembre de 2013, 8:46 am Asunto: [Freesurfer] delete skull part in GM by tkmedit A: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Dear all, > I have read the troubleshooting in the website http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_tktools. I want to know if thereis a similar method to remove skull part in GM? I donot want to use -gcut and watershed option. I think control point method is better than -gcut option in my case. > Thanks, > All the best. > > 2013-12-03 > Rujing Zha > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. -------------------------- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggonesc(a)upo.es http://www.upo.es/neuroaging/es/

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