Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

How to get aparcstats2table to output thickness and other parameters
by Salil Soman 04 Dec '13

04 Dec '13

Hi, Is there a way to get aparcstats2table to output all of the information for each subject, including thickness values? Thank you, Salil

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Re: [Freesurfer] Within group hemisphere comparison in QDec
by krista kelly 04 Dec '13

04 Dec '13

Great thanks Douglas! I'm glad that this is available, I wasn't too keen on using the 'flip the brain' method of looking for hemisphere asymmetries. Just a few questions regarding the first step - Apply an existing atlas (fsaverage_sym); this looks like a "for" loop, which I'm not great at figuring out. I would like to know how to actually do this. It seems like I would need to give it a list of all my subjects so that it can go through each subject separately without me having to run each participant separately. Is that correct? If so, and I have 40 participants, I'll need to leave the computer for a few days to do this. Is that correct? Lastly, how do I create the subject list? I tried just creating a list of my subjects using text mate and keeping it in the subjects folder, then using that in place of (subject list). This didn't work. Thanks again! On Sat, Nov 30, 2013 at 2:34 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > yep, we have an existing stream complete with documentation and a > publication you can cite! > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > > > On 11/30/13 12:59 PM, krista kelly wrote: > > Hello, > > I need to do a within group hemisphere comparison to see if there are > any hemisphere asymmetries in a patient group. I would like to do this in > QDec or if possible, somehow do it in freesurfer without using Qdec. I > asked this question two years ago and you mentioned that you were working > on this and it should be available soon. Has there been any progress? > > Thanks! > Krista > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 > > > 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. > >

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manual edits boundary 2 screenshots example for 3T adult
by Kaiming Yin 04 Dec '13

04 Dec '13

Dear guys, I have a simple question in the manual edits parts. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 with Ubuntu 13.10, for a trial on a 3T adult data, and I attached the data 2 screenshot common examples here, personally I am not sure if the wm boundary seems good or not. So I hope if you can help have a look and see if this data has any place need edits. And also usually, for a 3T data like this, how many edits will be approximately needed? I mean will it usually cost several corrections enough? Or 10s? 30s? or even more? Great thanks, Kaiming

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Fwd: Some problems of the brain image after recon-all
by Xiaojun.Huang 04 Dec '13

04 Dec '13

-------- 原始消息 -------- 主题: Some problems of the brain image after recon-all 日期: Tue, 03 Dec 2013 21:33:41 +0800 发件人: Xiaojun.Huang <lvdosha(a)gmail.com> 收件人: Freesurfer(a)nmr.mgh.harvard.edu Hi, I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is reverse. (eg. PDSub_02 in the attach files) It is the first time for me to use Freesurfer.I'm sorry for the trouble I'm giving you.And looking forward your reply. Thanks, Xiaojun 2013.12.3

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Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
by Jon Wieser 04 Dec '13

04 Dec '13

we install freesurfer 5.3 when we run trac-all -prep -c dmrirc the process ends with the error: tkreg2FSL: mov det = -64, ref det = 1 INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Tue Dec 3 13:32:26 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data flirt.fsl -ref /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/refvol.fslregister.nii -in /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Dec 3 13:32:26 CST 2013 flirt.fsl is not in the $FREESURFER_HOME/bin directory Jon ----- Original Message ----- From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> To: "Skyler Gabriel Shollenbarger" <shollen2(a)uwm.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed. You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok? a.y On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > Hi Anastasia, > > We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration? > > Thank you for the fast reply. Truly appreciated. > Skyler > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Skyler Gabriel Shollenbarger" <shollen2(a)uwm.edu> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Sent: Monday, December 2, 2013 4:27:37 PM > Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts > > > Hi Skyler - Are you using freesurfer 5.1 or 5.3? > > Most likely this issue is due to poor registration, either from the > individual DWI to the individual T1, or from the individual T1 to the > template space. Or it could be that there is a problem with the > aparc+aseg. > > a.y > > On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > >> Hi all, >> >> I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. >> See error below: >> >> INFO: Distances between consecutive points are 25 24 25 26 >> WARN: Could not find satisfactory control point fit - try 1665 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> INFO: Length of center streamline is 96 voxels >> Selecting 5 points on center streamline >> INFO: Step is 4 voxels >> WARN: Defaulting to equidistant control points >> INFO: Selected control points are >> 108 193 84 >> 112 173 72 >> 98 153 75 >> 74 157 75 >> 74 184 86 >> INFO: Distances between consecutive points are 24 25 24 29 >> WARN: Could not find satisfactory control point fit - try 1666 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> >> >> Best, >> Skyler >> >> > > > 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 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.

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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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