Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

1 0

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

2 1

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. > > >

1 0

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 > >

1 0

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/

1 0

delete skull part in GM by tkmedit
by Rujing Zha 03 Dec '13

03 Dec '13

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

1 0

Re: [Freesurfer] mri_vol2surf
by Douglas N Greve 02 Dec '13

02 Dec '13

On 12/01/2013 11:40 PM, Arash Nazeri wrote: > Hi all, > > I wanted to make sure how one could assign intensities from the > subjacent white matter voxels to the cortical surfaces using mri_vol2surf. > > Based on the documentation page --projfrac, if used with negative > values, would assign white matter values to the surface. I was > wondering if this holds true for other options such as projfrac-avg, > projfrac-max, projdist-max ... . Further, I wanted to make sure if the > third value, designated as del, means the minimum value that could be > projected to the surface. > For instance: --projdist-max 0 -4 0.1 means to assign the maximum > value in the distance 0-4 mm of the gray/white matter boundary to the > white matter, that is larger than 0.1 . You basically have the right idea (ie, negative values go into the white matter). I'm not sure exactly what you are asking in your example. If you want to go from the gray/white surface into the WM by 4 mm, I would use --projdist-max -4 0 0.1 or --projdist-max 0 4 -0.1 This will sample along the normal in 40 places spaced 0.1mm apart and return the maximum. Note that this does not assure that all points will be in WM because 4mm may put you into the GM on an adjacent bank (but for a T1 this will be dark so probably does not affect the max). > > In case of the local/global outliers, is there any good way of > finding, discarding, and replacement of these values, through > thresholding+resampling for instance? We don't have anything. > > Finally, I was wondering how it is possible to use these resulting mgh > files for group comparison in an uncached dataset, presumably using > mris_preproc. You can save them in the surf folder and then use "--meas yourfile.mgh" with mris_preproc. I'm not sure what you are aiming for, but David Salat did a similar analysis http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073 This was done using the pctsurfcon program, so you might want to take a look at that doug > > Bests, > Arash > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

Re: [Freesurfer] viewing slices dynamically by tkmedit
by Louis Nicholas Vinke 02 Dec '13

02 Dec '13

Hi Rujing, You can use a tcl script to take several snapshots in tkmedit, then you could use the convert command (part of ImageMagick distro) or something similar to create an animated gif. With the convert command you would use the -adjoin and -delay flags. You could use one of the tcl scripts from the QA tools scripts as a good start (e.g. snap_tkmedit.tcl). You could also get multiple snapshots with freeview using command line flags and a shell script. -Louis On Sat, 30 Nov 2013, Rujing Zha wrote: > Dear all, > I want to see the slices as a shape of movie in tkmedit. Do anyone can tell > me how to do it? > Thanks. > All the best. > > 2013-11-30 > > ____________________________________________________________________________ > Rujing Zha > >

3 2

Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
by Anastasia Yendiki 02 Dec '13

02 Dec '13

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 > >

1 0

Re: [Freesurfer] Which boost version is used in CVS, mris_resample
by Martin Kavec 02 Dec '13

02 Dec '13

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@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 >>>> >>>> >>>> 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 >> >>

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer