Freesurfer

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Remove From List
by Andrés Camarena 22 Feb '11

22 Feb '11

Remove from list amco1027(a)gmail.com

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Re: [Freesurfer] installation problem in ubuntu
by Pedro Paulo de Magalhães Oliveira Junior 21 Feb '11

21 Feb '11

run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> > Thanks Pedro, > > How I uninstall that version to re-install the correct version? > I look for some answers and try > > rm -rf $FREESURFER_HOME > > It says that I don't have permission,how I can unistall it, if i'm the > admin user? > > Thanks in advance, > > Carolina > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS >> >> >> 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> >> >> >>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >>> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >>> >>> Thanks, >>> >>> >>> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br >>> > >>> >>> Please send the result of the command: >>>> >>>> uname -a >>>> >>>> >>>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>>> cvalencia(a)linkdx.com.co> wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> I'm experimenting problems with the installation on Ubuntu too. >>>>> There's is warning in the welcome message, it seems that something is >>>>> missing: >>>>> >>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>>>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>>>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>>>> FSF_OUTPUT_FORMAT nii >>>>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>>>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>>>> FSL_DIR /usr/share/fsl/4.1 >>>>> >>>>> >>>>> I try to test it and it shows >>>>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit >>>>> /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de >>>>> ejecutable incorrecto. Binary file not executable. >>>>> >>>>> Thanks a lot, >>>>> >>>>> Carolina >>>>> >>>>> 2011/2/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>> >>>>>> Hi Jie, >>>>>> >>>>>> what hardware are you using? Is it a 64 bit operating system? >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> On Sat, 19 Feb 2011, Liukarl wrote: >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Hello, Freesurfer experts: >>>>>>> >>>>>>> >>>>>>> >>>>>>> I am new to freesurfer and try to >>>>>>> install the newest version of freesurfer in Ubuntu system. I closely >>>>>>> followed the instructions, and the only difference is that I >>>>>>> installed it in my Documents, instead of local folder. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Below is the output after “source >>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh” >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------- >>>>>>> freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- >>>>>>> >>>>>>> Setting up environment for >>>>>>> FreeSurfer/FS-FAST (and FSL) >>>>>>> >>>>>>> FREESURFER_HOME >>>>>>> /home/jie/Documents/freesurfer/ >>>>>>> >>>>>>> FSFAST_HOME >>>>>>> /home/jie/Documents/freesurfer//fsfast >>>>>>> >>>>>>> FSF_OUTPUT_FORMAT nii >>>>>>> >>>>>>> SUBJECTS_DIR >>>>>>> /home/jie/Documents/freesurfer//subjects >>>>>>> >>>>>>> MNI_DIR >>>>>>> /home/jie/Documents/freesurfer//mni >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Everything seems fine and I also added >>>>>>> the .license file to the freesurfer folder. >>>>>>> >>>>>>> >>>>>>> >>>>>>> But when I test it by “tkmedit bert >>>>>>> orig.mgz”, it reponds “Illegal instruction” >>>>>>> >>>>>>> >>>>>>> >>>>>>> If I type in “recon-all”, it will >>>>>>> show >>>>>>> >>>>>>> “ Required Arguments: >>>>>>> >>>>>>> -subjid <subjid> >>>>>>> >>>>>>> -<process directive>…... >>>>>>> ” >>>>>>> and the other arguments. >>>>>>> >>>>>>> >>>>>>> >>>>>>> How to fix the problem and make >>>>>>> Fressurfer run? Any help is appreciated. Thanks a lot! >>>>>>> >>>>>>> >>>>>>> >>>>>>> Jie >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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. >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> _______________________________________________ >>>>> 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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mri_mask
by Gabriel Go.Es. 21 Feb '11

21 Feb '11

Hello Freesurfers, I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after doing some manual segmentation corrections by using mri_mask command, I have donne it before and it always works but with this subject, the command line is excacly the same so I have no idea what could be wrong: mri_mask rawavg.mgz brain.mgz outbrain.mgz ERROR: dimension mismatch between source and mask. Can any one help me with this? Bests, Gabriel

2 1

volume of CSF for hemispheres
by Tetiana Dadakova 21 Feb '11

21 Feb '11

Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, Tanja.

3 5

fixing hippocampus segmentation
by Tetiana Dadakova 21 Feb '11

21 Feb '11

Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, Tanja.

2 1

Re: [Freesurfer] installation problem in ubuntu
by Pedro Paulo de Magalhães Oliveira Junior 21 Feb '11

21 Feb '11

It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia <cvalencia(a)linkdx.com.co> > > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae > #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux > > Thanks, > > > 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > > Please send the result of the command: >> >> uname -a >> >> >> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia <cvalencia(a)linkdx.com.co >> > wrote: >> >>> Hi Bruce, >>> >>> I'm experimenting problems with the installation on Ubuntu too. >>> There's is warning in the welcome message, it seems that something is >>> missing: >>> >>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 -------- >>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>> WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist >>> FREESURFER_HOME /home/cvalencia/Descargas/freesurfer >>> FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast >>> FSF_OUTPUT_FORMAT nii >>> SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects >>> MNI_DIR /home/cvalencia/Descargas/freesurfer/mni >>> FSL_DIR /usr/share/fsl/4.1 >>> >>> >>> I try to test it and it shows >>> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit >>> /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de >>> ejecutable incorrecto. Binary file not executable. >>> >>> Thanks a lot, >>> >>> Carolina >>> >>> 2011/2/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> >>>> Hi Jie, >>>> >>>> what hardware are you using? Is it a 64 bit operating system? >>>> >>>> cheers >>>> Bruce >>>> >>>> On Sat, 19 Feb 2011, Liukarl wrote: >>>> >>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Hello, Freesurfer experts: >>>>> >>>>> >>>>> >>>>> I am new to freesurfer and try to >>>>> install the newest version of freesurfer in Ubuntu system. I closely >>>>> followed the instructions, and the only difference is that I >>>>> installed it in my Documents, instead of local folder. >>>>> >>>>> >>>>> >>>>> Below is the output after “source >>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh” >>>>> >>>>> >>>>> >>>>> -------- >>>>> freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- >>>>> >>>>> Setting up environment for >>>>> FreeSurfer/FS-FAST (and FSL) >>>>> >>>>> FREESURFER_HOME >>>>> /home/jie/Documents/freesurfer/ >>>>> >>>>> FSFAST_HOME >>>>> /home/jie/Documents/freesurfer//fsfast >>>>> >>>>> FSF_OUTPUT_FORMAT nii >>>>> >>>>> SUBJECTS_DIR >>>>> /home/jie/Documents/freesurfer//subjects >>>>> >>>>> MNI_DIR >>>>> /home/jie/Documents/freesurfer//mni >>>>> >>>>> >>>>> >>>>> >>>>> Everything seems fine and I also added >>>>> the .license file to the freesurfer folder. >>>>> >>>>> >>>>> >>>>> But when I test it by “tkmedit bert >>>>> orig.mgz”, it reponds “Illegal instruction” >>>>> >>>>> >>>>> >>>>> If I type in “recon-all”, it will >>>>> show >>>>> >>>>> “ Required Arguments: >>>>> >>>>> -subjid <subjid> >>>>> >>>>> -<process directive>…... >>>>> ” >>>>> and the other arguments. >>>>> >>>>> >>>>> >>>>> How to fix the problem and make >>>>> Fressurfer run? Any help is appreciated. Thanks a lot! >>>>> >>>>> >>>>> >>>>> Jie >>>>> >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> >>> >>> -- >>> >>> _______________________________________________ >>> 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. >>> >>> >> > >

1 0

installation problem in ubuntu
by Liukarl 21 Feb '11

21 Feb '11

Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” -------- freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid <subjid> -<process directive>…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie

4 3

segment lobes
by Adil Javed 19 Feb '11

19 Feb '11

Hi, This may be complicated, but ... I would like to segment various brain lobes, save them as mask files, convert them to NIFTI format, feed them to FSL for tractography. Can anyone tell me if it is possible to segment brain lobes in freesurfer and then feed them to fsl? many thanks in advance, AJ

1 0

Help ! Error for generating *.mgz files
by xiaotian yin 19 Feb '11

19 Feb '11

Hi, Thank you for reading this email ! I am a newbie to Medical Imaging, and am learning to use FreeSurfer for surface construction. Already installed FreeSurfer in Ubuntu, and the installation has been verified to be 100% successful. I got a bunch of data (coming in pairs of *.hdr and *.img), and I am trying to convert them to *.mgz files, so that I can use recon-all then. but when I call mri_convert as follows: mri_convert Rcing.img Rcing.mgz I got the following error : mri_convert Rcing.img Rcing.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from Rcing.img... ----------------------------------------------------------------- INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: -40, . INFO: if not valid, please provide the information in /mnt/Data/Rcing.mat file ----------------------------------------------------------------- Segmentation fault I have searched the freesurfer website ... no luck .... Would you mind to give me some advice or hints ? Thank you so much ! Best Tim

2 1

vertex coordinates: tksurfer vs sig.cluster.summary
by Marco Loggia, PhD 19 Feb '11

19 Feb '11

Dear Freesurfers, I have noticed a slight incongruity between the coordinates outputted by sig.cluster.summary and those in tksurfer. For instance, in the .summary file one of my maxima (VtxMax=92221) has the following "Tal" coordinates: -14.9, -62.2, 57.5. Now, if I open the fsaverage with tksurfer, and I enter 92221 as my Vertex Index, the Vertex Talairach coordinates are slightly different than those reported by the .summary file (-14.89, -61.61, 57.01). Is this because the Max in my significant cluster actually spans multiple adjacent vertices, and therefore the coordinates provided by the .summary file represent an average across those vertices? As for the "MNI Talairach", my understanding is that these are from the MNI305, right? If so, why the "Talairach" part of the name? Thanks, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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