Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

mri_glmfit-sim doubt
by Rafa x 22 Feb '11

22 Feb '11

Dear Freesurfers, I have performed a permutation test with the command: mri_glmfit-sim --glmdir rh.fsgd_subj_gauss005 --sim mc-z 10000 THRESHOLD csd --sim-sign pos --seed 1297708255 And after that I have obtained the clusters with: mri_surfcluster --subject CNTRL_MCI_RAFA_average –mask rh.fsgd_subj_gauss005/mask.mgh --sum rh.fsgd_subj_gauss005/contrast/clustsum.txt --in rh.fsgd_subj_gauss005/contrast/sig.mgh --cwsig rh.fsgd_subj_gauss005/contrast/cwsig.mgh --vwsig rh.fsgd_subj_gauss005/contrast/vwsig.mgh --sign pos --csd rh.fsgd_subj_gauss005/csd/csd.j001-contrast.csd I’ve did it over the same dataset but with two different thresholds, THRESHOLD: 2.301 (pvalue=0.005) and 1.301 (pvalue=0.05). As far I know the cwsig.mgh resulting using the 1.3 threshold should be similar than the cwsig.mgh from the second thr, but with a more restrictive significative clusters (some coloured areas should disappear, in other words, clusters returned in the first case should be included in clusters returned by the 1.3 threshold). My results didn’t show that behaviour, some of the cwsig clusters can be contained in the other, but others don’t (see attached Figure). It is my reasoning correct? If so, why the images mismatching? Thank you all in advance. Rafa.

3 2

Gammafit parameters
by Mandy Nagy 22 Feb '11

22 Feb '11

Hi all, We are trying to use -gammafit when running the mkanalysis-sess command. In the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those numbers the default? If not, what is the default? Thanks in advance. Best, Mandy Nagy

2 1

overlay sig.mgh onto T1 vol
by Fernanda Palhano 22 Feb '11

22 Feb '11

Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda

4 5

FW: Surface Generation Problem Pertaining to FreeSurfer
by Saad Shakeel 22 Feb '11

22 Feb '11

From: saad.akhun(a)hotmail.com To: fsregister(a)nmr.mgh.harvard.edu; freesurfer(a)nmr.mgh.harvard.edu Subject: Surface Generation Problem Pertaining to FreeSurfer Date: Tue, 22 Feb 2011 11:43:36 +0500 Hello, We are graduate students from Giki university, Pakistan. We are doing our Final Year Project on shape Analysis Techniques.Our Project steps are a. Segmentation b. Surface Generation c. Spherical Harmonics for shape Analysis. We need your help pertaining to Surface Generation module. I have certain problems:1. How to create : surface generation of hippo-campus ( Exists In Sub-cortical region of Human Brain)2. Can I use mri_vol2surf tool in FreeSurfer for this purpose. If so, then what are the advantages and dis-advantages Thankyou for your time. Kindly send me the supporter's email address if you don't deal with this kind of situation.

2 1

Remove From List
by Andrés Camarena 22 Feb '11

22 Feb '11

Remove from list amco1027(a)gmail.com

1 0

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. >>>>> >>>>> >>>> >>> >>> >> > > > -- >

1 0

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

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Freesurfer February 2011