Freesurfer September 2007

freesurfer@nmr.mgh.harvard.edu

69 participants
99 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

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parcellation problem
by Wang, Xin 04 Oct '07

04 Oct '07

Hello, Group, After I manually removed the skull around cerebellum in the brainmask.mgz, the parcellation of the final inflated brain is totally messed up. Manual corrections of talairach transform and white matter surface did not mess up the parcellation. Could anyone tell me what is wrong? Thank you in advance, Xin Wang

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significance in unknown region
by Kirk, Gregory 01 Oct '07

01 Oct '07

Hi All, I have wondered what is done in the medial and inferior region where a patch needs to be put across to seal each of the two hemispheres. The variables , thickness etc... have some value in the region as we see a representation on the thickness maps. Is something like averaging with a diffusion equation i.e. computing a distance weighted average of the border of the surounding real cortex performed ? thanks curious Greg.

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within group contrast vector
by Elizabeth Mormino 01 Oct '07

01 Oct '07

Hello. I am trying to do a within group analysis looking at the effect of cognitive performance on cortical thickness, controlling for age and gender. I only have one class declared and my variable of interest is listed as the first variable in the FSGD file (with age and gender second and third). Should my contrast vector look like this: 0 1 0 0 Thanks for you help! I have enjoyed using your software very much! Beth

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Re: [Freesurfer] convert mnc->analyze->mgz
by Olivier Coulon 01 Oct '07

01 Oct '07

Hi everyone, >> but then, when I do mri_convert -it analyze -i subject -o subject.mgz, >> the volume is shifted to one side (in addition to left/right swapped). >> If you look at the coronal sections I'm attaching, you see that a >> piece of ear the right ear is appearing at the left. I also have this problem of left/right inversion and I cannot figure out why this happens. Do we have to specify a --out_orientation string ? Thanks, Olivier -- --------------------------------------------------------------- Olivier Coulon, Chargé de Recherche CNRS Laboratoire LSIS, UMR CNRS 6168 Equipe I&M, ESIL Campus de Luminy - Case 925, 13288 Marseille cedex 09 - France Tél: +33 (0)4 91 82 85 27 Fax: +33 (0)4 91 82 85 51 email: olivier.coulon(a)univmed.fr http://olivier.coulon.perso.univmed.fr ---------------------------------------------------------------

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convert mnc->analyze->mgz
by roberto toro 29 Sep '07

29 Sep '07

(sorry. I just clicked reply, and didn't send the screenshots to the list) You can see in the images (I'm using neurolens) the contraction of the left-right axis and the shift: the black space at the left and right sides is even originally but uneven in the converted data. In another slice (not included) you can see a little bit of the right ear appearing from the left side. There's also the problem with the rotation, the nose is originally pointing to the right but then it's pointing down, which is why the axial slices look coronal and vice-versa. Keeping that in mind, you can see that left and right hemispheres are swapped (look at the shape of the posterior horn of the ventricles, which is longer in the left hemisphere) thanks, roberto ---------- Forwarded message ---------- From: roberto toro <rtoro(a)snv.jussieu.fr> Date: Sep 27, 2007 4:23 PM Subject: Re: [Freesurfer] convert mnc->analyze->mgz To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> On 9/27/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Roberto, > > can you send us the command line and full screen output of the minc to > mgz step? It shouldn't change the aspect ratio. > > thanks, > Bruce hi Bruce, here's the command: roberto% mri_convert P.mnc P.mgz mri_convert P.mnc P.mgz reading from P.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to P.mgz... roberto% and I attach screenshots of the result (which is scaled and shifted). thank you, roberto

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Simple_Surface_labels2005.txt
by Juranek, Jenifer 28 Sep '07

28 Sep '07

I'd like to identify the voxel locations of each vertex within each aparc label. I found the command "mri_annotation2label" and thought it might do the trick. However, I noticed that the examples http://surfer.nmr.mgh.harvard.edu/fswiki/mri_5fannotation2label?action=h ighlight&value=mri_annotation2label refer to a txt file which I do not seem to have in my $FREESURFER_HOME dir. While the table specified in the examples is <Simple_surface_labels2005.txt> I only seem to have <surface_labels.txt> which appears to have 95 lines of text. Using the surface_labels.txt file yields only 12 files rather than the expected 94. 1) Is strategy appropriate? 2) Which file should be specified with the -table flag? 3) Best guess as to where to find the proper file to be specified with the -table flag? Many Thanks for any assistance you can provide... Jenifer

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Re: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm]
by Pratap Kunwar 28 Sep '07

28 Sep '07

Nevermind, it works fine now with after i added "--sign < >" flag to the mri_volcluster ..command. thanks pratap ---------------------------- Original Message ---------------------------- Subject: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm From: PKUNWAR(a)nmr.mgh.harvard.edu Date: Thu, September 27, 2007 3:12 pm To: Freesurfer(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer September 2007