Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

segmentation of the dural sinuses
by Jonathan A Winawer 26 Mar '12

26 Mar '12

Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon ******************************* Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 winawer(a)stanford.edu http://www-psych.stanford.edu/~winawer/

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Re: [Freesurfer] volume mapping
by Anastasia Yendiki 26 Mar '12

26 Mar '12

Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: > Hi FS expert > I need to know the transformation matrix itself since I will do the > transformation in matlab. > I successfully transformed white matter fibers coordinates to T1 using AIR > 5.0 from LONI lab. > They provide a transformation matrix. > Now I want to transform the coordinates from T1 to Freesurfer space, so > my question is: what is the transformation matrix that relates the T1 > which FS have used for parcellation and segmentation with the aparc+aseg.mgz > file? > I searched the logs but couldn't find such matrix. > I don't want to do a registration step since it will be less accurate than > the one that was generated during the segmentation process. > Also is it just one transformation or a combination of transformations? > > thanks > >

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calculating DLPFC or frontal lobe grey and white matter volumes
by sam bedford 26 Mar '12

26 Mar '12

Dear All We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to be having problems finding this region on the processed data for white matter volume (after recon-all command). It was previously suggested in this mailing list that we can get grey matter volume for the DLPFC by combining the following volumes: $hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label We are wondering how to get white matter volumes in the same region... If getting the DLPFC volume is difficult then can we just use the frontal grey and white matter volumes to make between group comparisons. From aseg and aparc files in the stats folder, adding all the following values below would give us frontal white and grey matter volumes. Or is there a simpler and less time consuming way to calculate grey and white matter volume in the frontal lobe? Frontal lobes - White Matter volume caudalmiddlefrontal lateralorbitofrontal medialorbitofrontal paracentral parsopercularis parsorbitalis parstriangularis precentral rostralmiddlefrontal superiorfrontal frontalpole Frontal lobes - Grey Matter volumes G_and_S_frontomargin G_and_S_paracentral G_and_S_subcentral QQQ??? G_and_S_transv_frontopol G_front_inf-Opercular G_front_inf-Orbital G_front_inf-Triangul G_front_middle G_front_sup G_precentral S_front_inf S_front_middle S_front_sup Thanks in advance Sam

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Talairach registration problem
by Gregor Strobbe 26 Mar '12

26 Mar '12

Dear All, Did someone already figured out a solution for this problem? I get exactly the same error every time I run recon_all There seems to be no answer on the mailing list yet Thank you Kind regards Gregor ---- Hi Avi, do you have any advise for Dana? thanks Bruce On Tue, 30 Jun 2009, Dana W. Moore wrote: Doug Yes, there is an error message in the talairach_avi.log--I am not sure what it means. The end of the log gives me this message: Dana imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305/usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted At 06:34 PM 6/29/2009, Douglas N Greve wrote: The error msg asks you to look at transforms/talairach_avi.log. Have you and does it reveal anything? doug Dana W. Moore wrote: Hi all, I get the following error message during recon-all: ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305/usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Any idea why this is happening? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...(a)med.cornell.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...(a)med.cornell.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________

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normal vector projection
by Seok Lew 26 Mar '12

26 Mar '12

Hi, After freesurfer reconstruction, I tried to project surface normal vectors on the ribbon. I used the following scripts, but the projected vectors were out of the ribbon when I visualized it freeview. The vectors were placed outside of the ribbon. Anyone knows any idea ? fslregister --mov mri/orig.mgz --s xDS --reg rrr.dat --dof 12 --tmp ./tmp/ mri_surf2surf --s xDS --hemi lh --sval-nxyz pial --tval ./pl_100.mgz mri_surf2vol --surfval pl_100.mgz --hemi lh --surf pial --volreg rrr.dat --outvol pln_pribbon.mgz --fillribbon --template mri/orig.mgz Thank in advance, Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School slew(a)nmr.mgh.harvard.edu

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[BUG] epidewarp.fsl
by Satrajit Ghosh 26 Mar '12

26 Mar '12

epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra

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Freesurfer coordinate problem
by xiaoning wu 26 Mar '12

26 Mar '12

Hi all, Recently I have a problem about coordinate of freesurfer. I have reprocessed the MRI data to get the cortical thickness and then I want to get the indexes, coordinate and cortical thickness of a region of interest(ROI). I have use the Surfstat toolbox of matlab to process the data.Now I want to use the function SurfStatROI ( function maskROI = SurfStatROI( centre, radius, surf ) ) to get the ROI, however, I have known the MNI coordinates (x,y,z) only .I want to convert this MNI coordinates to the freesurfer coordinates which can be used by SurfStatROI.center. That is ,if I use the function SurfStatReadSurf to read surf files (surf=SurfStatReadSurf(..)) to get the variable surf, then I can get surf.coord(:,index) by a index. How can the surf.coord() corresponding to the MNI coordinate systems or Talairach systems. I have seen the website of Freesurfer coordinate systems ( http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but I can not solve my problem. Looking forward to your help sincerely. Your sincerely! Xiaoning Wu Mar 20,2012

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question about Cluster-wise Correction for Multiple Comparisions
by ZhiLiangLong 26 Mar '12

26 Mar '12

Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 10000 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite In this command, does the vertex-wise threshold (here, '4') mean that the vertex whose p value is lower than 0.0001 can be considered to used for the Correction for Multiple Comparisions ? likewise, does the sign (here,'neg') mean that only negtive vertexs can be considered? Is there a criterion which vertex-wise threshold and sign i should choose? Hope you can give me some suggestions !

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question about FSGD file
by ZhiLiangLong 26 Mar '12

26 Mar '12

Hi, FS experts: I'm scanning freesurfer pages about FSGD files here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V and i'm interested in one contrast file(the example of Contrast 5 right-left.intercept.mtx). The original FSGD file is list as follows: GroupDescriptorFile 1 Title OSGM Class MaleRight Class MaleLeft Class FemaleRight Class FemaleLeft Variables Age Input subject1 MaleRight 30 Input subject2 MaleLeft 40 Input subject3 FemaleRight 50 Input subject4 FemaleLeft 60 The contrast file is : 0.5 -0.5 0.5 -0.5 0 0 0 0, meaning to exame the difference between Righties and Lefties regressing out the effects of gender and age. Now i consider gender as the covariate variable ('1' represents the Male and '2' represents the Female), and i setup a new FSGD file: GroupDescriptorFile 2 Title OSGM Class Right Class Left Variables Age gender Input subject1 Right 30 1 Input subject2 Left 40 2 I also want to exame the difference as suggested above, and I setup the new contrast file as :1 -1 0 0 0 0. My question is that : are the new FSGD and contrast files correct to exame the difference as suggested by original FSGD and contrast files?

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make_average_subject
by sonya kaur 26 Mar '12

26 Mar '12

Dear all, I'm getting an error with the make_average_subject command on freesurfer. The error is vm_allocate (size=262144) failed (error code 3). According to the freesurfer helpdesk, it seems to be a problem with creating an "average" aseg. Is there any solution for this that you know of? Thank you in advance! -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E <sonya_kaur(a)mail.utexas.edu> sonya_kaur(a)mail.utexas.edu

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