Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30079 discussions

converting a region defined by a surface to a label file
by Michael Harms 14 Apr '08

14 Apr '08

Hello, We have some white matter surfaces created using non-FS software in which we have subsequently "cut-out" via hand contouring specific gyri and sulci of interest (e.g., cingulate). I would like to be able to use these extracted surfaces to create a label file in FS corresponding to the matching surface region within FS. Is there a way to accomplish this using existing Freesurfer binary or matlab functions? More specifically, we can define these extracted surfaces in the native scan space, and get them into a vtk format (which should be readable by mris_convert). Do you have any suggestions for the easiest way to then "translate" the region defined by this surface into a corresponding region on the FS white matter surface? Ideally, since our in-house surface defines an enclosed set of vertices, the ensuing label file in FS would represent an enclosed set of vertices as well. thanks for your suggestions, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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FSGD
by Jerry Yeou-Wei Chen 13 Apr '08

13 Apr '08

Hello, I am getting the following error when I try to load an FSGD file in tksurfer. The stats were processed using a custom design matrix without error and I am able to view the results. FSGD file doesn't contain a PlotFile entry. Error loading GDF /scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/vbmDesign_fsgd.txt I understand that others have encountered a similar problem with an earlier release due to a missing file (fsgdfPlot.tcl). However, if I understand correctly, this was updated in the current release (4.0.3) Thanks, - Jerry

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fsfast file question
by Scott Gorlin 12 Apr '08

12 Apr '08

Hi, I have a question about files produced by fsfast selxavg3-sess. After a successful run, I see that it produces contrast folders in the appropriate analysis folder inside of /bold/, but there is also a folder named res which is quite large (including a file 'all.nii' which, in my case, is over 1 gb). I don't see this folder described anywhere in the fsfast documentation. I presume these are the residuals after the glm analysis? Are they necessary for any other fsfast/freesurfer commands, or are they safe to delete if i don't need to examine the residuals? Thanks, Scott

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cortical surface in MNI space?
by Stark, David Ernest 12 Apr '08

12 Apr '08

Hi all, I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use. Thanks! David

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tksurfer buttons grayed out
by hranilovich＠ucla.edu 11 Apr '08

11 Apr '08

We're taking a look at using FreeSurfer for our lab's analysis of cortical thickness...just ran a fully automated recon-all on one of our lab's brains that generated no error messages and looks good in the "Inspection of Freesurfer Output" exercise from your tutorial. However, I noticed while moving through this exercise that the curvature file button, pial surface button, and the thickness map button are grayed out (not available for use) in the tksurfer toolbox. If this means there was some subtle error in the output - any ideas where to begin troubleshooting? Perhaps automatic topology defect correction? Not sure how obvious the topology defects you refer to would be on inspection; there were no holes or handles that I could see in the inflated surface, though ours was more lumpy than the tutorial's...Some dura was left in and was designated cortex, lying outside of the pial surface generated. Could this be the issue? If so, would the solution be an adjustment of the watershed parameters fix it, or is that really intended for large over-inclusions of skull? Thanks - Jennifer

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Re: [Freesurfer] Interactions for continuous variables
by Jerry Yeou-Wei Chen 11 Apr '08

11 Apr '08

Regarding custom design matrices, does the --X flag require a design matrix in matlab format? If so, can I simply create it in a text editor and name it with the suffix ".mat"? Also, if I use the --X to specify a design matrix, am I still supposed to specify the fsgd file? Thanks, - Jerry On Wed, Apr 9, 2008 at 4:58 PM, Jerry Yeou-Wei Chen <jyw.chen(a)utoronto.ca> wrote: > Great! Thanks! > - Jerry > > > On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <greve(a)nmr.mgh.harvard.edu> > wrote: > > > > > You can pass custom design and contrast matrices to mri_glmfit, so you > > can pass the same matrices to mri_glmfit that you would use with spm. > > Alternatively, you can set up an fsgd file with a 3rd continuous variable > > that is the produce of the first two. > > > > doug > > > > > > > > > > > > Jerry Yeou-Wei Chen wrote: > > > > Hello, > > I would like to know how to examine an interaction between continuous > > variables. > > In SPM, my understanding is that a new interaction regressor, comprised > > of the product of the two continuous variables of interest, can be coded and > > entered into the model. > > Would this be appropriate for CTA group analysis in FreeSurfer? Is there > > any difference if I use the old command line method or the QDEC GUI? > > Thanks, > > - Jerry > > > > ------------------------------ > > > > _______________________________________________ > > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Centergreve(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 > > > > >

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mri_watershed -> BEM surfaces problem
by Silviu Podariu 11 Apr '08

11 Apr '08

Hi, In order to get the three BEMs for 3D source reconstruction for subject X, I used: mri_watershed -atlas -useSRAS -surf X/bem/watershed/X X/mri/T1.mgz X/bem/watershed/ws which created the BEMs in X/bem/watershed/, but the inner_skull and the brain were significantly distorted, mainly on the left side (the scalp BEM is okay). I followed the tutorial on troubleshooting the surfaces in the X/surf/ folder, but that does not address fixing these BEMs, so I was wondering if anybody knows how to get around this problem (should I edit the T1.mgz volume and run again?). Thank you, Silviu Podariu UNMC Omaha, NE P.S. Also, I was wondering if there is a utility to reduce the number of vertices of a given surface (i.e. to make a less precise triangulation) at will. I thought I may use the pial left and right halves greatly reduced (from about 140k vertices to 10k or less) for the brain surface instead of the mri_watershed output. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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wmparc creation
by joel bruss 10 Apr '08

10 Apr '08

Hello- I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz and all was running well until it exited with the following error: Used brute-force search on 2690 voxels Writing output aseg to mri/wmparc.mgz sh: mri/wmparc.mgz: No such file or directory I thought that the point of running this command was to create the wmparc.mgz file. Did I do something wrong with my command? Also, shouldn't recon-all create this file as well? Thanks, Joel

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wmparc
by joel bruss 10 Apr '08

10 Apr '08

I'll try this again as I'm stuck and in need of help. I ran recon-all and it reported that everything ran with no errors but, when I go into mri, there is no wmparc.mgz file. I tried running: mri_aparc2aseg --s sub1_ani --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz and all was running well until it exited with the following error (after labeling all 256 slices): Used brute-force search on 2690 voxels Writing output aseg to mri/wmparc.mgz sh: mri/wmparc.mgz: No such file or directory I thought that the point of running this command was to create the wmparc.mgz file. Did I do something wrong with my command? Also, shouldn't recon-all create this file as well? Thanks, Joel

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Black digits and black background
by Juergen Haenggi 10 Apr '08

10 Apr '08

Dear FS experts When loading a thickness map in FS 4.0.3 for MacOS X Leopard the thickness values of the colour scale bar are not visible because they are printed in black like the background. How can I change the colour of these mm values from black to white? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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