Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

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(no subject)
by Guang Zeng 28 Jan '10

28 Jan '10

Hi, there, I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab? Is it possible to replace FS Atlas with our own Atlas and use it for analysis? Thanks a lot! Guang _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2472…

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Using Clusters as ROIs
by Dankner, Nathan (NIH/NIMH) [F] 25 Jan '10

25 Jan '10

Hello all, I sent this last week but I think it may have slipped through the cracks. I have recently run a cluster correction on some data, and was hoping to use these clusters as ROIs and pull stats from them. What is the best way to do so? Thank you in advance for your help, Nathan

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Re: [Freesurfer] images with poor resolution
by Nick Schmansky 25 Jan '10

25 Jan '10

Dana, First I would run: recon-all -s subid -clean to remove any prior control points and edits. Then I would open nu.mgz: tkmedit subjid nu.mgz and *sparingly* put control points well into white matter areas on a few different slices. you only need a half dozen or so. to add control points, see: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints except you will add them to nu.mgz, to make sure that T1.mgz gets created properly. Then create a file name xopts.txt containing these lines: mri_normalize -gentle Then run: recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt and when done, open brainmask.mgz tkmedit subjid brainmask.mgz and check again to get a sense of the low value for white matter and high value for gray matter, then run: recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi replacing wlo and ghi with those values. if the surfaces still look bad, you can add a line to the xopts.txt file : mris_make_surfaces -max_gray val -min_gray_at_white_border val replacing the two 'val's with something you find appropriate, then run: recon-all -s subjid -autorecon2-pial -autorecon3 \ -expert <path_to>/xopts.txt good luck! Nick On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > Hi Nick, > > Below is Bruce's response to a problem I'm having with the gray/white > segmentation. (Pasted below, you can see the brainmask.mgz volume and > surfaces--the entire brain is labeled as white matter). I could use > some guidance in carrying out his advice. He says to adjust the > intensity normalization using control points and then use expert opts > for mri_segment and mris_make_surfaces. > > When I look at the brain.mgz volume, the white matter tends to have an > intensity of 110, as it should, but the gray matter at times goes as > high as 115. I was thinking, I could set ghi to 115 and wlo to 110. > Then, I am not sure how to actually run the corrections and what > language to use to implement the control points and mri_segment > adjustments. I will save control points and then run: recon-all > -autorecon2-cp -autorecon3 -subjed <subject>. Can I somehow include > the mri_segment adjustments into this command, or do I have to run > that separately? > > I am also not sure how options for mris_make_surfaces might help. > > I appreciate your help with this! > > Thanks, > dana > > > > > [] > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > Hi Dana, > > > > it looks like the gray/white density estimation failed. Try setting > > them with the expert opts for mri_segment and mris_make_surfaces > > (Nick can point you in the right direction if you can't figure it > > out). Things like max gm at white border and such. > > > > cheers, > > Bruce > > > p.s. it also looks like the intensity normalization went too far due > to the low contrast. You'll probably need to add some control points > and run it with the -gentle option > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > Hi everyone, > > > > > > I am trying to salvage some images that were done with poor > > > gray/white boundary contrasts. First, FreeSurfer includes an area > > > of dura in the skull strip. I tried adjusting the watershed but > > > it made no differences. FreeSurfer is subsequently unable to > > > detect the gray/white boundary and labels the dura as cortex: > > > > > > [] > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries are faint but > > > visible. Is there anything I can adjust to try to make this work > > > with FreeSurfer? > > > > > > 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: 212-746-2823 > > > Fax: 212-746-5584 > > > Email: dwm2003(a)med.cornell.edu > > 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: 212-746-2823 > Fax: 212-746-5584 > Email: dwm2003(a)med.cornell.edu > >

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fsaverage to mni152
by Yigal Agam 17 Dec '09

17 Dec '09

Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal

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Comments in paradigm files
by Yigal Agam 30 Nov '09

30 Nov '09

Hi, Can you add comments to a paradigm file? Thanks, Yigal

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TKSURFER error- open GL in Fedora
by Massieh Moayedi 30 Nov '09

30 Nov '09

Hi, I can't seem to run tksurfer in Fedora 7. We are using a Wacom Tablet monitor, and since we installed it, we cannot run tksurfer. We get the following error: surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(fsaverage) Can't create a context! surfer: failed, trying double buffered window Can't create a context! surfer: failed, no suitable display found Does anyone know how to go about this? massih

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T1 and T2 in one recon-all
by Samuel Inverso 30 Nov '09

30 Nov '09

Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam

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Re: [Freesurfer] convert/reconstructing with mrdc
by Jesse Bledsoe 29 Nov '09

29 Nov '09

I have T1volume+org.BRIK - should I use those with mri_convert? Thanks again, Jesse On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz(a)mail.nih.gov> wrote: > mri_convert usually work with BRIK files. > > Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format > which FreeSurfer can read fine. > > cheers, > ziad > > On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote: > > > These are not the standard .BRIK files? Ziad (ccd) will know. > > > > Bruce > > > > > > On Tue, 24 Nov 2009, Jesse Bledsoe wrote: > > > >> Hello, > >> > >> So far I have had no problems running recon-all with .mnc files but > >> could > >> use some guidance converting/reconstructing brains processed with > >> AFNI > >> (MRDC). > >> > >> There are 120 MRDC files in the T1 directory. > >> > >> I believe I need to run mri_convert on these MRDC files but am > >> unsure of > >> what the correct command would be? > >> > >> Thanks in advance, > >> > >> Jesse > >> > > -- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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Freesurfer November 2009