Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 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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a question about mris_ca_train
by Guang Zeng 03 Feb '10

03 Feb '10

Hi, there, Recently, I sent sseveral emails to you to ask same kind of question about building our own template and atlas. Thanks a lot for your quick reply, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother you again. We have a surface labeling atlas in our lab, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. What we try to do is: 1. Send each subject in the training set to our toolbox which will use our atlas to do surface labeling. For each subject it will output a file just like wmparc.mgz in FS, but it is NIfTI file. 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc files. 3. Find a method to get my ?h. mylabels. annot files, and use mris_ca_train to build a new atlas. First of all, do you think what I try to do is reasonable? If yes, I know I need to get the FS .label files for each ROI, then I can call mris_label2annot to get ?h. mylabels. annot files. But how can I get the FS .label files for each ROI from our toolbox output ROI labeled NIfTI file? These qurstions trouble me for a long time, your help are really appreciate. Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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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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Pial surface of both hemispheres as specific ASCII output
by Denny Milakara 27 Jan '10

27 Jan '10

Dear Freesurfers, I wonder if there is a way to output the triangulated pial surface for both hemispheres into a single ASCII file according to OFF-file schema: ---------------------------------- OFF numVertices numFaces numEdges x y z x y z ... numVertices like above NVertices v1 v2 v3 ... vN MVertices v1 v2 v3 ... vM ... numFaces like above --------------------------------- ...where the number of edges is to be ignored. Thank you for your suggestions! Denny Milakara

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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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Order of structures in aparcstats2table
by Dankner, Nathan (NIH/NIMH) [F] 08 Jan '10

08 Jan '10

Hi All, I just started using version 4.5, and when I use aparcstats2table to create a table the structures are being listed in a strange order. The ?h.aparc.stats file itself has them in the order in which they were in previous versions (essentially alphabetical except for frontal pole), but for whatever reason when made into a .txt file with aparcs2statstable it seems to jumble them up (but in a consistent way). Any ideas regarding how to get the program to order them in the older standard way?

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Retinotopic mapping of only polar data
by f.leone＠donders.ru.nl 04 Jan '10

04 Jan '10

Dear all, I just started using FreeSurfer, specifically for retinotopic data, on the moment only polar data. So I followed the guide as mentioned on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . This does seem to work to some extend, except that it complains that I don't have eccentricity data. He is right about that, but is the analysis also doable with the eccentricity data? I really hope so, thanks a lot in advance, kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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white matter mask
by Oya, Hiroyuki 03 Jan '10

03 Jan '10

Hello All, I'd like to create mask of white matter. Would it be possible to use white matter surface to do this? Tx. Hhiroyuki

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Freesurfer December 2009