Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

80 participants
131 discussions

hardware recommendations
by Elina Pitri 30 Apr '09

30 Apr '09

Hello, Can you please recommend me hardware appropriate for Freesurfer? What are the programme's requirements? Thanks, Elina

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RE: [Freesurfer] Measuring cortical thickness with high resolution data
by Nick Schmansky 30 Apr '09

30 Apr '09

Falk, Because the -hires switch disables the use the atlas during the skull- strip step, skull-stripping is more subject to stripping too much or too little brain (which is why use of the atlas was introduced). See this tutorial for ways to correct badly stripped skull: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix I had to add the switch -wsthresh 30 to get your sample subject to skull-strip (although it still left bits and pieces which affected the white matter tesselation step). Nick On Wed, 2009-04-08 at 15:07 +0200, Falk Lüsebrink wrote: > Hi Nick, > > First I wanted to give you a little bit of feedback. I'm still processing > one volume with .6mm which is working perfectly fine until now. The skull > stripping was done really well and no manual intervention was needed. I'm > currently running autorecon3 and will have a look at the final results > pretty soon. Thanks again for your modification and the help you offered. > > But I recently tried to process the data I send to you simultaneously to see > the results of the erroneous segmentation for myself. I just ran autorecon1 > to view the brainmask.mgz and the result isn't as bad as the one you send to > me in terms of remaining dura and skull, but only the right hemisphere is > being shown and a small piece on the anterior is missing. > > I also created a new subject so no older files could somehow influence the > new process. The result is the same. The flags I used were simply -hires and > -autorecon1 (and -clean in case for the older subject), so I don't know what > might have caused this issue. > > Regards, > Falk > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve > Sent: Monday, April 06, 2009 6:25 PM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu; 'Nick Schmansky' > Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution > data > > > Falk, it looks like that file was somehow converted to DOS. try: > > dos2unix recon-all > chmod a+x recon-all > > then re-run > > doug > > > On Mon, 6 Apr 2009, Falk Lüsebrink wrote: > > > Hi Nick, > > > > I tried using your modified recon-all today but as soon as I try to > process any data I receive following error message: > > > > 'nknown option: `- > > Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...]. > > > > Also it doesn't matter at all which flags I add to recon-all or if I don't > use any flags at all, the error is the same. The unmodified recon-all > performs well. > > > > Regards, > > Falk > > > > -----Original Message----- > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick > > Schmansky > > Sent: Thursday, April 02, 2009 3:28 PM > > To: Falk Lüsebrink > > Cc: Freesurfer Mailing List > > Subject: RE: [Freesurfer] Measuring cortical thickness with high > > resolution data > > > > Falk, > > > > There are no plans in the near future, but in the long term we'd like to > remove the dependence on conforming the data. > > > > It just occurred to me that you could have the best of both worlds: > > first run your data through the normal stream (conforming) up through > autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same > resolution as that created using the -hires stream, and copy it over. > > At least that would eliminate having to edit the original hires brainmask, > which would save hours of work. If i get few minutes i will try this. > > > > You can copy that recon-all over top your existing v4.x freesurfer > installation (attached again for the list). > > > > Nick > > > > > > On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote: > >> Hi Nick, > >> > >> Thank you very much. I'll have to look into that and try to process some > other volumes which might work a bit better, with less manual intervention. > >> > >> Are there any plans to improve Freesurfer in the (near) future so that > hires data can be processed within the currently available stream? > >> > >> Regards, > >> Falk > >> > >> -----Original Message----- > >> From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > >> Sent: Wednesday, April 01, 2009 7:53 PM > >> To: Falk Lüsebrink > >> Cc: Freesurfer Mailing List > >> Subject: Re: [Freesurfer] Measuring cortical thickness with high > >> resolution data > >> > >> Falk, > >> > >> Attached is a modified recon-all script where I've added a -hires switch > to force the stream to not conform the data to 1mm^3, and to not use the > atlases. > >> > >> Note that you should add the -clean flag to delete any work that had been > done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz). > >> > >> However, in working with the .8mm data that you sent me, working with > hires data will require quite a bit of manual intervention due to the fact > that the atlases normally used cannot be used. The first problem occurs in > skull-stripping, where quite a bit of dura and skull remains, and seems to > have intensity values close to gray matter. This would have to be manually > erased on each of the slices. If it is not erased (I did not do this > because of the amount of time required), then the wm.mgz file, which is what > is tessellated to create the initial surface, will be very wrong (it > tessellates the garbage surrounding the gray matter). > >> > >> See also Bruce's prior posting on the problems of working with hires data > in freesurfer. > >> > >> Nick > >> > >> > >> On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: > >>> Hi Freesurfers, > >>> > >>> > >>> > >>> Iÿÿm trying to evaluate the usefulness of high resolution scans > >>> acquired at 7T with an isometric voxel size of .6mm for the > >>> measurement of cortical thickness. The inhomogeneities are taken > >>> care of by dividing the scans with another scan of another sequence, > >>> so they are not an issue anymore. > >>> > >>> > >>> > >>> My problem is that Freesurfer usually conforms the voxel size to 1mm > >>> which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags > >>> for the recon-all process to avoid the conformation and to skip the > >>> subcortical segmentation, but another problem arises while using > >>> these flags. > >>> > >>> > >>> > >>> The error I receive is occurring after the WM Segmentation and > >>> states as follows: > >>> > >>> > >>> > >>> #-------------------------------------------- > >>> > >>> #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 > >>> > >>> > >>> > >>> cp wm.mgz wm.seg.mgz > >>> > >>> > >>> > >>> > >>> > >>> mri_segment -keep brain.mgz wm.seg.mgz > >>> > >>> > >>> > >>> preserving editing changes in output volume... > >>> > >>> doing initial intensity segmentation... > >>> > >>> using local statistics to label ambiguous voxels... > >>> > >>> computing class statistics for intensity windows... > >>> > >>> WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] > >>> > >>> GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] > >>> > >>> setting bottom of white matter range to 77.9 > >>> > >>> setting top of gray matter range to 89.4 > >>> > >>> doing initial intensity segmentation... > >>> > >>> using local statistics to label ambiguous voxels... > >>> > >>> using local geometry to label remaining ambiguous voxels... > >>> > >>> > >>> > >>> reclassifying voxels using Gaussian border classifier... > >>> > >>> > >>> > >>> removing voxels with positive offset direction... > >>> > >>> smoothing T1 volume with sigma = 0.250 > >>> > >>> removing 1-dimensional structures... > >>> > >>> thickening thin strands.... > >>> > >>> 20 segments, 4813 filled > >>> > >>> 10270 bright non-wm voxels segmented. > >>> > >>> 5589 diagonally connected voxels added... > >>> > >>> white matter segmentation took 2.4 minutes > >>> > >>> writing output to wm.seg.mgz... > >>> > >>> ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 > >>> height=320. > >>> > >>> > >>> > >>> The dimensions of the data Iÿÿm trying to process is 320 x 320 x 224 > >>> and is changed to 320 x 320 x 320 while using the ÿÿcm flag. It > >>> seems the mri_segment process canÿÿt handle any dimensions above 256 > >>> or Iÿÿm missing another flag. > >>> > >>> > >>> > >>> Does someone has any ideas about that issue? > >>> > >>> > >>> > >>> Regards, > >>> > >>> Falk > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(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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Getting standard space coordinates for anatomical parcellations
by David Hawellek 30 Apr '09

30 Apr '09

Hello there, I'd like to extract standard space coordinates (in the end I would like to use MNI coods) for each vertex of a structure of an anatomical parcellation. This so far seems pretty straight forward from what I read, but I somehow got lost between coordinate systems while doing the following: - Having an aparc.annot file I created a .label file for each structure using mri_annotation2label (with the pial surface). - After reading the comments by Darren Weber, I used mris_info to get the transformation from the surfaceRAS to talairached surface RAS coordinates and applied it to the data in the label files in Matlab (Using read_label.m and Darren's freesurfer_label2tal.m instructions). - In order to get the information to MNI space then, I simply used tal2mni.m. What I see is not totally absurd, but I noticed a slight backward shift. Is it that I'm lacking a further transformation for the surface coordinates? Or do you perhaps even know a more elegant way of doing this? Thanks for the support! David ---------------------------------------------------------------- David Hawellek Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg, Germany +4940 7410 55132 d.hawellek(a)uke.uni-hamburg.de ---------------------------------------------------------------- -- Pflichtangaben gem�� Gesetz �ber elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universit�tsklinikum Hamburg-Eppendorf K�rperschaft des �ffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. J�rg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Ricarda Klein Prof. Dr. Dr. Uwe Koch-Gromus

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Surface area and curvature
by Richard Frye 30 Apr '09

30 Apr '09

What is the best reference regarding the calculation of surface area and surface curvature and are there any studies looking at the reliability of these measures? Thanks Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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tksurfer question
by Sebastian Moeller 29 Apr '09

29 Apr '09

Hi fellow Surfers, in 3.0.5 (Linux centos4_x86_64) I used to be able to the following from a subdirectory myscripts-anat in the subjects directory: tksurfer subjects_name lh inflated -overlay lh.sulc Now, on macosx 4.3.0 this does not work anymore. I get: ERROR: cannot find lh.sulc using: tksurfer subjects_name lh inflated -overlay ../surf/lh.sulc does work. Now, is this a difference related to the switch linux to macosx or to the switch 3.0.5 to 4.3.0? And more importantly do you consider this something you will fix, or is this something I will have to change in all my scripts? Please let me know... ahoi Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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mri_normalization, what do the command line switches do?
by Sebastian Moeller 29 Apr '09

29 Apr '09

Aloha, fellow freesurfers, currently I am in the process of switching from freesurfer 3.0.5 to 4.3.0 (hopefully I can do the same for fsfast later). In that process I am revisiting mzy old scripts and try to improve them (or at least get rid of some cargo-cult coding). One of the more crirtical early steps for processing monkey brains, at least that is my experience, are the two normalization steps. Now here is the help from mri_normalize: mri_normalize input output -n <int n> use n 3d normalization iterations (default=2) -no1d disable 1d normalization -conform interpolate and embed volume to be 256^3 -noconform do not conform the volume -gentle perform kinder gentler normalization -f <path to file> use control points file (usually control.dat) -fonly <fname> use only control points file -w <mri_vol c> <mri_vol b> : write ctrl point(c) and bias field(b) volumes -a <float a> use control point with intensity a above target (default=25.0) -b <float b> use control point with intensity b below target (default=10.0) -g <float g> use max intensity/mm gradient g (default=1.000) -prune <boolean> turn pruning of control points on/off (default=off). pruning useful if white is expanding into gm -MASK maskfile -monkey turns off 1d, sets num_3d_iter=1 -nosnr disable snr normalization -sigma sigma smooth bias field -aseg aseg -v Gvx Gvy Gvz for debugging -d Gx Gy Gz for debugging -r controlpoints biasfield : for reading -u or -h print usage initially I use "mri_normalize -n 1 -no1d -gentle nu.mgz $T1.mgz", this invocation was handed down to me and I always just used it. Could someone in the know, explain, why monkey data should be processed without 1d normalization (and what is 1d normalization), and why only one iteration of 3d normalization is recommended; and what is the difference between a default normalization and a normaization using - gentle? (Since I mainly use the T1 for skull stripping and as underlay I guess I can just play around with the parameters to optimize the skull strip). I wonder especially, as I usually take monkey data at 0.5mm resolution, but fudge the header information so freesurfer thinks it is at 1.0mm, that way the size difference between human and monkey data is much less, compared to using monkey data at real 1.0mm resolution. And I have a hunch that the size difference might be the reason for special casing monkey data during normalization. Later I use "mri_normalize -f ${controlpoints} -monkey -MASK ${mask} nu.mgz brain.unmasked.mgz". Again I am interested to learn whether there is any reasoning to use the -monkey parameter here. (Since the full recon takes a while, doing trial and error here is a bit less attractive) Thank you very much in advance for any insight, aloha Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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corpus callosum segmentation
by Wayne Su 29 Apr '09

29 Apr '09

The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both 5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think they should not co-exist. Maybe I¹m wrong. Wayne

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Volume-based Monte Carlo Restricted to a within mask area
by Dave Brohawn 29 Apr '09

29 Apr '09

Hello, Here is my bugr info if you need it: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090428 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd $SUBJECTS_DIR I have made a mask version of subcortical regions using mri_binarize: mri_binarize --i aseg.mgz --match 16 --match 10 --match 49 --match 13 --match 52 --match 12 --match 51 --match 11 --match 50 --match 18 --match 54 --match 17 --match 53 --match 26 --match 58 --match 28 --match 60 --o Subcortical.nii I am able to load this file into tkmedit over fsaverage and I see that it has all the structures I want to use as a mask for my volume-based monte carlo command. I tried running my monte carlo command as follows: mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --C $SUBJECTS_DIR/fsgd/All-18.mat --mask $SUBJECTS_DIR/fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37 It looks like it wants to work, but will say: gdfReadHeader: reading /autofs/space/ventzl_016/users//fsgd/All-18.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 CC 2 T INFO: gd2mtx_method is dods simbase /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/SubCortVol_MCSIM1 $Id: mri_glmfit.c,v 1.138.2.9 2009/01/17 02:08:58 greve Exp $ cwd /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s cmdline mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd /autofs/space/ventzl_016/users//fsgd/All-18.fsgd --C /autofs/space/ventzl_016/users//fsgd/All-18.mat --mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37 sysname Linux hostname seymour machine i686 user jroffman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.370000 OneSampleGroupMean 0 y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii logyflag 0 usedti 0 FSGD /autofs/space/ventzl_016/users//fsgd/All-18.fsgd mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii maskinv 0 glmdir (null) IllCondOK 0 DoFFx 0 Loading y from /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii INFO: gd2mtx_method is dods Matrix condition is 1 ERROR: dimension mismatch 1 between y and mask Do you have any ideas about how to fix this? I am not sure how to look at the matrix dimension mismatches, nor am I sure how to alter the mask I made to fit the dimensions of the ces.nii file for the analysis. Please let me know. Thanks! Dave

1 0

longitudinal processing
by Dana W. Moore 29 Apr '09

29 Apr '09

FreeSurfers, I am using the longitudinal processing stream to look at change in the lateral ventricles at several timepoints. As a control measure, we are running two consecutive baseline images in the scanner. These images were done back-to-back, exactly the same, and the subject did not get out of the scanner nor reposition. Motion was not a problem. I have processed this first subject, and the longitudinal stream gives me a 2% change in lateral ventricular volume, comparing the two baseline scans. This is bigger than I'd like to see, as we are interested in changes over time as small as 2%. Is this kind of variability expected, or am I doing something wrong? I just used the first baseline as tp1, processed it cross-sectionally, and then longitudinally, and then I used the second baseline as tp2. 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: dwm2003(a)med.cornell.edu

2 1

(no subject)
by Elina Pitri 29 Apr '09

29 Apr '09

Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all commands) take. thanks, Elina

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Freesurfer April 2009