Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Reprocessing subjects with new freesurfer
by Jeff Sadino 12 Nov '10

12 Nov '10

Hello, I have an easy question: If I want to reprocess my fs 4.3.1 and fs 4.5.0 subjects with the newest fs 5.0 (btw, I thought we had fs 5.1 and 5.2 out already?), but I also want to keep the 4.3.1 and 4.5.0 subject folders for future reference, how do I do that? Do I copy all the 4.3.1 and 4.5.0 subjects to a new fs 5.0 subjects folder and then run fs 5.0? Thank you! Jeff Sadino

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another recon-all error
by Joakim Vinberg 11 Nov '10

11 Nov '10

Sorry to add another! I ran recon-all on a subject of mine, and have recon-all exit with the error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact totally empty-definitely not enough values of 110. Is this due to a specific error that I might be able to bypass, or will adding in WM control points fix things? Thanks in advance! Joakim //******************************************************** mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010

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Marking four majors lobes: frontal, parietal, temporal, occipital
by Mustafa, Nazahah 11 Nov '10

11 Nov '10

Hi, We are using freesurfer version 4.4. We did fully run recon-all, but not clear which file should be used to get label of 4 main lobes; frontal, occipital, temporal and parietal. Could you please give some instruction on marking the lobes. Thank you. Naza The University of Aberdeen is a charity registered in Scotland, No SC013683.

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redraw failed: no gl window open
by Mustafa, Nazahah 11 Nov '10

11 Nov '10

Helo, We are now using freesurfer version 4.4 on Linux os. We tried to visualize surface of our subject using tksurfer but we failed to do that. What we got was only the following message. tksurfer Output_C001_E5364 lh inflated surfer: current subjects dir: /exa/Imaging/Projects/blobs/freesurfer_subjects/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /exa/Imaging/Projects/blobs/freesurfer_subjects/Output_C001_E5364/label surfer: Reading header info from /exa/Imaging/Projects/blobs/freesurfer_subjects//Output_C001_E5364/mri/T1.mgz surfer: vertices=144411, faces=288818 Loading /home/bio-d/r05nm9/fs/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(Output_C001_E5364) libGL warning: 3D driver claims to not support visual 0x5a Does anybody here facing the same problems before and how did you solve that? Any advice would be appreciated. Thank you Regards; Naza The University of Aberdeen is a charity registered in Scotland, No SC013683.

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Re: [Freesurfer] discrepancy between p-values computed from t.nii and those stored in sig.nii
by Douglas N Greve 11 Nov '10

11 Nov '10

Hi Pablo, you have found a bug in FSFAST in which the values in the t.nii file are actually the sqrt of the p-values. I have fixed it in our code base and it will be in the next version. Do you actually need the t-values? thanks! doug Pablo Polosecki wrote: > I understand the X.mat contains the variable DOF which tells me the > degrees of freedom for the analysis, right? In my case it is 5915. > This is what I get when I load X.mat into a structure named 'x': > > x = > > DoSynth: 0 > UseFloat: 0 > SynthSeed: -1 > flac0: [1x1 struct] > runflac: [1x21 struct] > X: [6048x133 double] > DOF: 5915 > rfm: [1x1 struct] > yrun_randn: [] > RescaleFactor: 5.6510 > ErrCovMtx: 0 > acfseg: [1x1 struct] > acfsegmn: [6048x1 double] > nrho1segmn: 0.1456 > W: [6048x6048 double] > > > > On Thu, Nov 11, 2010 at 11:35 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > what is your dof? > > Pablo Polosecki wrote: > > Oh, sure. It is: > > > t.vol(test_voxel_number) > > ans = > > -0.6368 > > > On Thu, Nov 11, 2010 at 10:25 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > sorry, I meant what is the actual value of the t in > t.vol(test_voxel_number)? > > Pablo Polosecki wrote: > > Firstly, thank you for the quickyresponse. > > t.vol is the t-volume, loaded from t.nii using the MRIread > function (i.e. t=MRIread('t.nii');). test_voxel_number > is just > some voxel of the volume that I'm using as an example > in this > sanity check (I set it to 4000 in the sample code but it > could have been anything else). I'm using > -(abs(t.vol(test_voxel_number) > )) because that is how I think the p-value is > calculated from > the t-statistic is a 2 tailed test. (See for instance the > matlab code of the built-in ttest.m function where you > have p > = 2 * tcdf(-abs(tval), df) with df being the degrees of > freedom.) Still if I used the alternative you sugggest, > without the minus sign, I get: > > my_pval=-log10(2*tcdf((abs(t.vol(test_voxel_number))), > x.DOF)) > > my_pval = > > -0.1690 > > While I still have the stored p-value of > > stored_pval = > > -0.4055 > > > Thanks again! > On Thu, Nov 11, 2010 at 10:02 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > what is t.vol(test_voxel_number)? Why do you use > -(abs(t.vol(test_voxel_number))) instead of > +(abs(t.vol(test_voxel_number)))? > > doug > > Pablo Polosecki wrote: > > Dear experts, > > For different reasons I found myself double > checking the > relationship between t-values in t.nii and p-values > stored in > sig.nii. If I use the following matlab code I > thought > that I > should get the values of my_pval and stored_pval > to be the > same (except perhaps for the sign): > > cd(fullfile(basedir,session,'bold',anal,contrast)) > x=load('../X.mat') > t=MRIread('t.nii'); > sig=MRIread('sig.nii'); > test_voxel_number=4000; > > my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))), > x.DOF)) > stored_pval=sig.vol(test_voxel_number) > > > > However I get: > stored_pval = > > -0.4055 > > my_pval = > > 0.2804 > > Am I doing something wrong here? My FreeSurfer > version > is 4.5 > Thank you! > > -- Pablo Polosecki > Graduate Fellow > Laboratory of Neural Systems > The Rockefeller University > 1230 York Avenue, Box 9 > New York, NY 10065 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the > Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the > e-mail was > sent to > you in error > but does not contain patient information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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FreeSurfer ROI masks for DTI tractograpy
by Jason Tourville 11 Nov '10

11 Nov '10

Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring. One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this? Many thanks for any feedback you can provide. Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Cognitive and Neural Systems Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755

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fsaverage6
by Goldman, Aaron (NIH/NIMH) [C] 11 Nov '10

11 Nov '10

Hi, I had a question in reference to the following message (posted by Nick Schmansky): "1. in freesurfer v5, there are now multiple fsaverage subjects with varying number of vertices. fsaverage6 has about 40,000 vertices per hemi, so you can just include the flag: --target fsaverage6 after the -qcache flag, and it will use that as the target instead of fsaverage (producing files like 'rh.thickness.fsaverage6.mgh', which will have 40K thickness samples)." As I was also interested in trying this out, I ran the following in v5: recon-all -qcache -target fsaverage6 -s $subject However, recon-all failed to find fsaverage6, and I also couldn't manually find it in $FREESURFER_HOME. If this is included in the current distribution, where do I need to look? Thanks, Aaron

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discrepancy between p-values computed from t.nii and those stored in sig.nii
by Pablo Polosecki 11 Nov '10

11 Nov '10

Dear experts, For different reasons I found myself double checking the relationship between t-values in t.nii and p-values stored in sig.nii. If I use the following matlab code I thought that I should get the values of my_pval and stored_pval to be the same (except perhaps for the sign): cd(fullfile(basedir,session,'bold',anal,contrast)) x=load('../X.mat') t=MRIread('t.nii'); sig=MRIread('sig.nii'); test_voxel_number=4000; my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))), x.DOF)) stored_pval=sig.vol(test_voxel_number) However I get: stored_pval = -0.4055 my_pval = 0.2804 Am I doing something wrong here? My FreeSurfer version is 4.5 Thank you! -- Pablo Polosecki Graduate Fellow Laboratory of Neural Systems The Rockefeller University 1230 York Avenue, Box 9 New York, NY 10065

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Re: [Freesurfer] shift in freeview
by Ruopeng Wang 10 Nov '10

10 Nov '10

Hi Alexander, Would it be possible to send me the volume file and one surface file that has this shift problem? Thanks, Ruopeng On 11/10/10 9:10 PM, Alexander Hunold wrote: > > Dear experts, > > I am perplexed how to fix the problem which is shown in the pictures. > The volume is the T1.mgz. The surfaces are computed by MNE (red -- > inner_skull, yellow -- outer_skull, green -- outer_skin). In TkMedit > the inner and outer skull are aligned to the T1.mgz, respectively. > > I used <mne_watershed_bem> and <mne_setup_forward_model> to get the > surfaces. > > I get the same shift with all surfaces I compute with > mne_write_surface, as well. > > Since I would like to visualize 3-4 surfaces with a mri volume I would > like to use freeview instead of TkMedit. > > Do you have any hint how to fix that shift problem? > > Thanks so much, > Alexander > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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shift in freeview
by Alexander Hunold 10 Nov '10

10 Nov '10

Dear experts, I am perplexed how to fix the problem which is shown in the pictures. The volume is the T1.mgz. The surfaces are computed by MNE (red - inner_skull, yellow - outer_skull, green - outer_skin). In TkMedit the inner and outer skull are aligned to the T1.mgz, respectively. I used <mne_watershed_bem> and <mne_setup_forward_model> to get the surfaces. I get the same shift with all surfaces I compute with mne_write_surface, as well. Since I would like to visualize 3-4 surfaces with a mri volume I would like to use freeview instead of TkMedit. Do you have any hint how to fix that shift problem? Thanks so much, Alexander

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Freesurfer