Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

mri_normalize -noconform flag doesn't work in FS 5.0
by Falk Lüsebrink 03 Nov '10

03 Nov '10

Dear FreeSurfers, The noconform flag of mri_normalize doesnt seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with an isotropic resolution of 0.7mm using recon-all cm autorecon1 s <subject id> as the command line. The conformation is skipped until mri_normalize, but afterwards the output volume T1.mgz is conformed. Although the log during mri_normalize says: not interpolating and embedding volume to be 256^3 I have been trying to run it using the recon-all script and running mri_normalize by hand, the error is the same. A fix is highly appreciated. Thanks, Falk Lüsebrink

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CSF Volume
by Elena Molina 02 Nov '10

02 Nov '10

Hi, I would like to calculate the total CSF volume using FS. How should I proceed? Thanks in advance. Elena

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[Fwd: Re: Segmentation fault during mri_segment]
by Diandra Lucia 01 Nov '10

01 Nov '10

Hi freesurfers, To summarize the forwarded thread, some months ago I was experiencing segmentation faults at the mri_segment step in the processing stream, and the fix turned out to be running that particular caselist with v5. My lab is still using 4.2.0 in general, however, since we would have to rerun a couple hundred cases with the new version; thus, we probably won't do an update until a future major version release, like v6 or something. So my question now is, we're experiencing this same problem with a couple scans in our general data set (my guess is that this is due to a relatively high, i.e. >10,000, number of "sparsely connected voxels"?). We want these scans' FreeSurfer data to be compatible with our other FreeSurfer data, so I was wondering if there is a solution to this problem that doesn't involve running these with v5. Is there any hope for us in that respect? Thanks, Diandra -------- Original Message -------- Subject: Re: [Freesurfer] Segmentation fault during mri_segment Date: Fri, 30 Jul 2010 08:19:29 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Diandra Lucia <diandra(a)bwh.harvard.edu> References: <AANLkTimMnZL_OcAvEs-wlMwckBaREviS97cwRqd_7_Dm(a)mail.gmail.com> <Pine.LNX.4.62.1007212054060.9035(a)gate.nmr.mgh.harvard.edu> <AANLkTil_Tzs_-6y0xbGE3sDjxTMfdxMAFDmdx-P8bJRp(a)mail.gmail.com> <Pine.LNX.4.62.1007231724570.30598(a)gate.nmr.mgh.harvard.edu> <AANLkTimVoVhDKe0K+3XyO5QpTJ-oncnCLcMh_w=Bx9Ho(a)mail.gmail.com> Hi Diandra, you can read the release notes when it's out and decide. There are a bunch of changes, and it depends on what you care about cheers Bruce On Thu, 29 Jul 2010, Diandra Lucia wrote: > Hi Bruce, > > Sorry for the delay -- yeah, I guess I can do that for these cases, as > this is actually a collaborator's data. We have such a large dataset > internally, though, that rerunning all of our cases would be a pain... > But this set is pretty small, so we can run them all on v5. (How > improved is v5? Would it be worth considering rerunning >100 cases?) > > Thanks, > Diandra > > On Fri, Jul 23, 2010 at 5:25 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Diandra, >> that one ran through fine for me. Do you want to wait a couple of weeks for >> V5 to be out and try it? >> >> Bruce >> On Thu, 22 Jul 2010, Diandra Lucia wrote: >> >>> Hi Bruce, >>> >>> I sent you a sample case via >>> https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html; please >>> let me know if you need anything else. I just sent it to your >>> address; let me know if I need to share it with others as well. >>> >>> Thanks so much, >>> Diandra >>> >>> >>> On Wed, Jul 21, 2010 at 8:54 PM, Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> Hi Diandra, >>>> >>>> can you send us one of these datasets so we can see if we can track it >>>> down? >>>> >>>> thanks >>>> Bruce >>>> On Wed, 21 Jul 2010, Diandra Lucia wrote: >>>> >>>>> Hi again, >>>>> >>>>> As we process more cases, we've run into four cases that have had the >>>>> same problem. Each has segfaulted during mri_segment during >>>>> autorecon2; here is one example: >>>>> >>>>> #@# Mask BFS Mon Jul 19 23:38:35 EDT 2010 >>>>> /home/pnlstaff/freesurfer/subjects/case2403/mri >>>>> >>>>> mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz >>>>> >>>>> threshold mask volume at 5 >>>>> Writing masked volume to brain.finalsurfs.mgz...done. >>>>> #-------------------------------------------- >>>>> #@# WM Segmentation Mon Jul 19 23:38:41 EDT 2010 >>>>> >>>>> mri_segment brain.mgz wm.seg.mgz >>>>> >>>>> doing initial intensity segmentation... >>>>> using local statistics to label ambiguous voxels... >>>>> computing class statistics for intensity windows... >>>>> WM (105.0): 105.7 +- 6.1 [80.0 --> 125.0] >>>>> GM (72.0) : 71.1 +- 8.6 [30.0 --> 96.0] >>>>> setting bottom of white matter range to 79.6 >>>>> setting top of gray matter range to 88.2 >>>>> 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... >>>>> 12443 sparsely connected voxels removed... >>>>> thickening thin strands.... >>>>> Segmentation fault >>>>> Linux compute-2-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST >>>>> 2006 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>> recon-all exited with ERRORS at Mon Jul 19 23:40:24 EDT 2010 >>>>> >>>>> >>>>> They all segfaulted at exactly the same place. These were run with >>>>> freesurfer-Linux-rh9-stable-pub-v4.2.0 (without the new version of the >>>>> mri_ca_normalize you sent me recently). Please let me know if you need >>>>> anything else (data, etc) to help troubleshoot this. >>>>> >>>>> Thanks, >>>>> Diandra >>>>> >>>>> >>>>> >>>> >>> >>> >>> >> > > > >

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Re: [Freesurfer] Source matrix with zero determinant
by Douglas N Greve 01 Nov '10

01 Nov '10

you need to make sure that the direction cosines are correct. You can check whether it is correct by looking at it in tkmedit, ie, tkmedit -f yourfile.nii It should look coronal in the coronal view, etc. If it is wrong, there's no easy way to fix it. I'd go back to the original dicoms if you can. doug Lisa F. Akiyama wrote: > Hi Doug, > > I was able to locate the original nifti files that contain all slices > in one file downloaded from NIHPediatrics. > > I was able to run : > > *recon-all -autorecon1 -notalairach -s 1433_1101 -i > $SUBJECTS_DIR/1433_1101/mri/orig/deface_1433_V1_t1w.nii -force* > > But the output file orientations are still rotated in a odd way. > Is there a way to fix these output orientations? > Listed below are the mri_info outputs for both the input and the > output files. I'll also attach the input and the output files. > > <INPUT FILE mri_info> > > type: nii > dimensions: 256 x 256 x 46 > voxel sizes: 0.9766, 0.9766, 3.0000 > type: FLOAT (3) > fov: 250.000 > dof: 0 > xstart: -125.0, xend: -125.0 > ystart: -125.0, yend: -125.0 > zstart: -69.0, zend: -69.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip > angle: 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, > c_r = -11.5117 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, > c_a = 9.4883 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, > c_s = -4.1000 > Orientation : RAS > Primary Slice Direction: axial > > voxel to ras transform: > 0.9766 0.0000 0.0000 -136.5116 > 0.0000 0.9766 0.0000 -115.5116 > 0.0000 0.0000 3.0000 -73.1000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 2.86102 > > ras to voxel transform: > 1.0240 -0.0000 -0.0000 139.7879 > -0.0000 1.0240 -0.0000 118.2839 > -0.0000 -0.0000 0.3333 24.3667 > 0.0000 0.0000 0.0000 1.0000 > > > <OUTPUT FILE mri_info> > > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip > angle: 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, > c_r = -11.5116 > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, > c_a = 9.4883 > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, > c_s = -4.1000 > > talairach xfm : > /usr/local/freesurfer/subjects/1433_v1_multinii/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1.0000 0.0000 0.0000 116.4884 > 0.0000 0.0000 1.0000 -118.5117 > 0.0000 -1.0000 0.0000 123.9000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 0.0000 0.0000 116.4884 > -0.0000 -0.0000 -1.0000 123.9000 > -0.0000 1.0000 -0.0000 118.5117 > 0.0000 0.0000 0.0000 1.0000 > > > > Thank you in advance. > > > Best, > Lisa Akiyama > ** > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 12:05 PM, Lisa F. Akiyama <lrisa87(a)uw.edu > <mailto:lrisa87@uw.edu>> wrote: > > Hi Doug, > > Thanks for the tips. I will look into putting all the slices into > one volume. > > > Best, > Lisa > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 11:53 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > You would have to take all 45 slices and put them into one > volume. It won''t work slice-by-slice. It is probably the case > that this won't work either as we usually use high res data. > For intensity normalization, maybe it will work. > > > doug > > Lisa F. Akiyama wrote: > > Hi Doug, > > There are approximately 40~45 slices of each individual's > brain, > each saved as separate nifti files. > I'm trying to use FreeSurfer for the Non-uniform intensity > normalization and skull strip functions. > So, if I edit the header of each nifti file so that the > slice thickness isn't 0, > recon-all -autorecon1 should work? > > Thanks. > > Best, > Lisa > > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 10:55 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: > > The problem is that the slice thickness is 0. BTW, I > don't know > what you are planning to do with this in freesurrfer, > but it's not > going to work with only one slice. > > > doug > > Lisa F. Akiyama wrote: > > Hi Doug, > > Here's the result of mri_info: > > ubuntu:~> mri_info > > $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > INFO: using NIfTI-1 qform > Volume information for > > /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > type: nii > dimensions: 256 x 256 x 1 > voxel sizes: 0.9766, 0.9766, 0.0000 > type: FLOAT (3) > fov: 250.000 > dof: 0 > xstart: -125.0, xend: -125.0 > ystart: -125.0, yend: -125.0 > zstart: -0.0, zend: -0.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 > msec, flip > angle: 0.00 degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 1.0000, y_r = 0.0000, z_r > = -0.0000, > c_r = -11.5117 > : x_a = 0.0000, y_a = -1.0000, z_a > = -0.0000, > c_a = 8.5118 > : x_s = 0.0000, y_s = 0.0000, z_s > = 1.0000, > c_s = -73.1000 > Orientation : RPS > Primary Slice Direction: axial > > voxel to ras transform: > 0.9766 0.0000 -0.0000 -136.5116 > 0.0000 -0.9766 -0.0000 133.5117 > 0.0000 0.0000 0.0000 -73.1000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 0 > > ras to voxel transform: > mat = NULL! > MatrixFree: NULL mat POINTER! > > > Thank you. > > Best, > Lisa > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing > this e-mail. > > > > On Thu, Oct 28, 2010 at 4:25 PM, 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: > > mri_info *deface_1433_V1_t1w_slice0.nii > > > > -- 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> > > > > > > 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> > 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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Running Recon-all without the skullstrip & neck removal steps
by Toren Stearns 01 Nov '10

01 Nov '10

I'm trying to run recon-all on brains that have already been skullstripped and had their necks removed. I ran autorecon1 without the skullstrip steps. To generate brainmask.mgz I just created a renamed copy of T1.mgz. Is this okay? I'm currently stuck on autorecon2's segstats step. (For autorecon2 I opted out of the neck removal.) At the segstats step I get an error that says that I am missing transforms/talairach_with_skull.lta. talairach_with_skull.lta is created from autorecon1's skullstripping step, but I skipped that step because my brain is already skullstripped. How would I generate this file so that I may proceed with segstats?

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Output dt_recon
by Ed Gronenschild 01 Nov '10

01 Nov '10

Hi, Is it possible to give the exact definition of the output of dt_recon, in particular: - adc - ra - radialdiff - ivc Ed

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Re: [Freesurfer] 3 button mouse for macintosh
by Ed Gronenschild 01 Nov '10

01 Nov '10

Dear Isabelle, In the System Preferences -> Keyboard & Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed > Hello, > > Just getting started with Freesurfer. > I'm hoping someone can recommend a 3-button mouse that works well > with Freesurfer, on a Macintosh. I purchased a Logitech wireless > mouse, but can't get it to work properly. Freesurfer does not seem > to recognize the 2nd and 3rd buttons as any different than the 1st/ > left button. So I cannot get edits to work, for example, when > trying to edit white matter. > > Any tips appreciated. > > -Isabelle > > > --------------------------------------------------------------------- > Isabelle M. Rosso, Ph.D. > Assistant Professor of Psychology > Licensed Psychologist -- Certified Health Service Provider > > McLean Hospital > Neuroimaging Center > 115 Mill Street > Belmont, MA 02478 > Phone: 617.855.2607 > Fax: 617.855.2770 > irosso(a)hms.harvard.edu

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Freesurfer November 2010