Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

data conversion
by Al-Radaideh Ali 15 May '09

15 May '09

Dear FreeSurfer experts, I used 0.6mm isotropic resolution MPRAGE ( matrix size 320 x 320 ) and 260 slices in freesurfer. The output (.mgz) has a different resolution and matrix size (1mm isotropic resolution and 256 x 256 matrix size). I used mri_convert to convert the output image from mgz to analyze. is there any way I can get back to the original resolution and matrix size, please? Thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Processing high resolution data
by Falk Lüsebrink 15 May '09

15 May '09

Hi FreeSurfers, Im still trying to process some high resolution data through the freesurfer stream, but it is constantly failing during several different stages. The biggest issue is the skull stripping and Im still trying to get good results here. Using the hires switch during autorecon1 normally leaves to much skull or cuts of too much tissue. Adjusting the parameters during mri_watershed (like changing the preflooding height or using the atlas switch) doesnt work too well in most cases. I tried to manually edit the brainmask.mgz with tkmedit but I encountered another problem. I was using data with an isometric voxel size of 0.6mm and removed every bit of left skull from the coronal view. Afterwards I ran autorecon2 but it did exit, so I viewed the brainmask in Slicer and noticed that probably every second slice was skipped in tkmedit. I also tried using the cm switch during autorecon1 to create the .lta file for the skull stripping stage, which I was hoping to improve the results. But either mri_watershed exists with an error in which it states that the WM intensity is 0 and therefore below the csf intensity and that I should check the volume, though I cant find anything unusual, or it exists with the error segmentation fault. I read that these segmentation fault errors seem to occur if the system runs out of memory, but as Im having 32gb ram and 16gb swap memory I dont think this is the reason. Another approach I was using is to use either a brainmask created by a stream of Slicer and then importing it to freesurfer or to use a brainmask created by a conformed stream, then using mri_vol2vol to resample it to the original resolution and process the other stages. The first approach should work fine, but the volume I used wasnt well processed during mri_fill. Most voxels were recognized as being part of the left hemisphere and only a few (about 150) were marked as belonging to the right hemisphere. And I was unable to fix this issue. The second approach seems also to be a good idea, but the resulting brainmask is blurred due to the upscaling. I noticed that using the hires switch the brainmask isnt really used as a mask during normalization2 but is just normalized again and the output is written as brain.mgz. If I want to use the brainmask as a mask (as it should be intended) should I use it to mask the T1.mgz? Like mri_normalize noconform mask brainmask.mgz T1.mgz brain.mgz? In the original stream the brainmask is used here to mask the norm.mgz, which I quite dont understand as the norm.mgz is already stripped. But maybe I just get something wrong. Yesterday I was able get a good skull stripping by running mri_nu_correct again with T1.mgz as the input and using the distance 25 stop 0.0001 switches (which I read of in another mail here on the list to improve results using 3T data). But recon-all exists at the beginning of mris_fix_topology with the segmentation fault error on both hemispheres. I apologize for the long text, but maybe someone can give me some input to try something else or help with existing issues. Thanks in advance, Regards, Falk

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segmentation
by Feng-Xian 14 May '09

14 May '09

Hi, I have some problem. Could you get me some suggestion? I get a simulation brain with no-adding noise from BrainWeb. Then, I add 1% noise and 5% noise, respectively, to the simulation brains. When I finished these simulation brains through FreeSurfer, I found that the cortical thickness of these two groups (1% vs 5%) has a bias. Would you get me some comment? I guess the finding of bias maybe has a great relationship with the process of segmentation. Would you tell me what to do segmentation in FreeSuefer? Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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cluster spanning multiple labels
by Siddharth Srivastava 14 May '09

14 May '09

Hi everyone, For a cluster spanning multiple labels based on a specific annotation, is it possible to automatically generate a list of labels (text) of the regions it overlaps with? What command/process should do this? mri_surfcluster is just providing me with the parcellation where the maxima is located. thanks, sid.

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FSL --> FreeSurfer
by Vina Goghari 14 May '09

14 May '09

Hello all, I have group contrast fMRI activations analzyed by FSL Flame 1 that I want to extract individual thickness data for each subject from data processed by FreeSurfer? Is that possible and if so, how? Thanks! Vina

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[Fwd: mri_convert batch converting]
by ozgun ozalay 14 May '09

14 May '09

also i've tried ; //mri_convert -it dicom -ot nii /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA /home/ozgun/AnV/ok.nii / output was; / $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA... Starting DICOMRead2() dcmfile = /home/ozgun/AnV/dti samples/KARABAY_NURI_.MR.EGE_HEAD.4.1.2008.07.21.21.20.51.578125.24527595.IMA dcmdir = /home/ozgun/AnV/dti samples Ref Series No = 4 Found 73 files, checking for dicoms Found 70 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 70 nslices = 1 ndcmfiles = 70 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10700.00, TE=103.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation *MRIresample(): error inverting matrix; determinant is nan, matrix is:* -2.000 -0.000 nan nan; -0.000 -2.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; /i think problem occurs because of the bold line. Does anyone have any idea to correct this ? Thanks anyway Yours Ozgun

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mri_convert batch converting
by ozgun ozalay 14 May '09

14 May '09

Hi; i have 70 Siemens .ima files in a single directory. Does anyone know how to convert ALL files in a folder into another format using mri_convert ? Do i have to convert them one by one? Does "--sdcmlist" option does this? Simple usage; /mri_convert <input file> <outputfile>/ ie: mri_convert /home/ozgun/AnV/aman.ima /home/ozgun/AnV/aman.nii Thanks anyway Ozgun

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RE: GLUT Error
by Andrew Jahn 14 May '09

14 May '09

Hi again, I have been encountering an error when attempting to use either tksurfer or tkmedit via VNC on a local server. Here is the output whenever I type tkmedit or tksurfer: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: 1.0 I looked through the threads regarding this problem, but still have been unable to find a solution. The output of 'cat /etc/redhat-release' is Red Hat Enterprise Linux WS release r (Nahant Update 7) and here is the output from the command ldd `which tkmedit.bin`: libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib64/libtk8.4.so (0x0000003d43d00000) libtcl8.4.so => /usr/lib64/libtcl8.4.so (0x0000003d43b00000) libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000003d48300000) libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003d48500000) libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000003d44f00000) libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000003d44d00000) libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x0000003d47900000) libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x0000003d47100000) libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x0000003d4c000000) libz.so.1 => /usr/lib64/libz.so.1 (0x0000003d45100000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x0000003d48a00000) libdl.so.2 => /lib64/libdl.so.2 (0x0000003d44b00000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003d45300000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003d47500000) libm.so.6 => /lib64/tls/libm.so.6 (0x0000003d44900000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003d47300000) libc.so.6 => /lib64/tls/libc.so.6 (0x0000003d44600000) libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000002a95586000) libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000003d44400000) libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x0000003d4a100000) libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x0000003d45700000) libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x0000003d45500000) /lib64/ld-linux-x86-64.so.2 (0x0000003d43900000) Also, here is the content of the .xdebug_tkmedit file following an unsuccessful tkmedit command: tkmedit started: Thu May 14 14:55:44 2009 tkmedit.bin $Id: tkmedit.c,v 1.320.2.9 2009/01/27 20:41:02 greve Exp $ $Name: stable4 $ Any help or advice is greatly appreciated in advance. Thanks! -Andrew

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License Key issue (not recognized)
by ozgun ozalay 14 May '09

14 May '09

Hi; I'm Ozgun Ozalay, researcher at Ege University/Turkey. One of my friends recommended FreeSurfer's "mri_convert" program to convert my Siemens .IMA files to a more common format .nii. i've downloaded freesurfer from your wiki pages and made my registration too. i've recieved an e-mail with details of my license. Upon installing "freesurfer" to /home/ozgun/AnV/freesurfer i configured enviroment too as described in wiki with bash shell; /export FREESURFER_HOME=/home/ozgun/freesurfer/ /source $FREESURFER_HOME/SetUpFreeSurfer.sh/ I recieved no errors during this process. /source /home/ozgun/AnV/freesurfer/SetUpFreeSurfer.sh/ /-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 --------/ /Setting up environment for FreeSurfer/FS-FAST (and FSL)/ /FREESURFER_HOME /home/ozgun/AnV/freesurfer// /FSFAST_HOME /home/ozgun/AnV/freesurfer//fsfast/ /FSF_OUTPUT_FORMAT nii/ /SUBJECTS_DIR /home/ozgun/AnV/freesurfer//subjects/ /MNI_DIR /home/ozgun/AnV/freesurfer//mni/ /FSL_DIR /home/ozgun/AnV/FSL/fsl/ But when i try to execute "mri_convert" it says my license isn't ok. /ozgun@linux-dkvs:~/AnV/freesurfer/bin> ./mri_convert /home/ozgun/AnV/orn.IMA/ //home/ozgun/orn.nii/ /./mri_convert /home/ozgun/AnV/orn.IMA /home/ozgun/orn.nii/ /$Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $/ /reading from /home/ozgun/AnV/orn.IMA.../ /--------------------------------------------------------------------------/ /ERROR: Invalid FreeSurfer license key found in license file/ //home/ozgun/AnV/freesurfer/.license/ /If you are outside the NMR-Martinos Center,/ /go to http://surfer.nmr.mgh.harvard.edu to/ /get a valid license file (it's free)./ /If you are inside the NMR-Martinos Center,/ /make sure to source the standard environment./ /--------------------------------------------------------------------------/ / / I created ".license" file in my freesurfer home directory (/home/ozgun/AnV/freesurfer) and pasted 3 lines from your e-mail to this empty document and saved. Also attaching the .license file i've created. Did i do something wrong? By the way, i'm using OpenSuse 11.1 with kernel 2.6.27.21-0.1-default, KDE 4.1 as desktop enviroment. Thanks anyway ;) #---------------CUT HERE--------------- ozgun.ozalay(a)gmail.com 7235 *CZag.N9G9Ekc #---------------CUT HERE---------------

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smoothing with mri_surf2surf
by Gregory Dierksen 14 May '09

14 May '09

Hi, I want to smooth a cortical thickness map using values only in a specific area. Basically I want to mask out all other segmentations, for example smooth with fwhm of 20 only in the postcentral region. I've used quite a few combinations of the -label-src and -label-trg flags and noticed a slight problem: Using the command line (which seems to give the "best" results): mri_surf2surf --hemi rh --s fsaverage --sval ./rh.Input.mgh --fwhm 20 --label-trg ./postcentral.label --tval rh.Output.mgz When the rh.Input.mgh has been masked before running surf2surf using postcentral.label (so only the postcentral region is non-zero), I get DIFFERENT values than if rh.Input.mgh is NOT previously masked by postcentral.label (ie ALL verticies have non-zero values inside and outside postcentral region). How can I get mri_surf2surf (or perhaps some other command) to smooth only within a specified region without taking values from outside this region? Thanks for the help, Greg

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