Freesurfer

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30099 discussions

Research Assistant Position at the University of Washington
by McLaughlin, Katie 28 Aug '14

28 Aug '14

Research Assistant Position Integrated Brain Imaging Center University of Washington An experienced, independent, and organized individual is sought for a full-time Research Coordinator position working with Natalia Kleinhans, Ph.D., and Katie McLaughlin, Ph.D., at the Integrated Brain Imaging Center at the University of Washington. The individual in this position would assist with data collection and data processing for two neuroimaging studies of children. Principal duties include: 1) assisting with the administration and support of research projects and activities, including participant recruitment, development of surveys and flyers, and programming fMRI tasks; 2) assisting in data collection through active interaction with child participants, including telephone screening interviews, in-person interviews, and fMRI data acquisition; and 3) conducting pre-processing and analysis of MRI, fMRI, DTI, and MRS data. Ability to work in command line operating systems (Linux) and perform basic shell scripting is required. Previous research or clinical experience with children and experience with other programming languages (e.g., python) is preferred. This position would be an excellent fit for applicants interested in obtaining doctoral training in cognitive neuroscience, clinical psychology, or developmental psychology.

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questions about mri_make_bem_surfaces
by gamaliel huerta urrea 28 Aug '14

28 Aug '14

Hi I have questions about the use of the function: mri_make_bem_surfaces I need to create a surface from a set of MRIs in DICOM format. I would like if someone could help me. The only reference I have of the function is: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_make_bem_surfaces and does not say much about its use. Any help is welcome. My idea then is to generate a 3D head model fieldtrip toolbox of Matlab. Regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

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3dvolreg.afni error during mc-sess
by Milde, Christopher 28 Aug '14

28 Aug '14

Dear Freesurfer Experts, I'm struggling with running only motion correction. After running mktemplate-sess which ran well, the mc-sess terminates with the following error. The terminal otput is attached: "3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni" Some important comments: 1.) 3dvolreg.afni is within the bin-folder of Freesurfer 2.) I use partial-field-of-view EPI 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a prerequisite to use unpacksdcmdir)? Thank you, for your support!!! Greets Christopher TERMINAL OUTPUT: mc-sess -s PM_00031 -d $FSF_DIR -per-run -fstem -outfmt nii.gz [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 -outfmt nii.gz fmt: Undefinierte Variable. [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run -fstem 20 Logfile is /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold.log ------------------------------------------- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923 RunList: 001 002 004 ------- ************************** ----------- ------- Motion Correcting Run 001 ----------- ------- ************************** ----------- sess = PM_00923 Fr 22. Aug 09:35:07 CEST 2014 mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz log file is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is 001/tmp.mc-afni2.19767 #@# -------------------------------- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/tempvol.nii.gz... #@# -------------------------------- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 001/20.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing to 001/tmp.mc-afni2.19767/invol.nii.gz... #@# -------------------------------- /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix 001/tmp.mc-afni2.19767/outvol.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Ungültiger leerer Befehl.

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Problems with mri_watershed: almost no skull stripping
by Úrsula Pérez Ramírez 28 Aug '14

28 Aug '14

Hello, I'm having troubles trying to obtain only the brain in T1-weighted RM images that contain metastases. First of all I have converted the DICOM images to mgz with "mri_convert /usr/local/freesurfer/subjects/A0D0C0.dcm /usr/local/freesurfer/subjects/case1.mgz" . Then, I have employed "mri_watershed -atlas /usr/local/freesurfer/subjects/case1.mgz /usr/local/freesurfer/subjects/brainmaskcase1.mgz" but as I see with freeview, I obtain the original images with a really bad or any skull stripping. For example, in one case, the left part is removed a lot and the right is intact. I have lowered the threshold but nothing changes. How could I solve it? I'm working in VirtualBox and I didn't find the ".license" file, so I haven't copied the three lines. Is it necessary? Thank you very much Regards, Úrsula

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error in pre-processing in TRACULA
by 渡辺杏里 28 Aug '14

28 Aug '14

Dear TRACULA experts Hello. I am running TRACULA, but it exited an error very early in pre-processing. My data is not a format in DICOM but .nii, does this cause the error? I set the dcmlist to .nii file (in attachment). Could anyone help me? This is the error log and I attached the configuration file. -error log- [watanabeanris-Mac-Pro:mybook/Anri/diffusion_tutorial] watanabeanri% trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Aug 22 11:03:45 JST 2014 mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii... TR=7175.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996496, -0.0735924, -0.0397398) j_ras = (-0.0756091, 0.995787, 0.0518831) k_ras = (-0.0357542, -0.0547061, 0.997862) writing to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz... cp /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs flip4fsl /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 fslswapdim /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz x y z /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory Darwin watanabeanris-Mac-Pro.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Aug 22 11:03:46 JST 2014 Many thanks for your help. Best Wishes, Anri WATANABE ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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Obtaining volume measures based on T2 image
by Nobuko Kemmotsu 27 Aug '14

27 Aug '14

Dear Freesurfer experts, I have a project where I would like to compute volumes of the olfactory bulb. I understand olfactory bulb is currently not in the freesurfer atlases, so I would need to manually trace it for me to get the volume measures. Given that olfactory bulb appears easier to be seen on T2 scans, I am considering using T2 images for this purpose, but I also plan on obtaining high resolution T1 for reconstruction purposes. It may also be of my interest to try to automate this segmentation for future usage. How would I go about this process using FreeSurfer?

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FW: does Tracula correct for CSF contamination
by Laura Christine Anderson 27 Aug '14

27 Aug '14

Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF contamination? Thanks for your time, Laura -- Laura Anderson, B.A. Graduate Student Clinical / Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112

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Re: [Freesurfer] problem with format of CT dicoms
by Borzello, Mia 27 Aug '14

27 Aug '14

Hi Freesurfers, Apologies, I've never used this format before. Here's the error: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz 3. UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped) Thanks so much, m ________________________________________ From: Borzello, Mia Sent: Friday, August 22, 2014 1:14 PM To: Freesurfer support list Subject: RE: [Freesurfer] problem with format of CT dicoms Hi Freesurfers, Apologies, I've never used this format before. Here's the error: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_SurferOutput/mri For additional information: 1. Neuropace2JB 2. mri_convert -i /autofs/space/huygens_001/users/mia/subjects/Neuropace2JB_PostOp_CT/BENNETT^JACOB^F/1.2.124.113532.80.22200.7094.20140812.155724.232143365/1.3.12.2.1107.5.1.4.11060.30000014081213381840600011010/IMG84.dcm -o ct.mgz 3. UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault (core dumped) Thanks so much, m ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 12:43 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with format of CT dicoms Hi Mia, please follow the instructions on the web site below for submitting bug reports. thanks doug On 08/22/2014 12:37 PM, Borzello, Mia wrote: > Right, sorry. I was running a command with mri_convert in order to convert the ct dicoms to mgz format. The error I ran into was: > UseSliceScaleFactor 0 (slice 0: 1) > Segmentation fault (core dumped) > > Thanks, > m > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, August 22, 2014 12:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] problem with format of CT dicoms > > Hi Mia, do you realize that your description of the problem is too vague > for us to help you? If you want help in a timely fashion, please include > more detail like the problem you ran, the command-line arguments, the > terminal output, etc. Please see the following web page for the types > information we are looking for: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > The easier you make it for us, the more likely you are to get help. > > thanks > doug > > > On 08/22/2014 12:17 PM, Borzello, Mia wrote: >> Hi Freesurfers, >> >> I'm in the process of creating the ct.mgz file, but it is erroring and >> saying there is a "segmentation fault (core dumped)." >> >> What can I do to remedy this? >> >> Thanks, >> m >> >> >> _______________________________________________ >> 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview: Creating and using a LUT with a single region
by Tamás Hauer 27 Aug '14

27 Aug '14

Hi, I am trying to use a LUT which picks out just one region of the segmentation, e.g.: $ cat HCOnlyColorLUT.txt #$Id: FreeSurferColorLUT.txt,v 1.70.2.7 2012/08/27 17:20:08 nicks Exp $ #No. Label Name: R G B A 0 Unknown 0 0 0 255 17 Left-Hippocampus 220 216 20 0 with which I expect the segmentation overlay to have only one yellow region corresponding to the left HC. I run the command line: $ freeview -v T1.mgz aseg.mgz:colormap=lut:lut=HCOnlyColorLUT.txt after which I am getting the overlay displayed as below. I must be doing something stupid, could you, please help me out? Thanks Tamás -- Tamás Hauer McMRI AG Neugasse 55 9000 St. Gallen, Switzerland Tel: (+41)-76-380-7379 Tel: (+41)-71-913-0580 Fax: (+41)-71-913-0589

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White matter lesions
by Elijah Mak 27 Aug '14

27 Aug '14

Dear Freesurfer Experts, I am hoping to do some WML analyses in some patient groups by using the measure of T1 hypointensities derived from the ASEG analyses. Is there a way to view and check the accuracy the WML mask for each subject? Also, how may I go about performing a voxelwise analyses of the WML masks between 2 groups? I am referring to the following paper: http://www.ncbi.nlm.nih.gov/pubmed/21518999 Any help and advice will be greatly appreciated. Thank you all for your time! Many Thanks, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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