Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

success and failure of wm surfaces in (almost) identical structural image
by Melanie Ganz 28 Aug '14

28 Aug '14

Dear Freesurfer community, We've encountered a strange situation where the pial and wm surface delineation is successful for one image but contains wm (and subsequent pial) errors for another, almost identical structural image (see attached image, red and yellow are for the successful surface and blue and green are for the failed one). We've tried to identify the source for this discrepancy but I'm at a loss. All voxels of the original input images are identical to the 4th decimal and when converted to orig.mgz only a few voxels appear to be different due to rounding, none of which overlap with the wm surface errors. Both images were processed on the same setup (hardware and software, Freesurfer stable 5.3). Unfortunately, this error is quite systematic in my dataset; about 10% of the images show this type of error. Any suggestions on how to investigate this? I've uploaded example of good and bad at recon ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming/failed_wm_recon.tar.gz in case you'd like to have a closer look. Thanks for your help. Vincent and Melanie

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watershed surface to volume rendering
by Sherwood, Matt 28 Aug '14

28 Aug '14

Freesurfer, We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, inner skull, outer skull and outer scalp surfaces. We are particularly interested in these volumes for our study. Is there a way to convert these surface to volumes representative of CSF (layer between brain/skull), skull (inner to outer skull surface) and skin (outer skull to outer scalp)? Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherwood(a)wright.edu<mailto:matt.sherwood@wright.edu>

2 1

freesurfer version vs cvs version
by Joel R Pieper 28 Aug '14

28 Aug '14

Hello, I have 80 subjects' MRIs that were segmented in 2009 with a version of freesurfer that included this (cvs_version $Id: mri_segstats.c,v 1.11.2.5 2006/04/13 18:57:07 nicks Exp $) in the aseg.stats output. The other 19 of my subjects segmented in 2013 display this (cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $) in the output. I think this latest version the 19 subjects were run on is freesurfer 4.4.0 but I'm not sure which freesurfer version the older segmentations were run on. The volumes I am looking at are significantly different between the subjects segmented in 2009 and those segmented in 2013. I would like to remove any bias in my data due to different software versions. Is there a way to know which freesurfer version output the older cvs_version so I can download that and resegment my 19 subjects to remove version bias? This would be much quicker than running all 100 subjects on the newest freesurfer version. Joel Pieper

2 2

recon-all -openmp N question
by Krieger, Donald N. 28 Aug '14

28 Aug '14

The documentation for the 5.2.0 release (2Mar2013) states that -openmp works for the CentOS 6 distribution only. Is this still the case? Or does it work for CentOS 7 ? any other Linux version ? Thanks, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

2 2

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. To find more information and apply, go to the following website: https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szLocationI… Enter req # 111826

1 0

recon-all normalization: bias field output
by Barbara Kreilkamp 28 Aug '14

28 Aug '14

Dear all, Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities. Thank you for your help, Barbara

3 5

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

28 Aug '14

1 0

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*

2 1

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.

2 2

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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Freesurfer August 2014