Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

recon-all fails with MCSRCH ERROR and tumors
by Joshua Goh 28 Aug '14

28 Aug '14

Dear FS List, I recently encountered a couple of issues with some patient data that caused recon-all not to work. Recon.log files attached. The first error seems to be during the EM alignment step and has an MCSRCH ERROR and applies to 1030813-1, 1030813-3, and P201503416. The T1s look generally fine except that there might be some WM degradation. But I’ve seen worse that worked. Is this because the brain is too far off the center for alignment to the GCA atlas? Would reorienting or manual centering here help? The second error applies to U200057992 and may be a segmentation problem. For this case, there is a tumor in the WM, along with WM degradation. Is Freesurfer able to handle WM tumors? Thanks! Josh

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recon-all fails with MCSRCH ERROR and tumors
by Joshua Goh 28 Aug '14

28 Aug '14

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Output Time
by Isaiah C. Smith 28 Aug '14

28 Aug '14

Hello Experts, I was wondering if there is a way to short time of recon-all; I see that by using some of the parameters, one can get rid of different outputs. For mne forward models and inverses is there a recommended list of necessary and unnecessary outputs? Isaiah Smith

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Creating ROI
by Diaz Rodriguez, Juan 28 Aug '14

28 Aug '14

I am trying to create a spherical ROI mask in the form of a volume file with 2.5 cm radius. I also have to specify the center of the ROI location. What is the best way to accomplish this? I intend to use this to extract freesurfer cortical thickness values for a region-of-interest (ROI) defined in volume space as described in https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

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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>

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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

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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

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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

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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

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