Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

ReconAll error
by Hao wen 24 Jun '16

24 Jun '16

Hi, FS experts: I run the reconAlll command with two nii file, and I got some error here, can you help me to check it out, cuz I think I use the command correctly... here is the info for the error: I think the problem is for the mri_convert command, I checked thr orig folder, there is no T1.mgz file! can you tell me why? crash-20160624-204118-guest-_recon_all0.pklz File: crash-20160624-204118-guest-_recon_all0.pklz Node: _recon_all0 Working directory: /tmp/tmpzZyfB0/reconall_workflow/recon_all/mapflow/_recon_all0 Node inputs: T1_files = ['/home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii'] T2_file = <undefined> args = -qcache directive = all environ = {} flags = <undefined> hemi = <undefined> ignore_exception = False openmp = <undefined> subject_id = example2 subjects_dir = /tmp/tmpzZyfB0 terminal_output = stream Traceback: Traceback (most recent call last): File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 18, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1428, in run self._run_interface() File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1538, in _run_interface self._result = self._run_command(execute) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1664, in _run_command result = self._interface.run() File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1033, in run runtime = self._run_wrapper(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1457, in _run_wrapper runtime = self._run_interface(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1491, in _run_interface self.raise_exception(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1415, in raise_exception raise RuntimeError(message) RuntimeError: Command: recon-all -all -i /home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii -qcache -subjid example2 -sd /tmp/tmpzZyfB0 Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /tmp/tmpzZyfB0 Actual FREESURFER_HOME /usr/local/freesurfer Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /tmp/tmpzZyfB0/example2 mri_convert /home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii /tmp/tmpzZyfB0/example2/mri/orig/001.mgz Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s example2 exited with ERRORS at vendredi 24 juin 2016, 20:40:29 (UTC+0200) For more details, see the log file /tmp/tmpzZyfB0/example2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Standard error: Return code: 1 Interface ReconAll failed to run. Thanks in advance

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reconall error
by Hao wen 24 Jun '16

24 Jun '16

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visualizing statistical maps in FreeView
by Lars M. Rimol 24 Jun '16

24 Jun '16

Hi, Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly in FreeView, for purposes of visualizing the results, the same way you can in tksurfer? When I try load an overlay in FreeView, it seems to be expecting a volume file. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Creating spheres in the volume
by Afzal, Afsana 24 Jun '16

24 Jun '16

Hi, This question might have already been answered before but is there a way to take a coordinate in MNI space and create, say, a 5mm sphere in the volume? My goal is to take the sphere in the volume and convert it to a label using something like mri_vol2surf. Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Qdec-correction for multiple comparison
by John Anderson 23 Jun '16

23 Jun '16

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Research Specialist Job Opening at the Center for Healthy Minds
by STACEY M SCHAEFER 23 Jun '16

23 Jun '16

Research Specialist-86782 The Center for Healthy Minds (CHM), a component of the Waisman Center, was founded and is led by neuroscientist Richard J. Davidson. CIHM's mission is to cultivate well-being and relieve suffering through a scientific understanding of the mind. CHM is a leader in rigorous, interdisciplinary basic and translational research aimed at understanding the mind and how to nurture well-being in ourselves and other. CHM communicates these findings to the world, inspires scientists to conduct further research and engages influencers to shift the culture to embrace well-being. The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant screening and scheduling for the longitudinal Midlife in the United States (MIDUS) study. MIDUS is a national longitudinal study of health and well-being. The primary purpose of the study is to examine how individual differences in the neural bases of emotional reactivity, recovery, and sustaining processes relate to health and well-being throughout the lifespan. Degree and area of specialization: A Bachelor's degree is required. A degree in Psychology, Neuroscience or a related field is preferred. Minimum number of years and type of relevant work experience: Well-qualified applicants will have the following required experience: · A minimum of 1 year of experience in a large human subjects' research laboratory. Relevant undergraduate experience may be considered. Well-qualified candidates will have the following preferred work experience: · Experience with community samples and/or minority or aged populations. · Research experience in behavioral, psychophysiological and/or neuroimaging data collection, processing and analysis. · Computer programming skills in Bash, Python, and/or MATLAB. · Familiarity with FSL and/or Freesurfer. · Familiarity with R or similar statistical programs. · Experience using Windows, Mac, and Linux in a secure environment. Principal duties: 80% Data Collection, Data Management, and Data Processing: · Conduct data collection involving self-report, behavioral, neuropsychological, psychophysiological, and neuroimaging-based methods. · Assist with data processing of self-report, behavioral, neuropsychological, psychophysiological, and neuroimaging data. · Ensure the quality and integrity of data collection by performing periodic quality assurance checks, problem solving, and managing research supplies. · Track all study participants and complete data collection logs. · Train personnel in data collection procedures. · Study team coordination and management of undergraduate student workers. 20% Research Participant Recruitment & Screening: · Screen participants and coordinate their participation schedules. · Provide additional information to potential participants as needed. · Work with participants to facilitate travel arrangements and provide support to ensure study retention. · Follow up with participants as necessary. Additional Information: · A criminal background check will be conducted prior to hiring. · A period of evaluation will be required · UW-Madison is an equal opportunity/affirmative action employer. · We promote excellence through diversity and encourage all qualified individuals to apply. · Please indicate in writing if you request that your identity be kept confidential. If you do not indicate your preference to remain confidential, the University may be required to disclose your identify and/or application materials. The identity of finalists and successful candidates will be revealed upon request. See Wis. Stat. sec. 19.36(7). TO ENSURE CONSIDERATION Application must be received by: JULY 06, 2016 In order to apply, please upload your resume and cover letter highlighting your qualifications for this position. Applications must be submitted online at: https://uwjobapply.wisc.edu/Apply.aspx?pvl=86782 Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior Center for Healthy Minds University of Wisconsin-Madison 1500 Highland Avenue Rm T127 (608) 263-9321

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qdec load error missing BLT
by Joshua Lee 23 Jun '16

23 Jun '16

When loading qdec I get can't find package BLT FsgdfPlot::InitFsgdf: Couldn't find fsgdfPlot.tcl on Ubuntu with FreeSurfer5.3

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patch error
by S.V.Shepherd [work] 23 Jun '16

23 Jun '16

Hello all, I'm trying to make a patch and have run into the 'bad vertex' error. It's come up a few times on the listserv, but I never saw a public resolution. One possible source of errors is that I had to do a manual correction in FreeView, including a 'remove intersections' in FreeView. However, tksurfer had no trouble mapping the curvature to the finished surface, so I assume this was not likely to be the source of the error. Details below: $ mris_flatten -w 0 -distances 20 7 lh.cort.patch.3d lh.cort.patch.flat using write iterations = 0 sampling 7 neighbors out to a distance of 20 mm reading patch lh.cort.patch.3d with 1919246708 vertices (2846533.5% of total) MRISreadPatch: bad vertex # (1701060705) found in patch file No such file or directory stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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Qdec
by j.anderson＠publicist.com 23 Jun '16

23 Jun '16

Dear Freesurfer experts, I wanted to run cortical thickness analysis between two groups to check the diffetence in thickness between the groups. I used Qdec My question is regarding correcting for multiple comparisons. There are two options FDR and montecarlo. Which option do you recommend? Are there any role that can force the analysis to be corrected with any of them Thanks John

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recon-all warnings
by Rockers, Elijah D. 23 Jun '16

23 Jun '16

Hello, Doing a recon-all -all yields some deprecation warnings. defined(@array) is deprecated at /freesurfer/mni/bin/nu_estimate_np_and_em line 165. Use of ?PATTERN? without explicit operator is deprecated at /freesurfer/mni/bin/sharpen_volume line 153. I think my results should still be OK because it's a warning, but I just wanted to make sure. Thanks, Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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