Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Surface doesn't match error
by pfotiad＠nmr.mgh.harvard.edu 25 Sep '13

25 Sep '13

Hi FS Community, I have been using control points and adding wm voxels in the wm.mgz volume of a subject, in order to fix the reconstruction, and after doing so for a number of times, when I tried to run the command: tkmedit <subj_ID> brainmask.mgz -aux wm.mgz -surfs the following message popped up: Reading 574 control points... Converting main surface: 100% done. Converting main surface: 100% done. mrisReadTriangleFile(/cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.pial): surface doesn't match /cluster/ichresearch/Petechial/MEG/1424_02042011_CTh_fixed/surf/lh.white No such file or directory mrisReadTriangleFile failed. No such file or directory Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Reading 574 control points... Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl % and after tkmedit loads, the lh.pial is not shown. I ran mris_euler_number on lh.pial and lh.white and they are both equal to 2 as they should. I was wondering whether you happen to know why is this happening and how to fix it. (I am using FS 5.3) Thank you for your time! Best, Panos

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Calculating surface values
by Jonathan Holt 25 Sep '13

25 Sep '13

I'm curious whether or not freesurfer, when calculating surface values, takes the original surface into account? If not, which surfaces are included in this calculation? jon

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Brodmann Area Atlas
by Michael Kranz 25 Sep '13

25 Sep '13

Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas? Thanks, Mike

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R: Re: Import FS data to FSL
by stdp82＠virgilio.it 25 Sep '13

25 Sep '13

Thanks Anastasia. I have some problem when I use mri_binarize.FSL list and guide advise me to use label2surf. There are a way to obtain specific labels in .label instead of .nii.gz? Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Import FS data to FSL 1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL. On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > Hi list, > > I have 2 questions, please. > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > (FSL)? > > 2-I'd like to export cortical masks from FS to FSL. > > An option is mri_binarize but this way failed in probtrackx (fsl). > FSL list have advised me that I should use label2surf command to convert > label to surface files. > > Where could find the .label (according to FreeSurferColorLUT.txt) to build > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > Do you have other ways that you advise me? > > > Thanks, > > > Stefano > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

Post-surgery volumes and hippocampal subfield segmentation
by Germeyan, Sierra (NIH/NINDS) [F] 25 Sep '13

25 Sep '13

Hi all, A few questions. 1. Is there a way to run scans of post-surgical brains that takes resections into account and gives more accurate results than "recon-all -all"? 2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do this indirectly by finding the difference between total intracranial volume that FreeSurfer gave for scans pre- and post- surgery. However, I rarely obtained reasonable numbers with this method. 3. After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would give me the total hippocampal volume), and compared the sum to the hippocampal volume that FreeSurfer gave after running recon-all -all. They weren't the same! Why would these differ? Thanks very much for any advice you can give!

1 0

Import FS data to FSL
by stdp82＠virgilio.it 25 Sep '13

25 Sep '13

Hi list, I have 2 questions, please. 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)? 2-I'd like to export cortical masks from FS to FSL. An option is mri_binarize but this way failed in probtrackx (fsl).FSL list have advised me that I should use label2surf command to convert label to surface files. Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes? Do you have other ways that you advise me? Thanks, Stefano

2 1

Technical position available at Columbia/NYPH MRI Unit
by Andrew Gerber 25 Sep '13

25 Sep '13

Direct link: http://rfmh.iapplicants.com/ViewJob-499585.html Please email me with any questions. Best, Andrew Andrew J. Gerber, M.D., Ph.D. Interim Director, MRI Unit Assistant Professor of Clinical Psychiatry New York State Psychiatric Insitute / Columbia University Division of Child and Adolescent Psychiatry Phone: (212) 543-5104 Fax: (917) 522-9588 Email: gerbera(a)nyspi.columbia.edu Research Foundation for Mental Hygiene, Inc. - Jobs<http://rfmh.iapplicants.com> ________________________________ * Senior Computer System Analyst I, Grade 21 Job #499585 - New York, NY Senior Computer System Analyst I, Grade 21 Job #499585 - New York, NY<http://feedproxy.google.com/~r/ResearchFoundationForMentalHygieneInc-Jobs/~…> Posted: DESCRIPTION The MRI Unit and IT Department are jointly seeking applicants for a Senior Computer System Analyst who would serve as a specialist in the design, maintenance, and training for computers and other technical devices required for research using the NYSPI MRI Unit. Specifically, this individual will be responsible for (a) computers and associated software which store and back up MRI acquired data, (b) computers and associated software which present functional stimuli to MRI research participants and record behavioral and psychophysiological responses from participants, and (c) electronic peripherals responsible for presenting and recording functional stimuli and behavioral/psychophysiological responses. This individual will also be responsible for training staff, investigators, and personnel who use the MRI Unit/Core in the use and maintenance of these devices. This individual will be asked to be available on a rotating schedule for emergencies during MRI scanning hours (8 am to 8 pm, 7 days a week but not including holidays) related to the computers and peripherals listed above. Finally, this individual may be trained in operation of the MRI console to serve as a backup operator when the technologists are sick or on vacation. DUTIES - Design, maintain, and train personnel in computers and associated software for storage and back up of MRI data - Design, maintain and train personnel in computers, associated software, and peripheral devices involved in presenting functional stimuli to MRI research participants and recording behavioral and psychophysiological responses. - Be available for emergency maintenance on a rotating schedule with other staff - Train and backup operation of MRI console QUALIFICATIONS - Possesses knowledge of installation and maintenance of systems running Windows, Mac, and Linux operating systems, including experience as a sys admin. - Has at least intermediate programming knowledge include familiarity with shell scripting - Has at least intermediate level skills in building simple electronic circuits, including soldering, building basic circuitry (Arduino or equivalent), and troubleshooting and repairing existing circuits. - An undergraduate or master's level degree in electrical engineering or a related field would be ideal, as well as the skills of an advanced hobbyist. - Must be able to think independently and creatively about solutions to electronic and computer problems, yet also work as part of a team in designing and implementing these tools. - Ideally would have at least some experience in image processing, advanced digital photography - Mandatory evening/weekend coverage as scheduled on a rotating basis. - Participation in medical surveillance required. The Research Foundation is a private not-for-profit corporation and is not an agency or instrumentality of the State of New York. Employees of the Research Foundation are not state employees, do not participate in any state retirement system and do not receive state fringe benefits. Excellent benefits package, AA/EEO Employer. Applications will only be accepted through website at: http://corporate.rfmh.org then click on Employment Opportunities. Applications will be accepted only during the posting dates as listed at the top of the job announcement.

1 0

Monte Carlo Simulation in Qdec
by Tara Ann Miskovich 24 Sep '13

24 Sep '13

Hello, I am conducting group analyses with LGI data in qdec, and I am having an issue with the monte carlo simulation I am hoping to get help with. Under design I leave the Smoothing (FWHM) at 10, and when I try to run the monte carlo simulation after running the analysis I get this error: Error in Monte Carlo simulation: Error running mri_surfcluster. Plus in the terminal I get an error: mri_surfclusterfwhm.dat: 37.226284, rounded to 38 Error: fwhm out-of-range (< 1 or > 30)! Should I be using fwhm0 for LGI data? Thank you for your help! Tara

3 4

Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 24 Sep '13

24 Sep '13

Dear FreeSurfer experts, I want to test linear, square and cubic effects of age on different parameters (thickness, lGI....) with qdec. I add age (square) and age (cubic) as column in my qdec table. Am i right to see only the square effects: Add Age square as continous factor and age (maybe age cubic too?) as nuisance factor in the model. Best wishes and thanks a lot. Daniel

2 1

Malloc(): memory corruption
by ye tian 24 Sep '13

24 Sep '13

Dear freesurfers, I am trying to run clusterwise correction for multiple comparisons. The command line executed smoothly if I run mri-glmfit-sim with --sim mc-z 5 4 mc-z.positive, but it throws the follow error glibc detected *** mri_segstats: malloc(): memory corruption 0x30050bf0 *** I searched the archive, but haven't found a readily executable solution. I have freesurfer 5.3 and my computer ram is 4.0GB. Thank you very much! Sincerely, Ye

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