Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

FreeSurfer Longitudinal analysis
by Глеб Макшаков 11 Jun '18

11 Jun '18

External Email - Use Caution Dear all, I’ve just started using FreeSurfer and I need your advice. I have two series of images made 1 year apart from each other. Is it correct to use a Longitudinal Stream to process those images instead of simple cross-sectional counting and then estimating the difference in volumes between them? Regards, Gleb Makshakov MD, neurologist City Clinical Hospital 31 City Center of Multiple Sclerosis and AID Neurology Department of FSBEI HE I.P.Pavlov SPbSMU MOH Russia gleb.makshakov(a)gmail.com +79213912101

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Full-Time Research Assistant Position in Clinical Neuroscience at Ohio State University
by Herring, Elizabeth J. 11 Jun '18

11 Jun '18

External Email - Use Caution Posted on behalf of Dr. Ruchika Prakash: Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University The Clinical Neuroscience Lab, in the Psychology Department, within the College of Arts and Sciences, seeks a Research Assistant 1-Social to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash. The Research Assistant 1 assists in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitates recruitment efforts between the laboratory and community partners for human subject payments; conducts neuropsychological assessment sessions with clinical populations; assists with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB; supervises undergraduate research assistants. Position available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com/postings/86981 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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Analyzing slice data with freesurfer?
by John Absher 11 Jun '18

11 Jun '18

External Email - Use Caution We are attempting to analyze archival MRI data obtained during routine clinical care. Unfortunately, the standard clinical MR sequences do not include 3D volumes. Will the freesurfer algorithm work on slice data so that each slice could be marked with the pial and white matter boundaries? Then, the next question is how to apply seg and parc templates to analyze correctly defined subcortical structures, and cortical regions? Has anyone tried to do this type of archival data analysis? Unfortunately, our standard sequences do not include 3D volumes, so to do the retrospective work we'll need a workaround. Thank you. John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Grad-unwarp
by Maryam Abaei 11 Jun '18

11 Jun '18

External Email - Use Caution Dear Team, I am trying to use gradunwarp function but I can't go furher than first command. I can run perl gradient_unwarp_converter.pl and there is no error at all ( and it says writing alpha/beta sections....) but doesn't create the coef files that I need in sext step. I was wondering if you know how I can fix this. Best wishes, Maryam

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Extracting the centroids from Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz atlas
by zuxfoucault Wong 11 Jun '18

11 Jun '18

External Email - Use Caution Dear Freesurfer experts, I intended to extract centroid of the atlas "Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz" According to the post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-May/057046.html I used the command as: """ source_img_fname=${FREESURFER_HOME}"/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz" color_lut=${FREESURFER_HOME}"/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_ColorLUT.txt" mri_segcentroids --i ${source_img_fname} --o ./Buckner2011_17Networks_centroid.txt --ctab ${color_lut} """ Am I use it the right way? Also, I am wondering how to transform the volumetric 17Networks centroids to embed to surface-based fsaverage network centroids (scripts as https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-February/056056.…) ? Thank you for your time! Best, Foucault

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I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels) but converges only on 30 %
by Knut J Bjuland 11 Jun '18

11 Jun '18

External Email - Use Caution Dear FreeSurfer experts, I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels). I adapted the code a little bit to accommodate the data format. I have a longitudinal design with 3 time points and two groups, the model is intercept (random factor) + group (patients, controls) + centered age + sex + a continuous clinical variable. Centered age = age - mean age for all observations (across all subjects, groups, and time points). The scripts run without crashing but lme_fit_FS.m converges in only ca. 30% of the voxels. lm_F produces F and p-values that I can use. However, I'm uncertain what to make of the messages about "Algorithm does not converge after 50 iterations!!!" Does that invalidate the analyses? Or can I use the resulting pvals even where lme_fit_FS did not converge? Also, I'm not used to such a high rate of non-convergence. Any idea what may be going wrong? The FA-data looks fine (between 0 and 1; mean = 0.49; SD = 0.15). Thank you! Knut Jørgen Bjuland

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Re: [Freesurfer] get thickness and gray volume
by Bruce Fischl 10 Jun '18

10 Jun '18

also in the stats dir (check aseg.stats) cheers Bruce On Mon, 11 Jun 2018, charujing123 wrote: > > External Email - Use Caution > > Hi Bruce and FS experts, > I have resolved that question. another one is that how to get subcortical gray volume or thickness? > Thanks. > Best. > Rujing > > 2018-06-11 > > ____________________________________________________________________________________________________ > charujing123 > > ____________________________________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2018-06-10 23:28 > 主题：Re: get thickness and gray volume > 收件人："charujing123"<charujing123(a)163.com> > 抄送："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Hi Rujing > > have you looked the the stats file in each subject's stats dir? They > should contain these measures in text format. > > cheers > Bruce > On Sun, 10 Jun 2018, > charujing123 wrote: > > > > > External Email - Use Caution > > > > Hi FS experts and Bruce > > I have done the recon-all, and -qcache -measure thickness. Then I want to get thickness and gray > > > volume for each fsaverage atlas regions, and it would be better in a txt format. > > Thanks. > > Looking forward any kindhearted reply. > > Best. > > Rujing > > > > 2018-06-10 > > > > _________________________________________________________________________________________________ > ___ > > charujing123 > > > > > > > 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. > > >

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Unusual hires T1 specs
by Juranek, Jenifer 10 Jun '18

10 Jun '18

External Email - Use Caution I offered to help a colleague with some Freesurfer analyses, but when I looked at the data they were processing, I found: 1) highly anisotropic voxdims 2) sub-mm in-plane resolution Data were acquired on a 3T Siemens Tim Trio. I don't think they were trying to deviate from the recommended 1x1x1mm specs, but somehow it looks like they did since the 001.mgz file does not conform to the FS standard. Output for mri_info on their 001.mgz file is listed below. They did not keep the file converted by mri_convert (nii or dicom) in their FS_sub directory, so I'm limited to the 001.mgz. I'm running FSv6 in my lab, is the hires flag appropriate in this situation? Any suggestions? Many Thanks, Jenifer [orig]$ mri_info 001.mgz Volume information for 001.mgz type: MGH dimensions: 448 x 512 x 192 voxel sizes: 0.478516, 0.478516, 1.000000 type: SHORT (4) fov: 245.000 dof: 0 xstart: -107.2, xend: 107.2 ystart: -122.5, yend: 122.5 zstart: -96.0, zend: 96.0

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Re: [Freesurfer] get thickness and gray volume
by Bruce Fischl 10 Jun '18

10 Jun '18

Hi Rujing have you looked the the stats file in each subject's stats dir? They should contain these measures in text format. cheers Bruce On Sun, 10 Jun 2018, charujing123 wrote: > > External Email - Use Caution > > Hi FS experts and Bruce > I have done the recon-all, and -qcache -measure thickness. Then I want to get thickness and gray > volume for each fsaverage atlas regions, and it would be better in a txt format. > Thanks. > Looking forward any kindhearted reply. > Best. > Rujing > > 2018-06-10 > > ____________________________________________________________________________________________________ > charujing123 > >

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recon-all -s subid exited with ERRORS
by Lee, Seonjoo 10 Jun '18

10 Jun '18

External Email - Use Caution Hi Bruce, recon-all did not run, and I could not figure out the problem. Do you have any clue what could be? The log file does not tell anything… The command was the most simplest one (using only t1). If you need more information to figure out the cause of this error, please let me know. Thank you. -Seonjoo ==== #@# MotionCor Sat Jun 9 21:04:46 EDT 2018 Found 1 runs subject/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp subject/mri/orig/001.mgz subject/mri/rawavg.mgz \n subject \n mri_convert subject/mri/rawavg.mgz subject/mri/orig.mgz --conform \n mri_convert.bin subject/mri/rawavg.mgz subject/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from subject/mri/rawavg.mgz... TR=6.81, TE=3.16, TI=0.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to subject/mri/orig.mgz... Darwin Seonjoos-iMac.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 recon-all -s subid exited with ERRORS at Sat Jun 9 21:04:51 EDT 2018

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Freesurfer