Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

Analysis of rates or percent changes
by Katarina Trojacanec 14 Feb '17

14 Feb '17

Hi, I have a question about the analysis of rates or percent changes. I use data with available scans at baseline (TP1) and the 6-month (TP2), 12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of some of the data in the appropriate qdec table is given below: fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06 ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12 ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24 ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06 ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12 ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24 The base is constructed using all four time points. The time variable is given in years. I am using long_stats_slopes for aseg.stats as follows: long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit --do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg ./qdec/long_AD_NL_TP1_2_3_4 (similarly for ?h.aparc.stats) Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated approximately 6 months and TP3 and TP4 are separated approximately 12 months, are the annualized percent change or atrophy rates using this scenario reasonable (statistically?). Is it maybe more reasonable to apply the same scenario using three time points (for example TP1, TP3 and TP4 from the previous example and the template based only on these time points with the same approximate difference between all of them of 12 months, or TP1, TP2 and TP3 from the previous example and the template based only on these time points with the same approximate difference between all of them of 6 months)? Best Regards, Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science and Engineering Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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Re: [Freesurfer] tractstats2table error
by Adarsh Nellore 14 Feb '17

14 Feb '17

Hi Anastasia, The file I have seems very similar to the file in that link. I've pasted my file below: # Title Pathway Statistics # # generating_program /usr/local/freesurfer/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/bin/dmri_pathstats --intrc /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200_recon-all/dpath/fmajor_PP_avg33_mni_flt --dtbase /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200_recon-all/dmri/dtifit --path fmajor --subj Control200_recon-all --out /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200_recon-all/dpath/fmajor_PP_avg33_mni_flt/pathstats.overall.txt --outvox /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200_recon-all/dpath/fmajor_PP_avg33_mni_flt/pathstats.byvoxel.txt # sysname Linux # hostname magbrain # machine x86_64 # user magbrain # anatomy_type pathway # # subjectname Control200_recon-all # pathwayname fmajor # Count 1500 Volume 1206 Len_Min 51 Len_Max 113 Len_Avg 78.2753 Len_Center 70 AD_Avg 0.00117037 AD_Avg_Weight 0.00116289 AD_Avg_Center 0.001153 RD_Avg 0.000596586 RD_Avg_Weight 0.000603718 RD_Avg_Center 0.000548966 MD_Avg 0.000787847 MD_Avg_Weight 0.000790108 MD_Avg_Center 0.000750311 FA_Avg 0.415954 FA_Avg_Weight 0.404395 FA_Avg_Center 0.444513

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fast_selxavg3() failed\n
by Fatemeh.Molaei-Vaneghi 14 Feb '17

14 Feb '17

Dear FreeSurfers, I'm trying to perform a block design analysis with fsfast. All the steps up until the selxavg3-sess works quite fine. However, upon using the selxavg3-sess as, for example, in "selxavg3-sess -s Sess01 -a motion.sm3.lh -no-preproc -overwrite" I receive the following error. I'd appreciate any feedbacks on what might be the problem. Thank you. selxavg3-sess log file /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess01 -a motion.sm3.lh -no-preproc -overwrite $Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $ uid=501(lab) gid=20(staff) groups=20(staff),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),398(com.apple.access_screensharing),401(com.apple.sharepoint.group.1),402(com.apple.sharepoint.group.2),33(_appstore),100(_lpoperator),204(_developer),399(com.apple.access_ssh) /Volumes/DATA/Studies/FS/Sessions Darwin labs-Mac-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 Sat Feb 11 19:31:58 CET 2017 ------------------------------------------- /Volumes/DATA/Studies/FS/Sessions/Sess01 Sat Feb 11 19:31:58 CET 2017 anadir = /Volumes/DATA/Studies/FS/Sessions/Sess01/bold/motion.sm3.lh ------------------------------------------ % Sat Feb 11 19:31:58 CET 2017 % /Volumes/DATA/Studies/FS/Sessions % motion.sm3.lh %-------------------------------- sxa3pwd = '/Volumes/DATA/Studies/FS/Sessions' sxa3cmd = '/Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess01 -a motion.sm3.lh -no-preproc -overwrite' which fast_selxavg3 okfile = '/tmp/selxavg3-sess-19691.ok'; if(fast_fileexists(okfile)) delete(okfile); end monly = 0; perrun = 0; jkrun = 0; DoGLMFit = 1; DoContrasts = 1; ConList = splitstring('obj-vs-ret objective pursuit retinal'); DoSynth = 0; SynthNoiseAmp = 1; SynthNoiseAR1 = .3; SynthSignalAmp = 0; SynthSeed = -1; sess = '/Volumes/DATA/Studies/FS/Sessions/Sess01'; analysis = 'motion.sm3.lh'; flacname = ''; outtop = ''; DoFWHM = 0; MatlabSaveRes = 0; SaveResUnwhitened = 0; fast_selxavg3; if(~fast_fileexists(okfile) && ~monly); quit; end quit; ------------------------------------------ ------------------------------------------ ------- matlab output -------------------- < M A T L A B (R) > Copyright 1984-2015 The MathWorks, Inc. R2015b (8.6.0.267246) 64-bit (maci64) August 20, 2015 Toolbox Path Cache read in 0.04 seconds. MATLAB Path initialized in 1.05 seconds. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Academic License >> >> >> >> >> >> >> sxa3pwd = /Volumes/DATA/Studies/FS/Sessions >> sxa3cmd = /Applications/freesurfer/fsfast/bin/selxavg3-sess -s Sess01 -a motion.sm3.lh -no-preproc -overwrite >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# Sess01 ############################### /Volumes/DATA/Studies/FS/Sessions/Sess01 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Users/lab/Documents/MATLAB/MRIread.m ------------------------- outtop = /Volumes/DATA/Studies/FS/Sessions Extension format = nii.gz ERROR: could not open motion.sm3.lh/analysis.info ------------------------------------------ Best, Fatemeh, Max Planck Institute for Biological Cybernetics Tübingen, Germany

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Re: [Freesurfer] tractstats2table error
by Adarsh Nellore 14 Feb '17

14 Feb '17

Hi Anastasia, This was the full command: tractstats2table --inputs /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt/pathstats.overall.txt --overall --tablefile /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt.All.table And this was the full output: File "/usr/local/freesurfer/bin/tractstats2table", line 138 print 'ERROR: inputs are not specified' ^ SyntaxError: Missing parentheses in call to 'print' Thanks a lot, Adarsh

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Error from tractstats2table
by Adarsh Nellore 14 Feb '17

14 Feb '17

Hi there, I generated tractographies using the TRACULA pipeline and I'm not trying to generate the necessary statistics for them using tractstats2table. This is the command I'm using: tractstats2table --inputs /usr/local/freesurfer/subjects/control_data/ diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt/pathstats.overall.txt --overall --tablefile /usr/local/freesurfer/subjects/control_data/ diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt.All.table However, no matter what I change in this command, whether it be parameters or syntax, I get the following error: File "/usr/local/freesurfer/bin/tractstats2table", line 138 print 'ERROR: inputs are not specified' ^ SyntaxError: Missing parentheses in call to 'print' I'd really appreciate any advice on how I may be able to get past this error as soon as possible. Thanks a lot!

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Control Points editing
by Andrea Gerardo Russo 14 Feb '17

14 Feb '17

Hi FreeSurfer experts, I have some questions (maybe trivial) about Control Points editing. 1) Following the guide in your website and exploring your tutorial subject "cp_before" I understood that a Control Point has to be placed in a region that is definitely white matter but the standard recon-all process has classified as gray matter. However in the section "General Tips" you suggest that a Control Point has not to be placed in a tissue different from the white matter, and in other questions posted on the this mailing list several scientists said that they place Control Points in the white matter voxels with an intensity lower than the 110 to adjust the local intensity. I'm a bit confused. What is the correct strategy? 2) I noticed that a Control Point can adjust the white matter surface in its neighborhood, but it can create unpredictable changes in surfaces in other regions. How is it possible? 3) What kind of index can I use to test the reliability of Control Point editing? In a test-retest protocol, considering a single subject, I noticed that although the Control Point positioning improves the FreeSurfer surfaces there is an increase of the covariance in the cortical thickness measurements between scans after the editing. How can I interpret this results? Best regards Andrea Gerardo Russo

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Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0
by Juhyoung Ryu 13 Feb '17

13 Feb '17

Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I installed freesurfer v6. I attached recon-all.log file below. I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in log file. Is there anything to check more? Thank you, Juhyoung > On Feb 9, 2017, at 12:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in your path? > > And can you email the list so others can answer? > > thanks > Bruce > > > On Thu, 9 Feb 2017, Juhyoung Ryu wrote: > >> Hi Bruce, >> I installed FREESURFER with version 6.0 for your recommendation and I got an >> error: >> mri_em_register: could not open GCA >> /Applications/freesurfer/average/RB_all_2008-03-26.gca. >> That file not exist in ‘average' folder, and there is one similar >> file: RB_all_2016-05-10.vc700.gca >> Do you think I should drop that file manually from FREESURFER v5.2? >> Thank you in advance,Juhyoung >> >> Begin forwarded message: >> From: Juhyoung Ryu <jh67753737(a)gmail.com> >> Subject: Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not >> finite at vno 0 >> Date: February 8, 2017 at 11:01:23 AM GMT+9 >> To: Z K <zkaufman(a)nmr.mgh.harvard.edu> >> Cc: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Zeke and Bruce, >> Thank you very much for your help. >> I’ll try it now and share the results. >> Thanks! >> Juhyoung. >> >> On Feb 8, 2017, at 8:13 AM, Z K >> <zkaufman(a)nmr.mgh.harvard.edu> wrote: >> Hello Juhyoung, >> I noticed from the recon-all.log files that you are using >> freesurfer v5.2. It was revealed that this version had issues >> regarding systematic white surface contraction and placement of >> the pial surface extending too far: >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html >> I would recommend processing these subjects with version 6.0 >> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall >> -Zeke >> On 02/06/2017 01:43 AM, Juhyoung Ryu wrote: >> >> Hi FS developers, >> >> I received errors in one of steps in recon-all. >> I analyzed 111 individual subjects' T1 data using >> same method, but there >> are errors in _only 14 subjects._ >> >> Below is screenshot image in the end of >> recon-all.log file. I attached >> log files from two exemplar subjects below, also. >> >> I’d appreciate if you might help me. >> Juhyoung. >> >> _______________________________________________ >> 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.

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Postdoctoral Position/Developmental Neuroimaging
by emma jane 13 Feb '17

13 Feb '17

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position is supported by a recently awarded NICHD Center Grant (i.e., a CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect; PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions Network (http://solutionsnetwork.psu.edu/) and the Prevention Research Center (www.prevention.psu.edu) both of which are located on the University Park campus in State College, PA. The primary responsibility of this position will be to provide neuroimaging research support (e.g., experimental design, implementation and data analysis) to a longitudinal project that will consider the biological embedding of child maltreatment in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic, epigenetic, immunologic) and the impact of embedding on health outcomes, including neurodevelopmental trajectories. Candidates must have a PhD in psychology, neuroscience, or an allied field, or have completed all requirements for a PhD by the time of appointment. Applicants must have expertise in human subjects MRI, preferably with developmental cohorts. Preference will be given to those candidates with experience working with children who have experienced maltreatment or other high-risk groups. The successful candidate will be expected to contribute to experimental design and co-ordination of the neuroimaging aspects of the project and data analysis. Candidates must demonstrate expertise in functional and structural MRI analysis methods using standard processing packages (e.g., SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and complex datasets would be advantageous. The postdoctoral researcher will also be expected to contribute to manuscript preparation and presentation of study-related outcomes at key scientific meetings. Extensive mentorship will be provided to the successful candidate in order to facilitate transition to an independent research career. This position will provide an opportunity to interact with several vibrant research communities at Penn State, including the Social Sciences Research Institute (www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging Center (www.imaging.psu.edu) among others. The initial appointment will be for one year, with the possibility of renewal in subsequent years. Salary and benefits are based on NIH guidelines, commensurate with experience and qualifications. Interested candidates should upload a CV, cover letter, statement of research interests, and 2-3 relevant publications. In addition, applicants should arrange for 3 professional references to be submitted separately to Dr. Emma Jane Rose (Associate Director for P-TRAN) at emmajanerose(a)psu.edu. Review of applications will begin immediately and will continue until the position is filled. Applications received by March 24, 2017 will be given full consideration, although the position will remain open until filled. The expected start date will be between April and June 2017. For further information about this appointment, please contact Dr. Emma Jane Rose at emmajanerose(a)psu.edu or 814-865-0114 <(814)%20865-0114>. Apply online at https://psu.jobs/job/69051 CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery/, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. -- *Emma Jane Rose PhD.* *Assistant Research Professor & * *Associate Director for the **Program for Translational Research on Adversity and Neurodevelopment (P-TRAN)* *Edna Bennett Pierce Prevention Research Center* *The Pennsylvania State University* *308 Biobehavioral Health Building* *University Park, PA 16802* *www.prevention.psu.edu <http://www.prevention.psu.edu/>* *www.npscoalition.org <http://www.npscoalition.org/>*

1 0

intensity normalisation hippocampus
by firetech＠web.de 13 Feb '17

13 Feb '17

2 1

hippocampal subfields analysis command
by Rizvi, Batool 13 Feb '17

13 Feb '17

Hi, I'm having trouble getting any output from the hippocampal subfield analysis command. I entered in: quantifyHippocampalSubfields.sh T1 hippo.txt /path/to/my/subjects/freesurferfolder I tried both ways of having the environmental variable subjects directory defined to the freesurfer folder of the subjects (used *'s here for subjects and their freesurfer folder), but it still gives no output. It just says: Gathering results from subjects in: /path/to/my/subjects/freesurferfolder Using the suffix name: T1 And writing them to: hippo.txt What am I doing wrong here? Thanks so much! Batool

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Freesurfer February 2017