Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

LTA transforms into AFNI's aff12.1D format
by Varada, Jan (NIH/NIMH) [C] 15 Feb '17

15 Feb '17

Greetings, I am interested in using mri_robust_template to create an average anatomical image across several sessions (to which EPI runs will be aligned to). Are there any guidelines on how to convert the output .lta transforms into AFNI’s .aff12.1D format for later concatenation with the non-linear transform from aligning the average template to an MNI template? Thank your for your time, Jan Varada Jan Varada, MHS [C] | Computer Programmer | NIMH Rm B1D708A – 10 Center Drive, Bethesda MD jan.varada(a)nih.gov, Phone: 301-496-8101

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Fwd: REMINDER Call for OHBM 2017 Replication Award
by Douglas N Greve 15 Feb '17

15 Feb '17

FYI -------- Forwarded Message -------- Subject: REMINDER Call for OHBM 2017 Replication Award Date: Wed, 15 Feb 2017 05:32:45 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *REMINDER: Call for OHBM 2017 Replication Award Nominations* The deadline for the *NEW OHBM Replication Award Nominations is Wednesday, February 22, 2017.* This award was established to recognize the best published replication study was announced. This award highlights OHBM’s commitment to reproducibility in neuroimaging research and helps begin to reshape the incentives towards replication. See below for additional information: Nomination process <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3731#top> Q&A with Chris Gorgolewski regarding the Replication Award <http://www.ohbmbrainmappingblog.com/blog/ohbm-replication-award-qa-with-chr…> ------------------------------------------------------------------------ /*Please note: Current OHBM elected leadership are ineligible to receive OHBM Awards. */ Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…>.

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postdoctoral Research Fellow position at Mayo Clinic
by Senjem, Matthew L., M.S. 15 Feb '17

15 Feb '17

The Department of Radiology at Mayo Clinic has an open position for a talented post-doc to work on a novel 3T MR scanner. The compact system sports 85mT/m gradients with slew rates in excess of 700T/m/s. DOI’s for a few papers on this system are: doi: 10.1002/mrm.26044 doi: 10.1118/1.4941362 doi: 10.1002/mrm.26315 The job posting is: http://www.mayo-clinic-jobs.com/job/Rochester-Research-Fellow-Job-MN-55901/… Please contact mbernstein(a)mayo.edu<mailto:mbernstein@mayo.edu> with questions.

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Re: [Freesurfer] tractstats2table error
by Antonin Skoch 15 Feb '17

15 Feb '17

Hi, could not be the issue python version mismatch? tractstats2table is python script, maybe there is a problem. Antonin Hi Adarsh – What operating system are you running this on? It runs fine for me with this input file when I test it on both a mac and a linux computer.a.y From: <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Adarsh Nellore <adarsh.nellore...(a)gmail.com<mailto:adarsh.nellore...@gmail.com>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, February 14, 2017 at 3:19 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] tractstats2table error 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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General question about freesurfer
by Arsene Ella 15 Feb '17

15 Feb '17

Hi everyone, I am a newbie in freesurfer. I went a little bit throughout the tutorials and few questions arose: 1) Is freesurfer was only built to process data acquired on primates (especially humans)? In other words, is freesurfer unable to process data from other animal models (rat, mouse, sheep....)? 2) Is a spatial resolution of 1mm iso voxel size a prerequisite for using freesurfer? If my data have a better spatial resolution (0.5 mm iso voxel size for example), do they necessarily have to be transformed to a resolution of 1mm iso voxel prior to be used in freesurfer? 3) If I want to use my own atlas in freesurfer, in which form (label, annotation, format ...) should it be? And in which directory do I have to put it? I would really appreciate any help. Thanks.

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Q&A for posting on listserv
by Dawn C. Matthews 15 Feb '17

15 Feb '17

To FreeSurfer ListServ: Dr. Iglesius recently responded to the questions below and asked that the question and response (also included below) be posted on the Freesurfer ListServ…Thanks very much. Questions on 13 Feb 2017: In the manuscript Iglesius et al, “A computational atlas of the hippocampal formation…”, Neuroimage. 2015 July 15; 115: 117–137, there is a Table 7, repasted below. I wondered if you could help me to make sure that I am correctly interpreting what each one of the permutations involved. The first line (aseg, 5.3) was clear. I believe that the second line refers to the summation of the subregion volumes generated using version 5.3. I was unsure as to how “in vivo 5.3” of the third line differs from the first two lines? In the final line, was “this study and ex vivo” a different data set or were all using the exact same data? The impression that I received was that there is benefit in calculating hippocampal volume by adding up the subfields, but that the subfield accuracy is better in 6.0 which further increases the value of subfield addition for calculating overall hippocampal volume. Accuracy and area under the curve for the AD discrimination task. AtlasAccuracy at elbowAUROC Whole hippocampus (“aseg”, FreeSurfer v5.3)82.1%0.887 Whole hippocampus (adding up the volumes of the subregions)84.0%0.901 In vivo (FreeSurfer v5.3)86.3%0.917 Ex vivo (this study and FreeSurfer v6.0)88.0%0.931 Freesurfer may be used to generate hippocampal volumes for an enrichment study of MCI patients, to identify which subjects are most likely to worsen clinically at greater rates. I am trying to understand whether the performance of Freesurfer in this regard will be affected by whether the version used is 5.3 vs. 6.0. One further question is how the high resolution atlas used in 6.0 compares to multi atlas techniques. I believe that your paper did make a comparison to at least one multi-atlas approach, and performance was superior for certain subfields. However, others have found that multi-atlas approaches may perform better than FS (versions prior to 6.0). If there is a point to be made about FS 6.0 and its comparison to multi-atlas techniques, this could be helpful as well. Any insights on these questions would be appreciated. Responses from E Iglesius: Thank you for your email. I really appreciate that people seem to be finding this atlas useful. I agree that the table is not as clear as it should have: Whole hippocampus (“aseg”, FreeSurfer v5.3): this is just the estimate from the main FS recon-all script (“aseg”), stored in aseg.stats Whole hippocampus (adding up the volumes of the subregions): adding up the subfield volumes. It works a bit better than the aseg version (there’s actually 2-3 cases in which aseg fails badly but the hippocampal module manages to recover). In vivo (FreeSurfer v5.3): multivariate classification using the volumes of the subfields, as estimated by the in-vivo atlas in FS5.3 (Van Leemput 2009) Ex vivo (this study and FreeSurfer v6.0): multivariate classification with the ex vivo atlas. Regarding your specific question: people have written papers about how terrible the 5.3 subfield segmentation was. So, if you’re doing subfields, you should use 6.0. If you’re doing whole hippocampal volumes by adding subfields, it doesn’t matter much if you’re using 5.3 or 6.0, but I’d still use 6.0 because with 5.3 you’re looking for trouble for the reason mentioned above. And, of course, if you’re using the whole hippocampal volume, you can always use the aseg volume. My two cents regarding Freesurfer 6.0 vs. multi-atlas techniques: - If you have training data that is matched (in terms of MRI acquisition and contrast) to you test data, go for multi-atlas. It’s slow, but will work well. - If you do not, then generative models like ours do better- because they are independent of the modality of the test scan. This is important when you publicly release your code, e.g., as part of FreeSurfer (you need algorithms to be robust). - In our case: if the training data is ex vivo, there’s no choice. You have to do generative - there’s no way to register the intensities with good accuracy. Cheers, /Eugenio

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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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