Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

error when running eddy_correct
by Куликова Софья Петровна 28 Jun '18

28 Jun '18

External Email - Use Caution Hello FreeSurfer Developers, I was trying to run dt_recon (on centos7 system) but have got an error at the eddy_correct stage, saying there is no $FSLDIR/bin/imglob file. Indeed, it is not there. However, I gave installed FSL according to their tutorial without any errors and have no problem with running dt_recon on another machine. Could you kindly tell me how can I deal with this issue? Best regards, Sofya Kulikova PhD Neuroscience, HSE-Perm

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Hypothalamus
by 郑凤莲 27 Jun '18

27 Jun '18

External Email - Use Caution Hi FS experts, I want to study the volume changes of Hypothalamus in FS 6.0. However, I cannot find information about Hypothalamus in Wiki. Is there any description about Hypothalamus? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Best way to elaborate multiple .nii file for multiple subjects
by Ottavio Morciano 27 Jun '18

27 Jun '18

External Email - Use Caution Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours. Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....) Wich is the best way to finish the work more rapidly? Sorry for my bad english and i hope for a reply.Thanks Morciano Ottavio MD.Student

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Recon-all run time too long
by Ottavio Morciano 27 Jun '18

27 Jun '18

External Email - Use Caution Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7 ghz) and 16 gb of ram with El Capitan.This Macbook to run recon-all it takes 47 hours with -openmp 8 flag. A Dell with Intel Core i7 3632Q,8 GB RAM DDR3 1600mhz with Linux takes 8 hours...The same Dell on windows with linux virtualizated takes 13 hours. Why recon-all on mac is so slow? is the OS?the type of compilator used for each platform?freesurfer not optimized for El Capitan? the architecture of the cpu? Some Advice? Morciano Ottavio MD Student Università Di Foggia.Italy

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Resting-State and Brain Connectivity in Montreal: Early registration deadline is July 10 (fwd)
by Bruce Fischl 26 Jun '18

26 Jun '18

FYI ---------- Forwarded message ---------- Date: Tue, 26 Jun 2018 22:35:08 +0000 From: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> To: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> Subject: Resting-State and Brain Connectivity in Montreal: Early registration deadline is July 10 External Email - Use Caution The Sixth Biennial Conference on Resting-State and Brain Connectivity Conference: September 26 - 28, 2018 Educational workshop: September 24 - 25, 2018 Montreal, QC, Canada · Early registration deadline: July 10, 2018 · Registration fees will increase substantially on July 11 · To receive notice of acceptance by July 9: submit an abstract by July 2 · Late abstract submission can be made until August 1, 2018 See the conference web-site: http://restingstate.com/2018/ Amir Shmuel Chair of the organizing committee http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…. jpg [IMAGE]

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questions about freeview quit unexpectly
by 姜时泽 26 Jun '18

26 Jun '18

External Email - Use Caution | | Dear fresurfer experts, I am currently using freeview 2.0 to check some data. I am not sure why it always quit unexpectedly when I try to load a volume. my freeview is installed on OS 10.11.3 system. Would you please help me to solve this problem. Thank you. Best wishes Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

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Adjusting/accounting for between scanner variance
by Heidi Lindroth 26 Jun '18

26 Jun '18

External Email - Use Caution Hi there, Is there a standard method to use for adjusting for between scanner variance? In the sample I am analyzing, 4 different scanners were used. Thank you, Heidi Lindroth BSN RN PhD Candidate | School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindroth(a)wisc.edu<mailto:hlindroth@wisc.edu>

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Re: [Freesurfer] Question about GLM results in Freesurfer
by jahanvi patel 26 Jun '18

26 Jun '18

External Email - Use Caution Hello Doug, We are doing one test I supposed. Because we inputted all covariates into glm_fit. This is our command line. We entered all behavioral scores as covariates and obtained each folder named as covariate's name with sig.mgh in each folder. Does it mean we only have just one test, or several tests if we did the below way? Best regards, Jahanvi mri_glmfit \ --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \ --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --fsgd GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_age.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_CesD_score.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_state.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_STATI_trait.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_total_medi_min.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f1.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f2.mtx \ --surf fsaverage lh > Message: 4 > Date: Mon, 25 Jun 2018 10:45:42 -0400 > From: Douglas Greve <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about GLM results in Freesurfer > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <10e16d65-9ac1-c85c-875d-405e852ce9a5(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > Are you doing 5 different tests or just one test? It is a tricky > question as to whether you should correct across? 5 tests or not. > Ideally, one should, but I don't think I've ever seen it done in > practice. As a reviewer, I might not demand it for only 5 tests. On 6/20/18 9:17 AM, jahanvi patel wrote: > > > Hello, > > We have a question about using glm_fit in freesurfer. > > When we model several covariates (behavioral scores) in glm, and we > wanted to know the correlation between cortical thickness changes with > the changes of behavioral scores.? We obtained the correlation results > nicely after using freesurfer's monte carlo correction (eg. increase > of behavioral scores is correlated with the increase of cortical > thickness changes). > > Should we still perform the bonefferi corrections on the results we got ? > (because we have entered?5 covariates into the glm?model, so we are > wondering if it is still needed to divide the?alpha-value by 5 > to?determine the final significant findings)? > > > Thank you so much for helping us, > > Jahanvi > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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brainstem-structures different versions?
by Niels Janssen . 26 Jun '18

26 Jun '18

External Email - Use Caution Hi I see on the website of brainstem substructures that the '-brainstem-structures' option in freesurfer 6.0 stable release produces brainstem segmentations that are labeled v10 whereas the script 'segmentBS.sh' available in beta versions of freesurfer produces v11 or v12 segmentations. What is the difference between these versions of the brainstem segmentation? Under what circumstances is the latest version recommended? Thank you for any clarification.

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Using T2 or Flair data to improve pial surfaces
by Heidi Lindroth 25 Jun '18

25 Jun '18

External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thickness.fwhm10.fsaverage.mgz or .mgh file. . Instead, they have this file type: lh.smoothwm.FI.crv. Is there a way to convert the crv file to a mgz/mgh file? Is there an alternate way to analyze the T1/T2 data using QDEC? Thank you, Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindroth(a)wisc.edu

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Freesurfer June 2018