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30132 discussions

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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Question about GLM results in Freesurfer
by jahanvi patel 25 Jun '18

25 Jun '18

External Email - Use Caution 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

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 25 Jun '18

25 Jun '18

External Email - Use Caution Hi FreeSurfer experts, Just bringing this question back up to the top: I analyzed my data following the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. Is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)? Best, Jessica ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Saturday, June 23, 2018 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 172, Issue 36 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FreeSurfer Manual Edit Sequence (David S Lee) 2. Using grad_unwarp (James Gullickson) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Jun 2018 11:37:44 -0500 From: David S Lee <david.s.lee(a)wisc.edu> Subject: [Freesurfer] FreeSurfer Manual Edit Sequence To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAGcZjx8px96eS=O64q5nivBObJP9cqDha3_R87G3GHdjkVQnqA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Experts, When performing manual edits on brain masks, white matter, and gray matter, do I have to strictly follow the sequences(process stages) listed here <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>? For instance, the link suggests that "autorecon2-pial is used after editing brain volume *after running -autorecon2". In other words, is it okay to perform "autorecon2-pial" before "autorecon2-wm"? Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Amygdala nuclei - stable version -SOLVED
by Liza van Eijk 24 Jun '18

24 Jun '18

External Email - Use Caution Hi Lisa Thanks a lot for the interest! The tool itself is pretty Steele and unlikely to change any time soon. But the rest of FreeSurfer... who knows when 6.1 will come out. If you're worried about reproducibility of results, you can always process your subjects with FreeSurfer 6.0 and then run the subfields/amygdala on top. Cheers Eugenio PS would you mind posting this question on the list? It's be great to share (ill just copy-paste the answer) From: Liza van Eijk Sent: Wednesday, June 20, 02:39 Subject: Amygdala nuclei - stable version Dear Dr Iglesias, I am interested in using your amygdala nuclei segmentation tool. Would you happen to know when a stable release is coming out? Thanks again, Liza van Eijk PhD Candidate University of Queensland Brisbane, Australia

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differing display colors for 2+ labels in tksurfer
by Yagmur Ozdemir 19 23 Jun '18

23 Jun '18

External Email - Use Caution Hello freesurfer experts, I am aiming to view 3 to 8 different labels on one flattened surface patch created&viewed in tksurfer. Even if I can manually select the color of first label, the next ones end up sharing the same color and I cannot seem to change this from the interface and I didn't come across any command line options for this. Any advice on how to set these different colors? I see that freeview can handle this, but to my knowledge it cannot open flattened patches? Any help would be deeply appreciated. Best Idil

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