Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Multiple Comparison Question for surface-based analyses
by Ajay Kurani 28 Oct '16

28 Oct '16

Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay

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Group analysis Cortical Thickness
by Dev vasu 28 Oct '16

28 Oct '16

Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes in cortical thickness between 2 groups, could you please kindly inform me some methods that i should adapt to perform the analysis. Thanks Vasudev

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mris_left_right_register not found
by Daya P 28 Oct '16

28 Oct '16

Hi All, I was looking to flip a label I created on the left hemisphere to the right hemisphere and I read in previous messages that mris_left_right_register and then mri_apply_reg might be an option. I can find mri_apply_reg as a command but not mris_left_right_register. The links to it previously posted are not available anymore. Is there an updated link available? Daiana

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V6 beta update
by Bruce Fischl 27 Oct '16

27 Oct '16

Hi All, just an update on the status of the beta version of V6. We had hoped to have it out this week or early next week, but in our review of about ~250 hemispheres we found a small problem with one of them. We have a putative fix for the problem and are restarting our test suite. If it (finally!) passes everything we will have a version out in a couple of weeks. Sorry for the repeated delays, but we are doing everything we can to ensure that it will work well when we release it cheers Bruce

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mris_left_right_register
by Daya P 27 Oct '16

27 Oct '16

Hi all, How can I use mris_left_right_register, I tried downloading it but I get /home/daianapur/Documents/Dan/freesurfer/bin/mris_left_right_register: Permission denied. Is there an updated link that I can use to download it? Daiana

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Antwort: Re: TRACULA longitudinal stream: using multiple configuration files?
by j.oschwald＠psychologie.uzh.ch 26 Oct '16

26 Oct '16

Thank you, Michael! -----freesurfer-bounces(a)nmr.mgh.harvard.edu schrieb: ----- An: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Von: "Harms, Michael" Gesendet von: freesurfer-bounces(a)nmr.mgh.harvard.edu Datum: 25.10.2016 16:03 Betreff: Re: [Freesurfer] TRACULA longitudinal stream: using multiple configuration files? Hi, I remember looking into this — all the time points for a given subject need to be specified in the same configuration file, otherwise you don’t get the longitudinal aspect of the processing. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "j.oschwald(a)psychologie.uzh.ch" <j.oschwald(a)psychologie.uzh.ch> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, October 25, 2016 at 2:29 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA longitudinal stream: using multiple configuration files? Hi Freesurfer users I wonder wether it makes a difference when using longitudinal TRACULA if all timepoints are run within one process (1 configuration file including all three timepoints) or if it is possible to split it into several independent processes (with several different configuration files - one per time point)? Thank you for your help. Jessica The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ 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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Re: [Freesurfer] White matter surface don't change after editing
by Cong 26 Oct '16

26 Oct '16

Hi Dear Bruce My problem is bilateral high signal grey matter in T1 image. For example, in uploaded subject at coordinate of TkReg RAS -59.00 3.00 5.00, white matter surface is too far out even though I have erased extra white matter voxel in wm.mgz and rerun. Another problem is grey matter surface bend inward, for example at coordinate of TkReg RAS -61.00 3.00 -14.00. I tried to use expert options to improve min_border_white and max_gray but couldn’t get satisfied surface. So I want to know whether freesurfer can fix these two problems and how. I’m sorry to occupy you so much time. Thanks very much. Best Wishes Cong Chen > Date: Mon, 24 Oct 2016 23:22:58 -0400 > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > Can you send us specific coordinates of things to look at? > >> On Oct 24, 2016, at 10:44 PM, Cong <3110103623(a)zju.edu.cn> wrote: >> >> Hi Dear Bruce >> I have uploaded a subject named Cong2Bruce.zip through ftp. I can?t fix it by myself. Could you help me how to use expert options to get correct white matter and gray matter surface. Thank you very much. >> >> Best Wished >> Cong Chen >> >>> Date: Tue, 20 Sep 2016 10:45:30 -0400 (EDT) >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] White matter surface don't change after >>> editing >>> >>> Hi Cong >>> >>> we are experiencing serious disk problems at Martinos, so the ftp site is >>> down. >>> >>> Try changing the values for mri_segment also. Note that what you are >>> seeing are NOT topological defects as mris_make_surfaces preserves the >>> input topology whatever its settings. Make sure to look in 3D and scoll >>> through your slices. You can also try changing the gm thresholds >>> >>> cheers >>> Bruce >>> >>>> On Tue, 20 Sep 2016, Cong wrote: >>>> >>>> Hi Dear Bruce >>>> ? ? ?Thanks very much for your reply, I ?improved min_border_white to >>>> 100, the lh.white line shrinks but still is far out in some area, ?and >>>> I notice many topological defect appears as a result. >>>> ? ? ?I failed to upload subject through ftp, it's always appear an >>>> error called "550 Failed to change directory", so I send a subject to >>>> you through FileDrop. Can you receive a file named Cong2Bruce.zip?? >>>> >>>> ? ? ?Thanks again for your help. >>>> >>>> Best Wishes >>>> Cong Chen >>>> >>>> Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT) >>>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>> Hi Cong >>>> >>>> you could try using expert options to modify the >>>> mris_make_surfaces? >>>> parameters. It looks like you white surface is too far out. Try? >>>> increasing min_border_white and/or increasing max_gray. If you >>>> can't get it? >>>> working feel free to upload the entire subject dir and we will >>>> take a look >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Thu, 8 Sep 2016, Cong wrote: >>>> >>>> Hi dear all >>>> ? ? I attach a new picture to illustrate this problem. ?I erased >>>> some voxels in wm.mgz and rerun. The lh.orig(blue line) looks >>>> well, but lh.white(yellow line) don?t along the white surface in >>>> some area. Could anyone give me some advice? Thanks very much. >>>> >>>> Best wishes >>>> Cong Chen >>>> >>>> >>>> Date: Sun, 4 Sep 2016 15:15:42 +0800 >>>> From: Cong <3110103623(a)zju.edu.cn> >>>> Subject: [Freesurfer] White matter surface don't change after >>>> editing >>>> >>>> Dear freesurfer team? >>>> ?I have some MRI images from a GE scanner, ?it seems that >>>> images? quality is poor because grey matter is bright in so much >>>> area and these grey matter is included in wm.mgz. So I deleted >>>> wrong voxels in wm.mgz by freeview and rerun through command ? >>>> recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But >>>> ?h.white (yellow line) don?t change after rerunning as you can >>>> see in the attached picture. ?Is this problem caused by deleting >>>> too many voxels and how to fix it? ?Thanks very much. >>>> >>>> Regards >>>> Cong Chen >> >>

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Protocol for Ventricle Segmentation
by Tamara Tavares 25 Oct '16

25 Oct '16

Hello, I am wondering where I find the protocol used to segment the ventricles for Freesurfer version 5.1. Looking at the citations in Fischl et al 2002, I have found some information regarding the segmentation of the surfaces and some subcortical areas but not the ventricles. I was hoping to compare the segmentation protocol Freesurfer uses with another program. Thank you in advance for your help! Tamara

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TRACULA longitudinal stream: using multiple configuration files?
by j.oschwald＠psychologie.uzh.ch 25 Oct '16

25 Oct '16

Hi Freesurfer users I wonder wether it makes a difference when using longitudinal TRACULA if all timepoints are run within one process (1 configuration file including all three timepoints) or if it is possible to split it into several independent processes (with several different configuration files - one per time point)? Thank you for your help. Jessica

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3D Mesh of hemispheric surfaces does not match space of acquisition sequence
by Conrad Christoffer Prillwitz 25 Oct '16

25 Oct '16

Dear Freesurfer-Expert, We are currently trying to develop a 3D-Model from MRI data using combined files from Freesurfer and FSL. For this purpose we run recon-all on our subject and furthermore get some ROIs from FSL-based scripts. When visualizing the Freesurfer surfaces together with the FSL ROIs in any 3D modelling software (like e.g. Meshlab or 3D Slicer), there seems to be a space mismatch meaning: the FSL-based ROIs lie more inferior relative to the Freesurfer surfaces than they should (a shift in any other direction might be there but is at least not visible by eye; see attached screenshot). If we further add a single 2D slice of the original T1.mgz file to the 3D model, it seems to be consistent with the spatial position of the FSL ROIs, while the Freesurfer surfaces are clearly shifted (at least in z-direction; see attached screenshot). However opening the surfaces and the T1.mgz in freeview instead of 3D-Slicer, the spatial position fits. Do you have any idea of why this is the case or even more important, how to bring both structures in the same "space"? As we need to continue modelling in 3D-Slicer, we are looking for a way to correct the spatial shift independent of freeview. We are very thankful for any input on this matter! Best regards, Bastian David Bastian David, M.Sc. Ph.D. candidate .............................................................. Department of Epileptology University of Bonn .............................................................. Sigmund-Freud-Str. 25 53127 Bonn .............................................................. bastian.david(a)ukb.uni-bonn.de www.epileptologie-bonn.de

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