Freesurfer

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[How to perform z-statistic of the combination of multiple MRI features?]
by 김정식 08 Jun '17

08 Jun '17

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Extracting lgi cluster values over label
by Katherine Damme 07 Jun '17

07 Jun '17

Hello Everyone! I have run LGI analyses according to the JoVE article: https://www.jove.com/video/3417/how-to-measure-cortical-folding-from-mr-ima… I created labels from the significant clusters and would like to extract the lgi values from these labels and found that past email chains suggested the following: >>>* mris_anatomical_stats -l ?h_lgi_significant_cluster.label -t **SUBJ/surf/?h.pial_lgi -f ${subj}/stats/?h.aparc_lgi.stats **${subj}** ?h*>>>* aparcstats2table --subjects ALL_YOUR_SUBJECTS --hemi ?h --meas thickness** --parc aparc_lgi --tablefile aparc_lgi_?h.txt* *However the output results in a stats table with the following headings:* ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd Thusly, I am not confident that any of these values represent the lgi value. Can someone confirm that the correct value would appear under the thickness column in this case? Thank you Kate

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FSFAST Full Model Residuals?
by Taylor, Johnmark 07 Jun '17

07 Jun '17

Hello, I had a quick question. Is there a way to make FSFAST output a 4D volume of all the residuals? In other words: is there a way to see, for each voxel and timepoint, how much of the BOLD response was unexplained by the GLM? I know that it outputs a volume containing the residual variances, but I am interested in looking at the residuals in more detail. I see that there is a directory called "res", but for all of the GLMs I've run it appears to be empty... Thank you very much, JohnMark

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(no subject)
by Emily Rogers 07 Jun '17

07 Jun '17

Apologies-- This email contains attachment. Thank you. ____________________________________________________ Hello, I am trying to implement using Freesurfer segmentation in my analysis for MEG data. I am trying to segment this structural MRI (1400composite.dcm) and I keep getting errors. I have attached the log file. Any help is appreciated. Thank you, Emily

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How to capture missing grey matter after recon-all
by Shane Schofield 07 Jun '17

07 Jun '17

Hi Freesurfer Experts, Does anyone know how to deal with situations where the part of the brain is not being captured in aseg.mgz or in the surfaces? I have attached some screenshots. I have tried adding control points but it is not working. Thanks for helping. Best,Shane

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7T recon
by Hibert, Matthew Louis 07 Jun '17

07 Jun '17

Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2. How can I go about correcting this issue? Thanks, Matt

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Re: [Freesurfer] 7T recon
by Hibert, Matthew Louis 07 Jun '17

07 Jun '17

Hi Kevin, Thanks for the suggestion, but I don't think control points would help in this situation. The region of white matter being excluded has been been correctly normalized to approximately 110 and is included in the wm.mgz. Thanks, Matt ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Kevin Aquino [aquino(a)physics.usyd.edu.au] Sent: Wednesday, June 07, 2017 10:50 AM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon {Disarmed} Does adding control points help? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview Cheers, Dr Kevin Aquino Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney E Kevin.aquino(a)nottingham.ac.uk<mailto:Kevin.aquino@nottingham.ac.uk>, aquino(a)physics.usyd.edu.au<mailto:aquino@physics.usyd.edu.au> | W MailScanner has detected a possible fraud attempt from "www.physics.usyd.edu.au" claiming to be https://kevinaquino.github.io<http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary. On Wed, Jun 7, 2017 at 3:39 PM, Hibert, Matthew Louis <MHIBERT(a)mgh.harvard.edu<mailto:MHIBERT@mgh.harvard.edu>> wrote: Hi Bruce, I edited the wm.mgz with the recon-editing tool this time, removing the problem areas near this defect (primarily lots of dura originally included), and confirmed that my edits remained after re-processing. However, the left STG is still being removed, images attached (red is the lh.orig.nofix with lh.defect_labels overlayed, yellow is lh.white). The entire left STG is still being marked as a defect despite my edits. Any suggestions? Thanks, Matt ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Hibert, Matthew Louis [MHIBERT(a)mgh.harvard.edu<mailto:MHIBERT@mgh.harvard.edu>] Sent: Tuesday, June 06, 2017 5:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon Ah ok, thanks Bruce. Matt ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>] Sent: Tuesday, June 06, 2017 4:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] 7T recon Hi Matt we keep track of edits by setting erased voxels to 1, not 0. If you do the editing within freeview using the "recon edit" tool, this will happen automatically cheers Bruce On Tue, 6 Jun 2017, Hibert, Matthew Louis wrote: > Hi Bruce, > Thanks again for your help so far. I've tried removing the problem voxels from the wm.mgz (setting their value to 0), saving the wm.mgz, and then running "recon-all -autorecon2-wm -autorecon3 -hires -s $SUBJECT -xopts-use -openmp 2". However, the edits to the wm.mgz are not incorporated and the surfaces are not changed; when I open the wm.mgz again, the voxels I removed are now present again. What am I doing wrong? > > Thanks, > Matt > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>] > Sent: Friday, May 26, 2017 1:57 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] 7T recon > > yes, and autorecon3 > On Fri, 26 May 2017, Hibert, Matthew Louis wrote: > >> Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm? >> >> Thanks, >> Matt >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>] >> Sent: Friday, May 26, 2017 1:40 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] 7T recon >> >> Hi Matt >> >> yes, that means there was a topological defect that was incorrectly >> fixed. If you load the wm.mgz over the lh.orig.nofix, then in the >> orig.nofix load the file defect_labels as an overlay and change the overlay >> settings to that the min is 1 and click the "use overlay color" button it >> will show you the regions of the surface that are defective. You will then >> need to edit the wm.mgz to remove the handle/hole that is the defect. >> >> cheers >> Bruce >> >> >> On Fri, 26 May 2017, Hibert, Matthew Louis wrote: >> >>> Hi All, >>> I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T >>> and while most look good, 4 of the subjects have a similar section of the >>> left STG removed from the final surfaces (picture attached). In all 4 >>> subjects the entire left STG is included in the wm.mgz and lh.orig.nofix >>> (red), but a portion has been removed in lh.orig (yellow), so the problem >>> seems to occur in the -fix stage of autorecon2. >>> >>> How can I go about correcting this issue? >>> >>> Thanks, >>> Matt >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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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Subject creation got terminated after Subcortical Segmentation processing
by M Janani 07 Jun '17

07 Jun '17

Hello FreeSurfer Developers, I'm attempting to create subject for PiB MRI. I get an error during the Subcortical Segmentation value processing. The last thing it says is: "saving intensity scales to aseg.auto_noCCseg.label_intensities.txt". After that it got terminated like mentioned below Terminal Error: saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt Terminated I've searched the list and a similar error have been reported in V4.5. But we are using FS version 6. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux sand 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 4)recon-all.log: see attached Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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TRACULA (dmri_motion)
by John Anderson 06 Jun '17

06 Jun '17

Dear TRACULA experts, I plan to use TRACULA in freesurfer 6 to analyze DTI data. I want to kindly to inquire about the command "dmri_motion". This script,nicely, generates: the SNR, drop out score, # drop out slices and motion parameters. I highly appreciate if you can guide me to a method, so I can benefit from these numbers in my evaluation to motion in the data. I tried to plot SNR and Fa, or SNR and motion parameters and I found outliers consistent with more motion and less SNR. In this case is it healthy procedure just to remove the outliers?! Are there any ranges of safety for SNR and motion parameters that can be used to include/exclude the images. Thanks Jon

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recon-all: .md and .txt format
by 곽유나 06 Jun '17

06 Jun '17

Hello FS experts, I ran recon-all, and got an error saying that it can't read certain txt files from the freesurfer folder. I'm not sure if this is the main reason for exiting with ERRORS, but when I looked into the folder I found that FreeSurferColorLUT.txt , ASegStatsLUT.txt, and others were all stored in .md files. So I changed all of them into .txt, ran recon-all -make (to start from where it left off?), and now it seems to be working. Below is the output in the terminal when the error occurred (for the ASegStatsLUT.txt case) CTABreadASCII(/Applications/freesurfer/ASegStatsLUT.txt): could not open file Computing euler number orig.nofix lheno = -28, rheno = -16 orig.nofix lhholes = 15, rhholes = 9 Loading mri/aseg.mgz No such file or directory ERROR: reading /Applications/freesurfer/ASegStatsLUT.txt Darwin S-Yui-MacBook.local 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 recon-all -s yuna exited with ERRORS at Mon Jun 5 22:20:13 KST 2017 I want to ask if I'm doing this correctly, if it's okay to change the format to .txt and run recon-all -make. Best, Yuna. p.s. I posted a question on the list one or two days ago and for some reason I wasn't able to reply through the archive with the e-mail address I was using, so I wasn't able to thank you guys for your help. Now I'm posting with a new e-mail address, and I wanted to thank you for your replies!

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