Freesurfer

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Re: [Freesurfer] left-right flip?
by Ellen Ji 18 Sep '20

18 Sep '20

External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: > Hi Ellen > > Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? > > Cheers > Bruce > > -----Original Message----- > From: Ellen Ji <ellen.ji(a)bli.uzh.ch> > Sent: Tuesday, September 15, 2020 12:38 PM > To: Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] left-right flip? > > External Email - Use Caution > > Hi Bruce, > > Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again? > > Thanks, > > Ellen > > On 9/15/2020 5:44 PM, Fischl, Bruce wrote: >> And what is your input to recon-all? If it is dicom you should be >> pretty confident that we will get it correct >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve >> Sent: Tuesday, September 15, 2020 10:17 AM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] left-right flip? >> >> How are you checking the LR orientation? >> >> On 9/15/2020 4:10 AM, Ellen Ji wrote: >>> External Email - Use Caution >>> >>> Dear experts, >>> >>> I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. >>> >>> For example, in our dataset, the lateral ventricle volume is on >>> average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. >>> >>> In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. >>> >>> Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! >>> >>> I found this website on Left-right reversal, and it seems relevant to >>> my issue, but I'm not fully understanding what this means (how would >>> bias occur during segmentation?) - >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >>> >>> Many thanks for your input, >>> Ellen >>> >>> --- >>> >>> Ellen Ji, PhD >>> Postdoctoral Research Fellow >>> Psychiatric University Hospital >>> University of Zürich >>> ellen.ji(a)bli.uzh.ch >>> homanlab.github.io/ellen/ >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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] Freesurfer Digest, Vol 199, Issue 7
by James Hartzell 17 Sep '20

17 Sep '20

External Email - Use Caution HI Andrew Thanks. I've run autorecon 1, 2, and 3 so far for this one participant. There's an error in autorecon 1 but I see from older list discussion that it can be safely ignored. Even though autorecon 2 claims to finish without error, the error I reported seemed likely significant and I thought probably it should not be ignored--perhaps I am mistaken. I've attached a zip file with all the logs in the scripts folder. Cheers James On Fri, Sep 4, 2020 at 6:01 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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. Re: autorecon2, error MRISreadCurvature: (Hoopes, Andrew) > 2. Re: recon-all error (Jie Zhao) > 3. Re: mri_cvs_register with sub-millimeter recons > (Zollei, Lilla,Ph.D.) > 4. Re: recon-all error (Fischl, Bruce) > 5. mri_segstats quetsion (Nasiriavanaki, Zahra) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Sep 2020 20:18:22 +0000 > From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] autorecon2, error MRISreadCurvature: > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <67B3E641-B123-4261-880B-BF3E194A8B87(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi James, > > Can you send the full recon-all.log for this subject? > > Thanks, > Andrew > > From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of James > Hartzell <james.hartzell(a)gmail.com> > Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Date: Thursday, September 3, 2020 at 10:20 AM > To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] autorecon2, error MRISreadCurvature: > > > External Email - Use Caution > Hi > > When running recon-all autorecon2, on a single subject with > (Macbook Pro 10.15.6 (19G2021), > freesurfer-darwin-macOS-7.1.0-20200511-813297b) > > it handles the rh.curv without a problem, but for the lh kicks out this > error: > > /Users...$subj.../surf > \n mris_curvature_stats -m --writeCurvatureFiles -G -o > ../stats/lh.curv.stats -F smoothwm $subj lh curv sulc \n > Toggling save flag on curvature files [ > ok ] > Outputting results using filestem [ > ../stats/lh.curv.stats ] > Toggling save flag on curvature files [ > ok ] > Setting surface [ $subj./lh.smoothwm ] > Reading surface... [ > ok ] > Setting texture [ > curv ] > Reading texture...error: No such file or > directory > error: MRISreadCurvature: could not open /Users/$subj./surf/lh.curv > > ***WARNING!*** > Some error has occurred while reading 'lh.curv'. > This might be due a vertex incompatibility > between the surface 'lh.smoothwm' and curv 'lh.curv'. > > You might be able to correct this by re-running > 'mris_make_surfaces' on this dataset. > > Skipping this (and any remaining) curvature files. > Any measurements / calcuations that depend on the > curvature file will be skipped. > ************* > Note /Users/$subj./surf/lh.curv does exist in the subject's surf folder. > > I ran it twice just to be sure. I don't find an answer for the problem in > the freesurfer list. Any guidance will be much appreciated! > Cheers > James Hartzell, PhD (2x) > Donostia-San Sebati?n, Spain > > >

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Tracula FS 6 vs FS 7.1.1
by Alexopoulos, Dimitrios 17 Sep '20

17 Sep '20

External Email - Use Caution Are there any differences in usage /outputs from Tracula in FS 6 vs FS 7.1.1? Specifically as it relates to the customized dmrirc config file? The wiki mentions a beta version of Tracula in FS. 7.2. Will the general usage be similar to 6/7.1.1? Jim ________________________________ 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.

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display P-values for T-test on differences in mean FA/MD/… between groups
by Zeng, Qi 17 Sep '20

17 Sep '20

External Email - Use Caution Hi, In Tracula Wiki, there is a slice of displaying P-values for T-test on differences in mean FA/MD/… between groups following this link and sample plot attached below. https://ftp.nmr.mgh.harvard.edu/pub/docs/TraculaNov2013/tracula.workshop.ii… . I want to know what is the command for this and is there a useful link to demonstrate the process? Thank you so much! Best, Qi --

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outputs from step of trac- all prep
by Zeng, Qi 17 Sep '20

17 Sep '20

External Email - Use Caution Hi, Where is the nifti output stored from running trac-all preprocess? Is it dmri/dwi.nii.gz? Is there an additional step segment this nifti file into the grey matter and white matter for later tensor-fitting? Best, Qi

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Config File For Tracula Question
by Ledesma, Jason 17 Sep '20

17 Sep '20

External Email - Use Caution Hi, See attached for my Configfile for Tracula. See attached. What might be the issue with this? Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)lundquist.org ___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________

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Re: [Freesurfer] Hippocampal segmentation -quality check
by Iglesias Gonzalez, Juan E. 17 Sep '20

17 Sep '20

Hi Liz, I cannot say for sure without seeing the posteriors, but that totally looks like it is part of the alveus – which we leave out of the hippo subfield segmentation. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lizbeth Ayoub <lizbeth.ayoub(a)utoronto.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 16, 2020 at 23:41 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal segmentation -quality check External Email - Use Caution Hi everyone, I am in the process of checking my hippocampal segmentations. I am finding that the hippocampal mask is often underestimating certain grey matter areas perhaps pertaining to the hippocampus? For example, the area pointed by the red arrow, here below, was initially covered by the apart + aseg hippocampal mask. Would the FS voxel space mask of the hippocampus pass quality check or would you say that a part of the hippocampal grey matter would be missing ? Thank you for your helpful insight, Liz Liz[cid:image001.png@01D68C86.C1F12140]

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Hippocampal segmentation -quality check
by Lizbeth Ayoub 16 Sep '20

16 Sep '20

External Email - Use Caution Hi everyone, I am in the process of checking my hippocampal segmentations. I am finding that the hippocampal mask is often underestimating certain grey matter areas perhaps pertaining to the hippocampus? For example, the area pointed by the red arrow, here below, was initially covered by the apart + aseg hippocampal mask. Would the FS voxel space mask of the hippocampus pass quality check or would you say that a part of the hippocampal grey matter would be missing ? Thank you for your helpful insight, Liz Liz[cid:82F8A34D-D97A-4DD7-BE98-4C7CDA79D3E4@home]

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Hippocampal and amygdala subregions using earlier freesurfer version segmentations
by Keith Harenski 16 Sep '20

16 Sep '20

External Email - Use Caution Hello, I just wanted to verify that using segmentations from earlier freesurfer versions (5.3) are valid as input into the subsequent further segmentation into the hippocampal and amygdala subregions. I understand the input volumes will vary based on version. Thank you, Keith -- Keith Harenski Mobile MRI Manager / Data Analyst II Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski(a)mrn.org | www.mrn.org | www.lrri.org

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Freeview 7.1.1 won't start on Mac: segmentation fault
by Alex White 16 Sep '20

16 Sep '20

External Email - Use Caution Hello again dear Freesurfer experts I recently updated to v7.1.1, in order to get the latest version of Freeview. I’m using Mac OS 10.15.6. Freeview seems to start once each time I boot up my machine, but if I quite it, I can’t re-start it again (until re-booting the machine). In the terminal I get an error like this: /Applications/freesurfer/7.1.1/bin/freeview: line 2: 6667 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“ The number after “line 2” isn’t always the same. If I try to start Freeview by clicking on its icon, I get a window that says, “freeview quit unexpectedly.” I can send you the full crash report if you like. Any advice? Thanks again, Alex White

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