Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Unable to run recon all successfully !
by Sahil Bajaj 18 Feb '21

18 Feb '21

External Email - Use Caution Hello FreeSurfer experts, I am trying to run recon all pipeline on infants' brains. Somehow, out of 7 subjects, I am getting error for four subjects (S28, S69, S149 and S233) and for the other three (S36, S90 and S119) I do not see any progress in the terminal (for about the last 5 hours). Here I am attaching recon all logs for all these subjects. I would really appreciate any help. Thanks, Sahil

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Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 17 Feb '21

17 Feb '21

External Email - Use Caution Dear Freesurfer experts, I've been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the "Segmentation of thalamic nuclei" tool by Iglesias, J.E. et al. The "recon-all" as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases - regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://secure-web.cisco.com/13NyoIuwpnsiHWemQxkjh3X8nFYXTG9wpVXrDAWJsCjxur… Thanks for your help! Best, Franziska

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VB password
by バキット・ムダシル 17 Feb '21

17 Feb '21

External Email - Use Caution Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the “Developed” password. Is it possible to have it? Best Mudathir

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Re: [Freesurfer] overlap/intersection of labels?
by Trisanna Sprung-Much 16 Feb '21

16 Feb '21

External Email - Use Caution Hi Cornelius I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean: https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4… See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer<https://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8f…> 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2). I know there is also a command merge_labels that may help? Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Dr. Cornelius Kronlage" <Cornelius.Kronlage(a)med.uni-tuebingen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] overlap/intersection of labels? External Email - Use Caution Dear freesurfers, is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations? I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnw…<https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naU…> ) which is awfully slow. In case this is of use for anyone else, I attached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac. >time labels_intersect precentral.label frontal.label out1.label > /dev/null real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label out2.label real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label > Thank you and best wishes Cornelius -- Cornelius Kronlage Assistenzarzt Klinik für Neurologie | Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen Hoppe-Seyler-Str. 3 | 72076 Tübingen

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Re: [Freesurfer] ubuntu 20.4?
by Olga Kepinska 15 Feb '21

15 Feb '21

External Email - Use Caution Dear all, If in the meantime any of you has had any experience with FS on Ubuntu 20.4, please let us know the details. Thank you and kind regards, Olga Kepinska From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Olga Kepinska <olga.kepinska(a)univie.ac.at> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, December 22, 2020 at 5:24 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] ubuntu 20.4? External Email - Use Caution Dear FS community, I’m following up on my previous communications about FS on Ubuntu (if interested see thread ‘FS on Ubuntu’). The advice (very useful, thank you!) given by the fsbuild team is to go with Ubuntu 18. If however, anyone out there has successfully used FS 7.1 (to run the structural pipeline) on Ubuntu 20.4, please reach out! Thank you, Olga -- Olga Kepinska, PhD  Postdoctoral Researcher Brain and Language Lab (http://secure-web.cisco.com/1tPNPxrJsfZ-1q3XZeGBTdgWWtCKqGIdkSeXQvHSNzL5VMC…) @olgakepinska _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1V76lYf0Y94a8t749ME0OQqbTYt2ZVXuAfhfwcw2v9mDPF…

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white matter parcellation of Brodmann areas
by Vinny K 12 Feb '21

12 Feb '21

External Email - Use Caution Hello, I'd like to obtain white matter parcellations of the Brodmann areas. I am not certain that the generated wmparc file from recon-all has this type of parcellation. I was able to convert Brodmann area label files to mgz format using mris_label2annot and mri_aparc2aseg commands. How can I obtain white matter parcellation of the individual Brodmann area volumes? Thanks, Vinny

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White Spots shifts Pials - How to solve this
by Nils B. 12 Feb '21

12 Feb '21

External Email - Use Caution Hello everyone, I'm having problems with one of my participants' data (over 60 years old, subjective memory impairment). Due to White Spots in the Gray/White Matter the piles are shifted and I'm unsure how to change this. My outcome will be the Gray Matter thickness, which is why problems in the GM pials are problematic. I added a screenshot of the area (in the Green lines) where you can see several White Spots which cause the Pials to look weird. Is there a way that I could manually move the Gray matter pial to fit better or would you advise to not use this data set? I'm thankful for any feedback. Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://secure-web.cisco.com/1SB-q0kxQpAY3jY4W9qylyFQqq-5553HniFphTOa1lDwnN… https://secure-web.cisco.com/1YEExuqAHZEkxQlrIwlNwucYUa5Pz4hBCN2-gtdA_KZ_eL… <https://secure-web.cisco.com/1SB-q0kxQpAY3jY4W9qylyFQqq-5553HniFphTOa1lDwnN…>

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Re: [Freesurfer] Different results on same MRI in different space ?
by Funk, Quentin 12 Feb '21

12 Feb '21

External Email - Use Caution I used the SPM default coregistration settings -- which it calls "4th degree B-spline". From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Different results on same MRI in different space ? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <ebbb0121-2744-472e-a726-9578d4b5570b(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" When you mapped to the new space, what kind of interpolation did you use? Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care and safety and one of the top 20 hospitals in the nation. In addition, we are nationally ranked in 11 specialties, the most in the state, and have been national leaders throughout the COVID-19 pandemic in research, offering innovative treatments and surpassing CDC safety standards. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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cortical thickness values for each point in a ctx label file
by Krieger, Donald N. 12 Feb '21

12 Feb '21

External Email - Use Caution Dear freesurfer group, I wish to measure a cortical thickness value for each entry in a label file, e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label . Is there a function in the freesurfer distribution which includes this capability? Also, is there a function in the distribution that produces regional label files from the surf/[lr]h.pial files? Thanks - Don [cid:image003.jpg@01D70075.1EC687E0] Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

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LME model
by Víctor Leiva 12 Feb '21

12 Feb '21

External Email - Use Caution Dear Freesurfer experts,I'm using the LME model for longitudinal study and I'm running the part of parameter estimation but MATLAB "told me" than the file "libgeodesic.so" is not available or does not exist. So check in FreeSurfer' folder and it's not there. So I don't know where to find it because I can't found it on the internet Thanks for your help Best, -- Víctor Leiva Ormeño

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