Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

Queries in qdec
by Koustav Chatterjee 19 Feb '21

19 Feb '21

External Email - Use Caution Dear Forum members, May I get your help please to resolve 2 queries below? 1. I am unable to see .tiff files taken through 'quicksnaps.tiff' of the 'qdec' analysed data. Even after completing the process of 'quicksnaps.tiff' successfully, I can see only black screen while opening the file. Please find a sample pic of how those files look. [image: image.png] 2. I am using FreeSurfer version 6 where I am *missing 'Design Matrix Type'* inside the 'design' tab of 'qdec' command. [image: image.png] Thank you for your time and help. Regards, Koustav

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Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS
by Ishi Tandon 18 Feb '21

18 Feb '21

External Email - Use Caution Hello experts, I have recently installed freesurfer on Ubuntu 20 (which is on virtualbox). I want to use hippocampal subfield segmentation in freesurfer. I have installed MATLAB run time (2014b) through the following command - fs_install_mcr M2014b However, this displayed the following warning - on the target computer , append the following to your LD_LIBRARY_PATH environment variable : /tmp/tmp.HvgiEwe6Av/install-target/v84/runtime/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/bin/glnx864://tmp/tmp.HvgiEwe6Av/install-target/v84/sys/os/glnx864 Next, set the XAPPLRESDIR environment variable to /tmp/tmp.HvgiEwe6Av/install-target/v84/X11/app-defaults Having set that to the bashrc script. It gives me an error when I try the following command. segmentHA_T1.sh <https://secure-web.cisco.com/11MSQv2e7FuBi1XZjDt6ZitEBRceHDC8rRcDsdx1Fq1aC1…> bert. (error attached below). I am also attaching the changes that I made in bashrc. It would be great if you help me out. Thank you in advance. *Regards,* *Ishi Tandon* *B.tech <https://secure-web.cisco.com/1CFi-inHeHrntmx2nGqrNhbOMeLCIYQPJUzxpcsRSry9KD…> + M.tech <https://secure-web.cisco.com/1dcU_xiUsYUlrguN9SAjy7_K6ZMhQa0p9ALjneRAYlfaMX…> - Cognitive & Neuroscience* *Amity University, Rajasthan* *contact - +918239259846 ; Email- ishi.tandon99(a)gmail.com <ishi.tandon99(a)gmail.com>*

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What exactly are the BA_exvivo.thresh label and annotation files?
by julienbesle 18 Feb '21

18 Feb '21

External Email - Use Caution Hello, The ex-vivo BA label and annotation files named ?h.BA??_exvivo.thresh.label and BA_exvivo.thresh.annot seem to be thresholded versions of the corresponding probabilistic BA labels. Was a simple threshold on the probability used and if yes, what was the value? In addition the annotation files, whether thresholded or not, only have one label per vertex. Are the labels based on the maximum probability across all BA labels? Thanks Julien -- ------------------------------------------------------ Julien Besle Assistant Professor Department of Psychology Faculty of Arts and Sciences American University of Beirut Riad El-Solh / Beirut 1107 2020 Lebanon Jesup Hall, Room 103E Tel: +961 1 350 000 ext. 4927 -----------------------------------------------------

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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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Freesurfer February 2021