Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm
by Dalton Bermudez 18 Nov '19

18 Nov '19

External Email - Use Caution ---------- Forwarded message --------- From: Dalton Bermudez <daltonhbermudez(a)gmail.com> Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: <freesurfer(a)nmr.mgh.harvard.edu> Dear FreeSurfer Developers, I am attempting to obtain a average cortical surface for two structural MRI nii dataset. However, when I run the command, I obtain the following errors. error: No such file or directory error: ltMNIreadEx: could not open file transforms/talairach.xfm error: mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz, -1): could not open file ERROR readMNI: cannot read src MRIorig.mgz FreeSurfer version: freesurfer-linux-centos6_x86_64-dev Platform: Linux Ubuntu 18.05 recon-all.log: see attachment

3 3

HBT hippocampal segmentation
by Daniel Callow 18 Nov '19

18 Nov '19

External Email - Use Caution Hello, I was just asked by a reviewer how the head body and tail of the Freesurfer subfield segmentation is determined. I know that there is no differentiation of the tail, however, there are differentiations between the head and body of the different subfields. Are there specific anatomical boundary rules that drive the algorithm to differentiate between head and body in the HBT segmentation output. Thank you for any guidance you can provide! Best, *Daniel Callow* *Graduate Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

2 2

Fwd: Regarding Issue in reading binary files inside DICOM Directory
by sudhakar Mishra 18 Nov '19

18 Nov '19

External Email - Use Caution Hi, I am facing problem in reading dicom files arranged in a way described in attached image. I want to convert from this format to .nii format. Please help me with this. Thanks very much for considering my request Sudhakar Mishra Research Scholar

4 5

Request regarding Lobular pooling
by Samson Nivins 17 Nov '19

17 Nov '19

External Email - Use Caution Hi, I am interested in summing up the lobes or make individual lobes like frontal, parietal etc. I tried using lobes strict, however, I am unable to get the data in the label format. Rather I get as annot form. Can you please help me Looking forward to hear from you " mri_annotation2label --subject 1008 --hemi rh --lobesStrict --outdir ./location" Best regards, Sam Samson Nivins | PhD Student A The University of Auckland, Liggins Institute Building 505, Level 2, 85 Park Road, Auckland Ph +(64) 21 256 5964 E samson.nivins(a)gmail.com<mailto:samson.nivins@gmail.com> [cid:image001.png@01D4C1F6.9273DF90]

1 0

bias field correction Freesurfer
by Adam Rytina 16 Nov '19

16 Nov '19

External Email - Use Caution Hello all, I have an input MR T1w series of images. I want to apply the bias field correction. According to some articles that I´ve read, bias field correction is automatically done in the standard "recon-all". Is that right - in which of 31 stages of recon-all bias filed correction is implemented? Moreover, I´ve read it´s possible to run "nu_correct" - does it perform also bias field correction? Or does it perform only intensity inhomogenity? Thanks a lot Adam

2 2

Re: [Freesurfer] mri_cvs_register: no such file or directory
by Vinny K 16 Nov '19

16 Nov '19

External Email - Use Caution Hi, I'm using the development version of FreeSurfer and am attempting to register two subjects using mri_cvs_register. This is the command I ran: mri_cvs_register --mov subjb/ --template subja/ Below was the outputted message: The outdir: /home/vinny/Tools/freesurfer/subjects/subjb//cvs Log file is /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log: No such file or directory. Thanks, Vinny

2 3

Re: [Freesurfer] Processor speed/cores vs cache size
by fsbuild 15 Nov '19

15 Nov '19

External Email - Use Caution Hello Pradyumna, I have not read thru the mailing list posts so see what other comments there may be about this, but the posted system requirements,https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements- do not mention anything like Xeon class server chips. Desktop (non-server class) machines with a modern Intel i7 or i9 chip with base (non-turbo, non-overclocked) CPU speeds of ~3 GHz are common.  I’ve run a complete recon-all in about 7-8 hours on a mid-2016 MacBook Pro with a 2.9Ghz  i7 chip (4 physical, 8 virtual cores) with 16GB of old higher latency DDR3 memory using all SSD disk storage (with the machine doing nothing else). I don’t have any data w.r.t the pros/cons of L2 or L3 level cache.  I don’t know the details of how many threads the commands executed by recon-all can exploit.  From my own experience of running various commands, 4 or 8 physical cores (hyperthreaded to yield 8 or 16 cores) should be fine.   I’ve also found that 24G to 32G of RAM is helpful with performance.  Since data/files will be read/written from disk, at certain points performance could be I/O bound by how fast disk read/writes occur.  This can be helped by having your data stored on a 7200, 10,000 RPM disk drive (or better an SSD drive) to speed things up that is physically separate from the drive with the boot partition. But you could certainly meet or upgrade the specs to outfit a server machine with Xeon class chips and drives for multiple users. - R. On Nov 13, 2019, at 15:00, Pradyumna Bharadwaj <prad(a)email.arizona.edu> wrote:        External Email - Use Caution        Hello,For running recon-all or tracula on a local workstation, is it recommended to go for a higher processor speed/number of cores, or a larger cache size for the processor (Intel Xeon W series). Or is it likely to be a more complex interplay between the number of recon-all processes running at any given time?Thanks,Pradyumna_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Custom location of license file
by fsbuild 15 Nov '19

15 Nov '19

External Email - Use Caution Hello Karsten, I think the location for license.txt in the freesurfer 6 release needs to be under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and cannot be relocated from there by an environment variable..  But you can try using a soft link to point to it in another location.   While it does not work to preserve $HOME/license.txt as a reference in another environment variable like FREESURFER_HOME or within a soft link, I believe the shorthand notation ~/license.txt does work in a soft link.   So in your common installation under $FREESURFER_HOME you could try, $ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt - and see if freesurfer complains if an individual users $HOME/license.txt (or ~/license.txt) is missing. In the newer code base on the freesurfer development branch, it should work to set the FS_LICENSE environment variable to point to the path of the license.txt file, but I don’t think that works in the 6.0.0 release. Ideally, I think the freesurfer group would prefer if each user signed up for their own license in order to track usage, so maybe try the soft link. - R. On Nov 14, 2019, at 12:58, Siller, Karsten H (khs3z) <khs3z(a)virginia.edu> wrote:        External Email - Use Caution        Hi, We’d like to install FreeSurfer globally for our users on a CentOS HPC system.  Is it possible to define an alternative location for the FreeSurfer license file, e.g.  ~/.license, so that users can use their individual license files with the globally installed software?  Perhaps the license file location and name can be customized via an environment variable at runtime? If that is not possible, is it ok to install a single “global” license file for all users in the shared FreeSurfer installation directory? Thanks,Karsten -- Karsten SillerResearch ComputingUniversity of Virginia _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Volume (WM Parcellation) of RightCerebralCortex -- Freesurfer 6.0
by An Lijun 15 Nov '19

15 Nov '19

External Email - Use Caution Dear Freesurfer experts, I am trying to use ADNI MERGE R package to get 'wholebrain' volume. It requires <Left/Right>CerebralCortex. The information I get from ADNI merge is "Volume (WM Parcellation) of RightCerebralCortex". But when I ran Freesurfer reconall 6.0, I could not find <Left/Right>CerebralCortex under 'stats' folder, do you know where it could be? Thanks so much. Best Regards, An Lijun

2 1

Custom location of license file
by Siller, Karsten H (khs3z) 14 Nov '19

14 Nov '19

External Email - Use Caution Hi, We’d like to install FreeSurfer globally for our users on a CentOS HPC system. Is it possible to define an alternative location for the FreeSurfer license file, e.g. ~/.license, so that users can use their individual license files with the globally installed software? Perhaps the license file location and name can be customized via an environment variable at runtime? If that is not possible, is it ok to install a single “global” license file for all users in the shared FreeSurfer installation directory? Thanks, Karsten -- Karsten Siller Research Computing University of Virginia

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer