Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Hippocampal Subfields (6.0) Error
by Andrew Schoen 11 Jan '16

11 Jan '16

Hi all, We are running some hippocampal subfield segmentations for two independent studies. They have already been processed through the standard pipeline (5.3), so I was just running the following command: *recon-all -s ${subjectid} -hippocampal-subfields-T1* For both test cases, the processing seems to have halted (no more updates to the log file), but the command keeps running. For one study, it trailed off here: ************************************************************************************************************************ Resolution level 1 iteration 2 deformation iterations 13 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0.00037944 voxels in 14.6033 seconds minLogLikelihoodTimesPrior = 2.3442e+06 Resolution level 1 iteration 2 deformation iterations 14 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 1.3541e-06 voxels in 3.5131 seconds minLogLikelihoodTimesPrior = 2.3442e+06 Resolution level 1 iteration 2 deformation iterations 15 Number of Meshes: 1 Using CG optimizer Did one deformation step of max. 0 voxels in 30.0807 seconds minLogLikelihoodTimesPrior = 2.3442e+06 maximalDeformation is too small; stopping Iteration 3 of 7 (eof) ************************************************************************************************************************ and the other here: ************************************************************************************************************************ Making Left-Accumbens-area map to reduced label 13 -------------- Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians parameters Estimating typical intensities of molecular layer and alveus For ML in T1, we assume gray with high N In T2, we actually assume the same hypermean Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0 Smoothing class: 1 Smoothing class: 2 Smoothing class: 3 Smoothing class: 4 Smoothing class: 5 Smoothing class: 6 Smoothing class: 7 Smoothing class: 8 Smoothing class: 9 Smoothing class: 10 Smoothing class: 11 Smoothing class: 12 Smoothing class: 13 done numberOfImages = 2 Image: 0 Image: 2 Iteration 1 of 7 (eof) ************************************************************************************************************************ Interestingly, for one study, we have T2-weighted images, and when I ran with that (same subject as second log, above), it ran to completion fine. Any idea what might be happening? Let me know if any other info would be useful! Thanks! Andrew Schoen Center for Healthy Minds Waisman Center University of Wisconsin - Madison

2 1

Recon-all get stucked without error during processing
by Matthieu Vanhoutte 07 Jan '16

07 Jan '16

Dear FS epxerts, I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step without error. Please found the recon-all.log associated attached to this mail. Thanks in advance for helping ! Best regards, Matthieu

2 9

.w file for freeview
by peng 06 Jan '16

06 Jan '16

Hi Freesurfers, I tried to overlay .w file onto a surface, and failed. I dug the previous posts and know this file format is obsolete now. However I wish to know in which version of freeview can I still use this file format, if possible. It will be great if you can provide the link for it. If this is not possible, is there a matlab tool similar to 'write_file.m' so I can output my data in matlab to the newer format (substitution of w-file)? Thanks in advance. best Peng

3 5

Recon-all Run Time
by Marissa Pifer 06 Jan '16

06 Jan '16

Hi Freesurfers, I've recently downloaded free surfer onto a new computer. It's working correctly, but the running time for the recon-all -all command is 30-50 hours. This is in contrast to when I've used free surfer on previous computers where the run time was 6-12 hours. I'm wondering why this would be the case and if anyone else has run into this problem. Marissa

2 2

how to display individual Desikan parcels?
by Mihaela Stefan 05 Jan '16

05 Jan '16

Hello Freesurfers, I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview. There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this? Thanks! Mihaela

2 6

Freesurfer 6.0 -hires mri_segment potential issue
by Ajay Kurani 05 Jan '16

05 Jan '16

Hello Freesurfer experts, I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu 14.04 with a high resolution image (0.5mm isotropic). I set OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags in my autorecon 2 line command. Autorecon1 and the beginning parts of Autorecon2 ran in a reasonable amount of time. Currently the program is running the mri_segment -keep -mprage brain.mgz wm.seg.mgz line command however it has been at this step for approximately 5 days! I used top line command to verify that the program is still running and it seems to be still running. I wasn't sure if this time for this step is typical for a high-res image (as this is my first time processing data higher than 1mm iso), or if there is a potential bug. I ran this same subject on another computer using the same version of Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been running for over a day so far. Any feedback would be appreciated as to if this amount of processing time is typical for this type of resolution, or if it could be a potential bug and that I should wait for a new beta release? Thanks, Ajay

2 1

problem with hard coded directory (/scratch)
by Fengji Geng 04 Jan '16

04 Jan '16

Dear all, I am currently using freesurfer 6.0 (development version) to run hippocampal subfields segmentation and encountered a 'mkdir' error, which is attached below. Our troubleshooting found that some scripts in the ...freesurfer/dev/sys/bin directory with things like: if(-e /scratch) set tmpdir = /scratch/tmpdir.bbmask.$$ if(! -e /scratch) set tmpdir = $outdir/tmpdir.bbmask.$$ However, /scratch is a directory that is not writable in our server. So, we made changes to all of the scripts that testing the existence of /scratch. However, there are several places where they incorrectly test for the /scratch directory using -e instead of -dw, the /scratch is hard coded in there so it can't be changed. Looking forward to hearing suggestions and comments. Fengji ----------------------------------------------------------------------------------------------------------- Here begins the error message: hippocampus:/<2>hippocampus/HMN/data/FG_Temp: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Nov 18 21:57:45 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Nov 18 21:57:50 EST 2015 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cell_root/software/freesurfer/dev/sys/MCRv80/runtime/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/bin/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/os/glnxa64:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/cell_root/software/freesurfer/dev/sys/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/cell_root/software/gsl/current/sys/lib:/cell_root/software/fastx/current/lib/fastx_server/lib Warning: application is running on a locale different from the original platform locale. Error using mkdir Read-only file system Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError End of error message.

4 8

Using custom segmentations with recon-all
by james pardon 02 Jan '16

02 Jan '16

Dear All, I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps? Thank you in advance, James

2 3

Fwd: LME FDR2 corrected results
by Hanbyul Cho 01 Jan '16

01 Jan '16

Dear FreeSurfer Team, My name is Han. I am wondering how I can save the FDR2 corrected results. I processed in MATLAB for Linear mixed effects models analysis, as follow: [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95); lhstats01 = lme_mass_fit_Rgw(X,[1],Y,ni, lhTh01, lhRgs01, lhsphere,[],'euc','exp',4) F_lhstats01=lme_mass_F(lhstats01,CM,4); dvtx = lme_mass_FDR2(F_lhstats01.pval, F_lhstats01.sgn, lhcortex, 0.05, 0); length(dvtx) ans = 8000 In this case, I search the corrected results that were 8000 vertices. I think the dvtx value was for saving the significant each vertex numbering label, is it right? However, I don't know the next step for save the 8000 corrected vertices. fs_write_fstats(F_lhstats01,mri,'%%$.mgh','sig'); I can save the whole results 'F_lhstats01' as the mgh format. However these were uncorrected results, is it right? Could you let me know the method for saving the FDR2 corrected results as a mgh format? Best Regards, Han.

2 2

Question on longitudinal stats directory
by Govindarajan, Koushik Athreya 01 Jan '16

01 Jan '16

Hi there, I have run my subjects from multiple time points through a cross-sectional stream and a longitudinal stream. When I look at the 'stats' directory for the same subject from the cross-sectional pipeline and the longitudinal pipeline, I see that the numbers are different. For example, the cortical thickness values in the lh.aparc file for the same subject are different. Is one estimation more accurate than the other? Where is the difference coming from? Thanks Koushik Govindarajan

2 3

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 December 2015