Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30066 discussions

Medial Surface Problem
by Bronwyn Overs 03 Aug '17

03 Aug '17

Hi mailing list, I am currently processing a longitudinal image and have come across a problem at the medial surface in the long image (step 3). As you can see in the attached image, the rh medial surface has been significantly overestimated and extends into the lh surface. This error showed up only in only 1 of the 2 long images for this subject, and both the time-point images and the base are perfectly fine. Do you know why this is happening? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

4 19

Univariate Linear Mixed Effects
by Worker, Amanda 03 Aug '17

03 Aug '17

Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could you explain why that is please? And also what hypotheses these three different contrasts are testing? C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]; At the moment I have a simple design with two groups, 4-5 time points so I have a design matrix with 4 columns (intercept, weeks, group, group*time) and the contrast I am using is [0 0 0 1] to test the interaction term. If I were to add covariates such as age and gender would I simply add two more columns to my design matrix and contrast to look like this...[0 0 0 1 0 0]? Thanks in advance for your help. Amanda

2 2

reducing a matrix
by Linda Eva Heidinger 02 Aug '17

02 Aug '17

Dear experts in freesurfer, I myself am a very beginner in freesurfer but I come with a difficult question to answer. As you can see from the script below, I am trying to obtain the Bold in CVS35MNI152 template space which hopefully has better properties for accuracy and determination of location of a voxel for targeting in use with TMS. One can see that bbregister and mri_cvs_register were used followed by mri_vol2vol to register the Bold and transform it from subject space to the above template. Unfortunately, the template space is in freesurfer space (1mm^3,256^3) . When we try to run the result that we obtain after transformation in our AFNI programs, they couldn't run on our computers because of the size of the Bold matrix being too large. I am wondering if it is possible for mri_cvs_register to use a template that is of the same size as the T1? or really we should just somehow reformulate the transformation matrix resulting from mri_cvs_register which I believe is: final_CVSmorph_tocvs_avg35_MNI152.m3z to allow for a reduced final Bold matrix from mri_vol2vol which will have the same dimensions as the subject space which the original Bold had? I appreciate the time and attention you give this question. Thanks, -Linda ? # FreeSurfer commands nmr-std-env setenv SUBJECTS_DIR <path to the directory where all MRI data for this study reside> setenv SUBJECT <my subject code> cd $SUBJECTS_DIR # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual. recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4 # Second, do co-registration at the individual level between the hires anatomical and the bold (functional) image. # In the below example the already motion corrected (and otherwise preprocessed) bold data for run 005 are in # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii # Use boundary-based registration (bbregister) - this by far the most accurate tool. # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF 6 for within-subject registration. bbregister --mov $SUBJECT/bold/005/005.mc.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg boldregister.dat --fslmat ${SUBJECT}_anat2bold.mat # Just in case, let us make FSL type coregistration matrices as well. convert_xfm -omat ${SUBJECT}_bold2anat.mat -inverse ${SUBJECT}_anat2bold.mat # Now, we will compute a group-level coregistration from the individual brain to a template brain for both volumetric non-linear morphing. # We will use the standard brain cvs_avg35_inMNI152 as the target/template. mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECT/cvs_CVS35MNI152 --openmp 8 # Finally, we can move the bold image from the individual spac into the standard space: mri_vol2vol \ --mov $SUBJECT/bold/005/005.mc.nii \ --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \ --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ --noDefM3zPath \ --interp nearest \ --reg $SUBJECT/bold/boldregister.dat \ --no-save-reg \

3 5

error with fcseed-config & fcseed-sess
by Jessica Huang 02 Aug '17

02 Aug '17

Hi freesurfer experts, I’m using the fcseed-config and fcseed-sess commands to create a seed at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…> Steps: *STEP 4: Use fcseed-config to configure the parameters you wish to pass to your connectivity analysis. Sample command: fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config *STEP 5: Create the FC seed for an individual fcseed-sess -s sessionid -cfg L_Posteriorcingulate.config V1 corresponds to the number 400 in $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m running is B101. The data is rest data but I named the file bold. Overall, with this information specific to my data, I ran the following commands: INPUT $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg mean.V1.config OUTPUT fcname is V1.dat fcseed-config done INPUT $ fcseed-sess -s B101 -cfg mean.V1.config OUTPUT Logfile is /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/fcseed-sess.V1.dat.log.B101 Wed Jul 26 12:27:17 EDT 2017 Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir /Applications/freesurfer/fsfast/bin/fcseed-sess -s B101 -cfg mean.V1.config freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Wed Jul 26 12:27:17 EDT 2017 Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir /Applications/freesurfer/fsfast/bin/fcseed-sess -s B101 -cfg mean.V1.config freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c mri_label2vol --seg /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz --reg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta --temp /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz --fillthresh .5 --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --pvf /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz PVF /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz Outut Volume: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz Registration File: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.50000 -0.00000 -0.00000 56.00000; -0.00000 -0.00000 -0.50000 56.00000; -0.00000 0.45455 -0.00000 32.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8.8 nHits Thresh: 4.4 Loading registration from /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta regio_read_register: loading lta RegMat: -------- 0.99785 0.02664 0.05987 0.19449; -0.06077 0.03415 0.99757 -39.76084; -0.02453 0.99906 -0.03570 2.27075; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -0.49893 -0.01332 -0.02994 55.90276; 0.01227 -0.49953 0.01785 54.86462; -0.02762 0.01552 0.45344 13.92689; 0.00000 0.00000 0.00000 1.00000; PVF /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz Computing PVF 8.8 mri_label2vol done mri_binarize --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --match 400 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir cmdline mri_binarize.bin --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --match 400 sysname Darwin hostname Caramazza-Labs-Mac-Pro.local machine x86_64 user caramazzalab input /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz Binarizing based on matching values nMatch 1 0 400 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 802816 0.000000 mri_binarize done mri_segstats --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz --seg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --id 1 --sum /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum --avgwfvol /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz --seg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --id 1 --sum /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum --avgwfvol /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh sysname Darwin hostname Caramazza-Labs-Mac-Pro.local machine x86_64 user caramazzalab UseRobust 0 Loading /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz Loading /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz Voxel Volume is 8.8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Using PrintSegStat Computing spatial average of each frame ERROR: no voxels found in segmentation I attached the error log below - any idea what happened? Is there something I can change in these commands to yield the timecourse of V1? These are all subjects 18+ years of age. What do you think? Thank you in advance, any and all feedback would be greatly appreciated. Thanks, Jess

3 9

fsfast
by John Anderson 02 Aug '17

02 Aug '17

Dear Dr Greve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. I want to study the difference in functional connectivity between two groups My questions are regarding motion evaluation and the contrasts. 1. The attached figure is an output of "plot-twf-sess". Given the plotted data can we say that including run 003 is more reliable that all the other runs? 2. In the attached figure the command "plot-twf-sess" provides the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? 3. I used the following commands to study the differnc ein functional connectivity between two groups (each group has one run): ## preprocessing preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm -fsd bold -per-run -init-spm ### First-Level (Group) Analysis mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run #####Analyze First Level selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok Now for the next step I need to concatenate the sessions using isxconcat but this command needs a contrast which I didn't create it in the previous step. Given that I am looking for a differnce in the functional connectivity between two groups how can I create the contrast for this anlaysis. Thank you for any help and feedback!! John

2 7

FreeSurfer is now available on OpenNeuro.org
by Chris Gorgolewski 02 Aug '17

02 Aug '17

Dear all, FreeSurfer BIDS App is now available on the OpenNeuro.org platform. This means that you can run recon-all on your datasets (with longitudinal pipeline and study specific template estimation) in the cloud for free (see example results here <https://openneuro.org/datasets/ds000108/versions/00001?app=FreeSurfer&versi…> ). You can learn more about OpenNeuro.org in the FAQ <https://openneuro.org/faq> and about the details of the FreeSurfer BIDS App here <https://github.com/BIDS-Apps/freesurfer>. Let us know if you have any questions! Best, The OpenNeuro Team PS If you are developing a neuroimaging pipeline and would like to host it on OpenNeuro.org please get in touch. We a non-profit project dedicated to enabling access to cutting edge neuroimaging methods and incentivizing data sharing.

1 0

FSFAST (plot-twf-sess)
by John Anderson 02 Aug '17

02 Aug '17

Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. My questions is regarding motion evaluation. The attached figure is an output of "plot-twf-sess". 1. Given the plotted data can we say that including run 003 is more reliable that all the other runs? 2. In the attached figure the command "plot-twf-sess" provide the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? Thank you for help John

2 1

Error: trac-all -prep "Segmentation fault (core dumped)"
by Walter Hugo Lopez Pinaya 02 Aug '17

02 Aug '17

Hello FreeSurfer Developers, I am attempting to compute the tracula preprocessing directive (-prep), but for all my subjects I get the following error when it computes the pathway priors from atlas to T1. ... WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels INFO: Length of center streamline is 9 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 1 INFO: Minimum allowable curvature at a dominant point is 0.070643 INFO: Points where local peeks in curvature occur are 121 129 57 (curv = 0.0819549) INFO: Intermediate dominant points are 123 130 49 123 130 51 123 129 54 122 129 56 120 130 58 *Segmentation fault (core dumped) * Linux hardleste 4.8.0-58-generic #63~16.04.1-Ubuntu SMP Mon Jun 26 18:08:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Qui Jul 27 21:23:25 BRT 2017 I have searched the list and no similar errors with reply have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the trac-all.log and trac-all.error in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.2 LTS xenial 3) trac-all.log and trac-all.error: see attached trac-all.error <https://drive.google.com/file/d/0Bz-56qlsQ1xDbjEzZ3NkUG1XVlk/view?usp=drive…> trac-all.log <https://drive.google.com/file/d/0Bz-56qlsQ1xDMk1FUHI2QlZkMGc/view?usp=drive…>

2 2

using -make all with base
by Emily Grossnickle Peterson 02 Aug '17

02 Aug '17

Hello all, I made edits to the brainmask and wm of a base image (in the longitudinal stream) and am getting stuck when trying to re-process recon-all. Specifically, I can't seem to get the -make flag to work. I think it is probably either a silly error on my part or perhaps -make isn't designed for base edits? The command and error output are below. Thanks in advance, Emily *This is the command I ran on an HPC:* recon-all -base template_${SGE_TASK_ID} -tp T1_$SGE_TASK_ID -tp T2_$SGE_TASK_ID -make all *This is the error message:* Running on compute-0-0.local Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c rm: cannot remove `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/patchdir.txt': Permission denied cp: cannot create regular file `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/lastcall.build-stamp.txt': Permission denied Subject 'template_4047': make all recon-all -s /share/aeg58/Freesurfer/4047_both/template_4047 -nuintensitycor ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base): template_4047 If you are trying to re-run a -base template you need to pass the -base and all -tp flags: \' -base <templateid> -tp <tpNid> ... -all \' (Instead of -all you can pass other flags, such as -autorecon2 -autorecon3 to run only parts.) make: *** [/share/aeg58/Freesurfer/4047_both/template_4047/mri/nu.mgz] Error 1

1 0

output with input matrix size and referential
by pierre deman 02 Aug '17

02 Aug '17

Hello, I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation. what is the best way to do it ? Cheers, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

4 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