Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion
by Matthieu Vanhoutte 19 Sep '14

19 Sep '14

Dear Freesurfer's experts, I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data. The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006). I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link... Where can I find this package and how to use it ? Many thanks ! Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France

2 4

segmentation fault mri_convert Ubuntu 14.04
by Alessandra Griffa 19 Sep '14

19 Sep '14

Dear all, I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an Ubuntu machine. After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a segmentation fault when I try to resample images using mri_convert: /mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled image.nii.gz // //$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $// //reading from /folder/original_image.nii.gz...// //Segmentation fault (core dumped)/ Any help on this? (for consistency with an on-going study I would like not to install a newer FreeSurfer version) Thank you very much! Alessandra -- ------------------------------ Alessandra Griffa Doctoral assistant Signal Processing Laboratory 5 EPFL STI IEL LTS5 ELD 233 (Bâtiment ELD) Station 11 CH-1015 Lausanne Tel.: +41216934807 web: http://lts5www.epfl.ch/ personal page: http://people.epfl.ch/alessandra.griffa?lang=en ------------------------------

2 1

Freeview screenshot automation questions
by Eric Xiuming ZHANG 19 Sep '14

19 Sep '14

Dear FreeSurfer experts, I understand that > freeview -v brain.nii.gz -ss screenshot takes the screenshots and quits the freeview. Regarding this, I have the following two questions. (1) Is it possible to suppress the redundant GUI flashing? It is really a pain when many images are batch-processed, because the GUI keeps flashing up and closing. (2) Is it possible to take multiple screenshots with one session? I wish to screenshot multiple slices of one image. I have tried > freeview -v brain.nii.gz\ > -viewport sagittal -slice 80 127 127 -ss sag1 \ > -viewport sagittal -slice 127 127 127 -ss sag2 \ > -viewport sagittal -slice 156 127 127 -ss sag3 \ However, the session ends right after the first -ss, producing only one screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to get these 3 screenshots, but that is very inefficient. Thank you very much for your help in advance! Best regards, Xiuming ZHANG (Eric) Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) :: National University of Singapore (NUS)

2 1

fsaverage subject does not exist in SUBJECTS_DIR
by Mahmoud 18 Sep '14

18 Sep '14

Dear All, I ran the following script: #!/bin/bash SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all and got the error below at the end. Could anybody please let me know how to fix it. Thank you, Mahmoud Reporting on 70 segmentations mri_segstats done /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label #-------------------------------------------- #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 INFO: *fsaverage subject does not exist in SUBJECTS_DIR* INFO: Creating symlink to fsaverage subject... cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - ln: *failed to create symbolic link './fsaverage': Operation not supported* mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case022_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/hgfs/DBSI/volumetric/MGZ FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014 For more details, see the log file /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 13

Re: [Freesurfer] displaying a single label from aparc in tksurfer
by Daniel Carey 18 Sep '14

18 Sep '14

Hi Maria, You can display a single label (or labels) in tksurfer by loading the aparc annotation onto fsaverage; then, simply click on the label you're interested in, and click File, then Label, and Save Selected Label. This will let you save out a single label from aparc, which can these easily be loaded onto fsaverage on its own. You can of course also overlay multiple labels in tksurfer that you've saved out in this way (and naturally change colour schemes if you're so inclined). Best, Dan --- On 18 Sep 2014, at 22:03, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > displaying a single label from aparc in tksurfer Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

1 0

quick quality assessment for MPRAGE images
by Wegbreit, Ezra 18 Sep '14

18 Sep '14

Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbreit(a)brown.edu (preferred) ewegbreit(a)lifespan.org *___________________________________________________________*

3 4

displaying a single label from aparc in tksurfer
by Maria Kharitonova 18 Sep '14

18 Sep '14

Hi all, I would like make a figure where only 1 or 2 regions (labels from the aparc.a2009s atlas are displayed). I know how to turn on/off all labels, but how do I only display 1? (e.g. rh_G_and_S_cingul-Mid-Ant). Turning off all but the one I need is tedious and I was wondering if there was a better way. I was able to change the color of the ACC region I needed to make it more apparent (see attached), but was looking for a way that the white region is only label that is shown. I looked through the archives but could not find anything. Thanks in advance for the help! Best, Maria -- Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.kharitonova(a)northwestern.edu<mailto:maria.kharitonova@northwestern.edu>

2 1

problem with mris_preproc
by Lars M. Rimol 18 Sep '14

18 Sep '14

Hi, I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?: Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file This subject, 007, seems to have all the files it should: [rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thickness rh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pial rh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.orig lh.smoothwm.BE.crv lh.smoothwm.S.crv lh.white rh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.pial lh.smoothwm.H.crv lh.sulc rh.area.pial rh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh Here's the entire output: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 -------------- ----------------------- mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

2 1

mri_vol2surf
by Nicholas Heugel 18 Sep '14

18 Sep '14

I looked over the documentation but can;t seem to find what I am looking for. How exactly does the function project the mdi data onto the surface? What method is it using to accomplish this, is it just projecting to the nearest neighbor or is there something more complex occurring. I ask because I just want to make sure I completely understand what every step in my analysis is doing and not have it be a blackbox that I put data in and it gives me stuff out. Thanks for your help. Nicholas

3 2

exporting QDEC results
by elisa veronese 18 Sep '14

18 Sep '14

Dear FreeSurfers, can anybody tell me if there is a way to export results in form of table (or text file) from the QDEC GUI after having performed analysis on thickness, area, volume, etc etc... ? I mean, is the infomation regarding the significant clusters saved in table format? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

2 1

← Newer
1
...
4
5
6
7
8
9
10
...
17
Older →

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 September 2014