Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

automatically expand surface label along the surface
by Martha Shiell 19 May '14

19 May '14

Hello Freesurfer users, Does anyone know a command to automatically expand (grow/dilute) a label file along the surface, e.g. add neighbouring vertices to the label? Thanks, Martha Shiell Ph.D. Candidate, Neuroscience McGill University

3 2

labels of surface vertices
by Tanya 19 May '14

19 May '14

Hi Freesurfers, I'm confused about surface vertices labels. One of the tutorial mentions that: " There is a one-to-one correspondence between surfaces which allows the user to cross-reference vertices from one surface to another (even across subjects) and to the volume." So there is a map between vertex index and label and it is universal for all subjects and all surfaces? Where can I find this map and is there a script to use it? Thank you! Tanya

2 1

Contrast vector in Qdec terminal and DOSS vs DODS
by Santosh Yadav 19 May '14

19 May '14

Dear FS Experts, I am asking same question again since did not get any reply. I processed my data with FS 5.3 version and running analysis in Qedc GUI with DODS that include 2 groups (control and heart Failure). I want to see the cortical thickness difference between these 2 groups, with age and gender as a covariate. In Qdec GUI, model factors have three options that include the fixed factor, continuous factor (covariate) and nuisance variable. So group (control and heart failure) belongs to fixed factor while age and gender belongs to both continuous factor and nuisance variable. When I am running this analysis in Qdec by selecting the model that include only group the contrast vector in the Qdec terminal is 1, -1, and I believe its fine. But when I am designing the model that includes age and gender as a nuisance factor, the contrast vector showing 1, -1, 0, 0, 0, 0, on the Qdec terminal. So my question is why we have two extra 0, 0 in contrast vector, as per my understanding it should be 1, -1, 0, 0, please explain. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. Another question: When I finished the analysis in Qdec and got the state data tables, that have 18 files, with volume, area, curv and thickness from both left and right sides. I am interested in cortical thickness and it's have four files with left and right with two versions. for example for left side one is lh.aparc.a2009s and one is lh.aparc. I am not sure which file should I used for the analysis. I believe for left side qdec is using lh.aparc, Is I am right? With Regards, Santosh K. Yadav -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

1 0

Rotated structurals
by Tudor Popescu 18 May '14

18 May '14

Hi everyone Are structurals that come out of the scanner somewhat rotated (a few degrees, but still visible, example - attached) processed normally by recon-all, or do they first have to be manually corrected (rotated)? Thanks! Tudor

2 1

Re: [Freesurfer] using multiple cores
by Lukas.Scheef＠ukb.uni-bonn.de 16 May '14

16 May '14

3 3

mri_convert frame error in tracula
by Pedro Rosa 16 May '14

16 May '14

Dear All, As suggest, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa.

1 0

TRACULA preprocessing error, FreeSurfer 5.2.0
by McGinnity, Colm 16 May '14

16 May '14

Dear Experts, I am very new to TRACULA, I apologise for what is probably a silly question. I've got the following error on running trac-all -prep (FreeSurfer 5.2.0): awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz Can anyone tell me what this means and how to fix this, please? I'm guessing I've set up my configuration wrong or have the files in the wrong place? Many thanks! Best wishes, Colm. King's College London

3 7

Setup and configuration problem ubuntu 12.04.LTS
by Alejandra Machado 16 May '14

16 May '14

Hello, i'm trying to setup freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. I think i've done downloading properly but i'm having some trouble with installation. I can set up enviroment and when testing freesurfer with some of the scripts from the page, sometimes it works but sometimes i get an error. Can you please help me? Thank you! Alejandra Ale:~> setenv FREESURFER_HOME /usr/local/freesurfer Ale:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni Ale:~> freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Ale:~> tkmedit bert orig.mgz Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl % Ale:~> freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Ale:~> qdec qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Ale:~>

2 1

Tracula - configuration file error
by Pedro Rosa 16 May '14

16 May '14

Dear all, I am facing an error at the configuration file for trac-all I am trying to run a single subject, 148, for who there is a folder ‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the configuration file. However, I am facing the following error, although no run list is specified: [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. red240green242blue245: Command not found. }: Command not found. margl1440margr1440vieww22600viewh9020viewkind0: Command not found. deftab720: Command not found. pardpardeftab720: Command not found. ERROR: run list is longer than subject list Any input is appreciated. Regards, Pedro Rosa.

2 3

gray matter around amygdala
by Harms, Michael 15 May '14

15 May '14

1 0

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Freesurfer May 2014