Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

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

Longitudinal Error: long_mris_slopes
by Jennifer Addicks 15 May '14

15 May '14

Hello, I recently installed FreeSurfer v5.3 on a Mac OS X 10.9.2. I am trying to run a longitudinal analysis (longitudinal two-stage model) on my data (26 participants, 2 time points each) which was processed (cross-sectionally and longitudinally) using a previous version of FreeSurfer (v4.5). When running the long_mris_slopes command: long_MRIS_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I get the following error message {CED01 is one of my fsid-base names}: Traceback (most recent call last): File "/Applications/freesurfer/bin/long_MRIS_slopes", line 862, in <module> dirname = tempfile.mkdtemp('',prefix,'') File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tempfile.py", line 329, in mkdtemp _os.mkdir(file, 0700) OSError: [Errno 13] Permission denied: './tmp-CED01_lh_thickness_34xA_9' Any suggestions? Sincerely, Jennifer

2 1

Re: [Freesurfer] aseg.stats volume mismatch
by Gabor Perlaki 15 May '14

15 May '14

Dear Bruce, Is there a file generated by freesurfer which stores the subcortical segmentations together with the information of partial volume estimates? Thanks, Gabor

2 5

Problems with tkmedit
by Esteve Cervantes Martin 15 May '14

15 May '14

Hi, I'm Esteve Cervantes an student from UPC. I'm trying to install Freesurferfrom the source and I'm having some problems with tkmedit. I previously had some problems with recon-all because I got segmentation faults. After installing the mni.srcbuilt.tgz from source and some fixes it runs ok. But when I wanted to run tkmedit to view my volumes I got only one window with the picture, but a blank window for the tools. Then I tried to install the tcltkticblt-8.4.6.tgz and after building again freesrufer, now I get nothing. The output is: ecervantes@v3:~/opt/freesurfer1/tktools>> vglrun tkmedit 002_S_0295 brainmask.mgz -surfs [VGL] NOTICE: Automatically setting VGL_CLIENT environment variable to [VGL] 192.168.1.31, the IP address of your SSh client. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. ecervantes@v3:~/opt/freesurfer1/tktools>> It starts and sudenly ends without showing any window... I'm out of ideas any help will be appreciated. Thank you, Esteve

1 0

Tksurfer will not accept key input in Ubuntu 14.04
by Knut J Bjuland 15 May '14

15 May '14

Bug report I am unable to enter number using the keyboard when using Tksurfer under Ubuntu 14.04. I have tried to enter a number in overlay configuration and smooth overlay. Is there any workaround? I have this bug on two different system with Ubuntu 14.04. Best regards Knut J Bjuland

1 0

BrainMask Edits
by David Tate 15 May '14

15 May '14

Question regarding the use of skull stripping errors. I am wondering if it is possible to correct (use the -wsthresh or -gcut) in longitudinal processed data or would these types of edits be required in the earlier processing steps (initial FreeSurfer recon-all)? Thanks in advance for any help with this. David F. Tate, Ph.D.

1 0

white matter surface (tkmedit -surfs) vs wm.mgz
by Mayer Kristina 15 May '14

15 May '14

Dear all I am segmenting data of 2 year olds and as freesurfer fails on segmneting inferior parts of the temporal lobe, I try to edit this manually using tkmedit (protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools, ControlPoints_tktools). I first add control points, with successfull amelioration of brainmask volumes. As this leads to integration of too much tissue in the white matter surface (displayed as tkmedit brainmask.mgz -surfs), i tried to manually edit wm.mgz. When I edit wm.mgz, there is no change in -surfs. When looking at the data in tkmedit (tkmedit subjid wm.mgz -surfs), total WM surface (-surfs), and wm.mgz are not the same. Where is the file generated that is shown in tkmedit as -surfs and which volume/file do I have to edit to ameliorate output of -surfs? Best, Kristina

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