[Freesurfer] error while loading shared libraries: libnewimage.so
Hello, I'm trying to prepare my diffusion data with track-all -prep but "trac-preproc exited with ERRORS" I think it is related to the FSL instructions, because it gives this message in the beginning: <...> flirt: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory trac-preproc -c /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/dmrirc.local -log /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/trac-all.log -cmd /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/trac-all.cmd <...> and it also cannot run the flip4fsl <...> flip4fsl /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig.nii.gz /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig.nii.gz x -y z /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz fslorient: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory <...> and consequently the eddy correct: <...> eddy_correct /home/rlavrador/proj/Freesurfer_diff/MCD20111024/dmri/dwi_orig_flip.nii.gz /home/rlavrador/proj/Freesurfer_diff/MCD20111024/dmri/dwi.nii.gz 0 Input does not exist or is not in a supported format <...> I think I have the variables well configured <...> HP-Z620-RLavrador:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 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 /home/rlavrador/proj/Freesurfer MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0/ <...> I would like to know what I am doing wrong. Some clues? Regards, -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error while loading shared libraries: libnewimage.so
It's solved, The problem has been solved by adding a line to .bashrc file. <...> export FSL_DIR=/usr/share/fsl/5.0 <...> Previously I manually corrected the FSL_DIR in the tcsh shell, were I run the Freesurfer, using: <...> HP-Z620-RLavrador:~> setenv FSL_DIR /usr/share/fsl/5.0/ HP-Z620-RLavrador:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 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 /home/rlavrador/proj/Freesurfer MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0/ <...> but it did not solve the problem. I had to add the line to .bashrc in order to solve the problem, as I explained. It worked for me! Best regards, 2015-03-27 14:10 GMT+00:00 Rui Lavrador : > Hello, > > I'm trying to prepare my diffusion data with track-all -prep but > "trac-preproc exited with ERRORS" > > I think it is related to the FSL instructions, because it gives this > message in the beginning: > > <...> > flirt: error while loading shared libraries: libnewimage.so: cannot open > shared object file: No such file or directory > trac-preproc -c > /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/dmrirc.local -log > /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/trac-all.log -cmd > /home/rlavrador/proj/Freesurfer_diff/AAA/scripts/trac-all.cmd > <...> > > and it also cannot run the flip4fsl > > <...> > flip4fsl /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig.nii.gz > /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz > INFO: input image orientation is LPS > INFO: input image determinant is 8 > fslswapdim /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig.nii.gz x > -y z /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz > fslorient -forceradiological > /home/rlavrador/proj/Freesurfer_diff/AAA/dmri/dwi_orig_flip.nii.gz > fslorient: error while loading shared libraries: libnewimage.so: cannot > open shared object file: No such file or directory > <...> > > and consequently the eddy correct: > > <...> > eddy_correct > /home/rlavrador/proj/Freesurfer_diff/MCD20111024/dmri/dwi_orig_flip.nii.gz > /home/rlavrador/proj/Freesurfer_diff/MCD20111024/dmri/dwi.nii.gz 0 > Input does not exist or is not in a supported format > <...> > > I think I have the variables well configured > > <...> > HP-Z620-RLavrador:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh > freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > 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 /home/rlavrador/proj/Freesurfer > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/share/fsl/5.0/ > <...> > > I would like to know what I am doing wrong. Some clues? > > Regards, > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Memory allocation problem trac-all -prior
Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Memory allocation problem trac-all -prior
-- Forwarded message -- From: Rui Lavrador Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki > > Hi Rui - How many voxels are in your diffusion volume? How many of them > are inside the mask? > > a.y > > > On Thu, 12 Jul 2012, Rui Lavrador wrote: > > Hi all, >> I'm running tracula and when doing the step: >> trac-all -prior -c single_subject >> >> After some time it gives this error: >> >> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice >> >> Cannot allocate memory >> >> I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is >> DTI with 64 directions. >> >> This happens many times? I need more memory? >> >> Best regards, >> >> -- >> Rui Lavrador >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi all, I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files. thanks 2012/7/16 Rui Lavrador > > > -- Forwarded message -- > From: Rui Lavrador > Date: 2012/7/16 > Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior > To: Anastasia Yendiki > > > Hi Anastasia, > Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels > inside of the brain mask. > > Rui > > 2012/7/12 Anastasia Yendiki > >> >> Hi Rui - How many voxels are in your diffusion volume? How many of them >> are inside the mask? >> >> a.y >> >> >> On Thu, 12 Jul 2012, Rui Lavrador wrote: >> >> Hi all, >>> I'm running tracula and when doing the step: >>> trac-all -prior -c single_subject >>> >>> After some time it gives this error: >>> >>> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice >>> >>> Cannot allocate memory >>> >>> I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is >>> DTI with 64 directions. >>> >>> This happens many times? I need more memory? >>> >>> Best regards, >>> >>> -- >>> Rui Lavrador >>> >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > > > > > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > > -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] running trac-all -path missing files
Hi FS users, I'm running “trac-all –path ” and when running it, it constantly gives the output ERROR: Degenerate spline segment 58 81 24 56 69 24 … But it runs until the end without exiting and says that it ran without errors. It’s normal? Plus, it seems that it fails to create the output files. When looking at the created folder “…/Diff001/dpath” there is only one folder “5cpts”, so I cannot visualize the WM pathways, with freeview, that should be located, for example at “…/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz” Any suggestions? -- Rui Lavrador ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
