[Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 -- Andrea Cristina de Lima Pardini CV: http://lattes.cnpq.br/0921194840474573 ___ 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] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
Em 30/09/2015 11:30, "andrea cristina Lima" escreveu: > I got the error below. Could you help me? I've already check the dti file > and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c > /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt > > INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer > > INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local > -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd > > #- > > /Applications/freesurfer/bin/trac-preproc > > #- > > #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... > > Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 > 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 > > -- > Andrea Cristina de Lima Pardini > CV: http://lattes.cnpq.br/0921194840474573 > ___ 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] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
Ok! Thank you! I will try again! 2015-09-30 19:16 GMT-03:00 andrea cristina Lima : > Em 30/09/2015 11:30, "andrea cristina Lima" > escreveu: > >> I got the error below. Could you help me? I've already check the dti file >> and it seems Ok. Tks >> >> macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c >> /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt >> >> INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer >> >> INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 >> >> Actual FREESURFER_HOME /Applications/freesurfer >> >> trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local >> -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd >> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd >> >> #- >> >> /Applications/freesurfer/bin/trac-preproc >> >> #- >> >> #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 >> >> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii >> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz >> >> mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii >> SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz >> >> niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii >> >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> >> reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... >> >> Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 >> 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 >> >> >> trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 >> >> -- >> Andrea Cristina de Lima Pardini >> CV: http://lattes.cnpq.br/0921194840474573 >> > -- Andrea Cristina de Lima Pardini CV: http://lattes.cnpq.br/0921194840474573 ___ 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] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep 2015, andrea cristina Lima wrote: I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 -- Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573 ___ 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.
