Re: [Freesurfer] Error running TRACULA
Dear Anastasia, using the command you told me I solved the problem with the bvecs file, however I get this error dmri_train(8994) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory Darwin dhcp-71-112.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Oct 2 10:04:53 CEST 2013 Is it a memory problem? Do I need to change memory allocation? Thanks again. Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 18:08, Anastasia Yendiki ha scritto: Hi Lucia - The bvecs file is full of 0,000. I'm guessing the problem is that your environment is set to use the comma instead of the point as the decimal separator. Can you try this and then rerun? setenv LANG en_US.UTF-8 Hope this helps, a.y On Fri, 27 Sep 2013, Lucia Billeci wrote: Hi Anastasia here are the files Thanks Lucia 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error running TRACULA
Hi Lucia - Glad to hear the bvecs problem got solved. About the memory problem: Can you please click on the apple on the top left of your screen and go to About This Mac and give me the info on the little window that pops up? Thanks, a.y On Wed, 2 Oct 2013, Lucia Billeci wrote: Dear Anastasia, using the command you told me I solved the problem with the bvecs file, however I get this error dmri_train(8994) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory Darwin dhcp-71-112.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Oct 2 10:04:53 CEST 2013 Is it a memory problem? Do I need to change memory allocation? Thanks again. Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 18:08, Anastasia Yendiki ha scritto: Hi Lucia - The bvecs file is full of 0,000. I'm guessing the problem is that your environment is set to use the comma instead of the point as the decimal separator. Can you try this and then rerun? setenv LANG en_US.UTF-8 Hope this helps, a.y On Fri, 27 Sep 2013, Lucia Billeci wrote: Hi Anastasia here are the files Thanks Lucia 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error running TRACULA
Thanks. And can you also check which freesurfer build you're using? Look for the line that says build-stamp towards the beginning of your trac-all.log file. On Wed, 2 Oct 2013, Lucia Billeci wrote: Hi Anastasia These are the information: Mac OS X 10.7.5 Processor 3.4 Ghz Intel Core i7 Memory 4 GB 1333 MHz DD3 Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 02/ott/2013, alle ore 16:21, Anastasia Yendiki ha scritto: Hi Lucia - Glad to hear the bvecs problem got solved. About the memory problem: Can you please click on the apple on the top left of your screen and go to About This Mac and give me the info on the little window that pops up? Thanks, a.y On Wed, 2 Oct 2013, Lucia Billeci wrote: Dear Anastasia, using the command you told me I solved the problem with the bvecs file, however I get this error dmri_train(8994) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice Cannot allocate memory Darwin dhcp-71-112.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Oct 2 10:04:53 CEST 2013 Is it a memory problem? Do I need to change memory allocation? Thanks again. Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 18:08, Anastasia Yendiki ha scritto: Hi Lucia - The bvecs file is full of 0,000. I'm guessing the problem is that your environment is set to use the comma instead of the point as the decimal separator. Can you try this and then rerun? setenv LANG en_US.UTF-8 Hope this helps, a.y On Fri, 27 Sep 2013, Lucia Billeci wrote: Hi Anastasia here are the files Thanks Lucia 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 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 running TRACULA
Hi Lucia - You are using an older version of tracula (from freesurfer 5.1 instead of 5.3). This version used to have memory issues in the mac build. There is an update of the 5.1 mac build that addresses the memory issue, but since you are just starting out, I *highly* recommend to use the 5.3 version. It has improved both speed and performance. All this info is here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Also, please make sure to send these messages to the freesuerfer list and not just to me personally. This way the messages are archived, which reduces the replication of questions. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ Thanks! a.y On Wed, 2 Oct 2013, Lucia Billeci wrote: I found this: build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 02/ott/2013, alle ore 16:38, Anastasia Yendiki ha scritto: build-stamp ___ 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 running TRACULA
Dear Anastasia, I added in the dmrirc file the following line: set nb0 = 1 because I red in the forum that it is necessary to indicate the number of b0 volume and I don't get the error about fslroi anymore. However now I have the following error: Error: bvecs and bvals don't have the same number of entries I removed the blank line as you suggested (see attach) so I don't understand the error Thanks Lucia bvals Description: Binary data bvecs Description: Binary data _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 26/set/2013, alle ore 18:31, Anastasia Yendiki ha scritto: Hi Lucia - Does it work if you remove the extra blank line at the end of the bvecs file? a.y On Thu, 26 Sep 2013, Lucia Billeci wrote: Dear all, I am trying to apply TRACULA on my DATA (GE data) but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after eddy current correction, I obtain this error: mv -f /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: -.93: expected numeric value printf: -.003594: expected numeric value printf: .000852: expected numeric value R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi input output xmin xsize ymin ysize zmin zsize fslroi input output tmin tsize fslroi input output xmin xsize ymin ysize zmin zsize tmin tsize Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Darwin dhcp225.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 26 Set 2013 10:12:38 CEST I attach my bvals and bvecs Could you help me? Thanks Lucia 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 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 running TRACULA
Hi Lucia - The nb0 thing isn't used any more, it was in the old version of tracula only (the one in freesurfer 5.1). Can you send the version of the bvecs and bvals files that are in the dmri/ directory? Thanks, a.y On Fri, 27 Sep 2013, Lucia Billeci wrote: Dear Anastasia, I added in the dmrirc file the following line: set nb0 = 1 because I red in the forum that it is necessary to indicate the number of b0 volume and I don't get the error about fslroi anymore. However now I have the following error: Error: bvecs and bvals don't have the same number of entries I removed the blank line as you suggested (see attach) so I don't understand the error Thanks Lucia ___ 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 running TRACULA
Hi Anastasia here are the files Thanks Lucia bvals Description: Binary data bvecs Description: Binary data _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.bill...@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Il giorno 27/set/2013, alle ore 17:06, Anastasia Yendiki ha scritto: Hi Lucia - The nb0 thing isn't used any more, it was in the old version of tracula only (the one in freesurfer 5.1). Can you send the version of the bvecs and bvals files that are in the dmri/ directory? Thanks, a.y On Fri, 27 Sep 2013, Lucia Billeci wrote: Dear Anastasia, I added in the dmrirc file the following line: set nb0 = 1 because I red in the forum that it is necessary to indicate the number of b0 volume and I don't get the error about fslroi anymore. However now I have the following error: Error: bvecs and bvals don't have the same number of entries I removed the blank line as you suggested (see attach) so I don't understand the error Thanks Lucia 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 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.
