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

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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.billeci@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: -.999993: 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

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Hi Anastasia

here are the files

Thanks 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.billeci@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.

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.billeci@ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

Il giorno 27/set/2013, alle ore 18:08, Anastasia Yendiki ha scritto:

Hi Lucia - The bvecs file is full of "0,0000000". 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.