Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs
Let me know if you need any other information. Thanks in advance for your help.
Dear Michele,
I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval?
Good luck, Barbara
On 28/08/2014 22:47, Michele Cavallari wrote:
Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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.
Hi Michelle - Your column-formatted gradient table (original_columns.bvec) shows up as having only 2 rows in unix (e.g. with the cat command). That's sometimes the case for text files saved from Excel or other non-unix applications. When I open your file in TextEdit on a mac and then copy-paste it into a unix text editor, it shows up fine.
For row-formatted gradient tables, you have to make sure you have the latest version of tracula, as that option was added more recently: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
Hope this helps, a.y
On Thu, 28 Aug 2014, Michele Cavallari wrote:
Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
Hi Barbara and Anastasia, thanks to your suggestions and help I was able to run the pre-processing step of tracula. I was using FreeSurfer 5.3, but didn't download any update. That's probably why the row configuration was not working. Anyway, I used the column configuration after manual correction for extra text due to excel formatting. Thanks again for your help. I'll get back to you as soon as the next error message pops up! Best, -Michele
On Thu, Sep 4, 2014 at 5:03 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Michelle - Your column-formatted gradient table (original_columns.bvec) shows up as having only 2 rows in unix (e.g. with the cat command). That's sometimes the case for text files saved from Excel or other non-unix applications. When I open your file in TextEdit on a mac and then copy-paste it into a unix text editor, it shows up fine.
For row-formatted gradient tables, you have to make sure you have the latest version of tracula, as that option was added more recently: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
Hope this helps, a.y
On Thu, 28 Aug 2014, Michele Cavallari wrote:
Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the
following
error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries
The original bvals and bvecs files seem to have the same numbers of
entries
to me. But the bvecs file produced by the processing - both the
bvecs.norot
and the bvecs files in the dmri folder - don't have all the information
of
the vectors.
I am enclosing a zip folder with attachments:
- original bvecs and bvals files organized in rows and columns
- bvecs and bvals files generated by tracula
- error logs
Let me know if you need any other information. Thanks in advance for your help.
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Barbara Kreilkamp -
Michele Cavallari -
Michele Cavallari