Hi Jared - We haven't reproduced this error on our end. So if I understand it correctly, replacing "bedpostx_seychelles" with "bedpostx" in trac-all would solve the problem?

a.y

On Wed, 29 Jun 2011, Jared Saletin wrote:

Hi Anatasia,

Thank you for the response.

I've reformatted the files and -prep ran fine.

I'm receiving a similar error to some other users upon running -bedp

Where bedpostx fails immediately

I wanted to point out, and wonder if other folks have had any luck, that if I try running bedpostx from FSL directly on the dmri folder, it starts normally. I can then kill the bedpostx process, and relaunch trac-all -bedp -c ... and things seem to be continuing...

It still returns the "unexpected operator" errors that other users have reported but it does not break to a command prompt anymore, and instead beings return the "0 slices processed" ... iterating message.

I'm curious, has anyone else had luck navigating around this bedpostx error? Or would it be best to just run bedpostx separately in FSL and return to trac-all after the bedpostx processing is complete?

Thanks again! Jared

On Jun 28, 2011, at 3:24 PM, Anastasia Yendiki wrote:

...

Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hopefully! :)

a.y

On Tue, 28 Jun 2011, Jared Saletin wrote:

...

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared

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Glad it worked. We'll have to make sure this agrees better with non-MGH installations in the next release.

On Fri, 1 Jul 2011, Jared Saletin wrote:

Hi Anastasia,

That did the trick! Thanks so much!

Cheers, Jared On Jun 30, 2011, at 12:28 PM, Anastasia Yendiki wrote:

...

Hi Jared - We haven't reproduced this error on our end. So if I understand it correctly, replacing "bedpostx_seychelles" with "bedpostx" in trac-all would solve the problem?

a.y

On Wed, 29 Jun 2011, Jared Saletin wrote:

...

Hi Anatasia,

Thank you for the response.

I've reformatted the files and -prep ran fine.

I'm receiving a similar error to some other users upon running -bedp

Where bedpostx fails immediately

I wanted to point out, and wonder if other folks have had any luck, that if I try running bedpostx from FSL directly on the dmri folder, it starts normally. I can then kill the bedpostx process, and relaunch trac-all -bedp -c ... and things seem to be continuing...

It still returns the "unexpected operator" errors that other users have reported but it does not break to a command prompt anymore, and instead beings return the "0 slices processed" ... iterating message.

I'm curious, has anyone else had luck navigating around this bedpostx error? Or would it be best to just run bedpostx separately in FSL and return to trac-all after the bedpostx processing is complete?

Thanks again! Jared

On Jun 28, 2011, at 3:24 PM, Anastasia Yendiki wrote:

...

Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hopefully! :)

a.y

On Tue, 28 Jun 2011, Jared Saletin wrote:

...

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared

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.