Re: [Freesurfer] Getting combined bvals/bvecs
Hi Marisa - Is there by any chance the same file saved with 2 different extensions, like .nii and .nii.gz? I'd have to look at the entire trac-all.log to get a better idea when this happens. Thanks, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Marissa Pifer [marissapi...@gmail.com] Sent: Monday, November 14, 2016 1:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Getting combined bvals/bvecs Hi Anatasia, Thank you for your reply, I'm sorry for responding so later, I have been trying a few different things in order to get tracula to work. I did what you suggested and compiled the bvals and bvecs into one file, in the same order as the images. This got me further, but the trac-all -prep step is still not completing without error. The lastest problem I can't get past is this: "WARNING Multiple image files detected: /users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri/dwi.nii /Users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri.dwi.nii.gz STOPPING PROGRAM Darwin Marcs-Macbook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016, root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Nov 11 14:46:42 EST 2016" But since I'm combining the AP and PA images files, wouldn't it be necessary for there to be multiple image files? Marissa On Wed, Sep 14, 2016 at 9:54 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>> wrote: Hi Marissa - You have to specify as many b-values and gradient vectors as there are volumes in your DWI data file. This means that, if you combine the AP and PA volumes, you also have to concatenate the bvals from the two into one file, and do the same with the bvecs. Make sure that the order in which the AP and PA volumes are combined is the same as the order in which the corresponding bvals and bvecs are combined. Hope this helps, a.y On Wed, 14 Sep 2016, Marissa Pifer wrote: Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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 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] Getting combined bvals/bvecs
Hi Anatasia, Thank you for your reply, I'm sorry for responding so later, I have been trying a few different things in order to get tracula to work. I did what you suggested and compiled the bvals and bvecs into one file, in the same order as the images. This got me further, but the trac-all -prep step is still not completing without error. The lastest problem I can't get past is this: "WARNING Multiple image files detected: /users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri/dwi.nii /Users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri.dwi.nii.gz STOPPING PROGRAM Darwin Marcs-Macbook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016, root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Nov 11 14:46:42 EST 2016" But since I'm combining the AP and PA images files, wouldn't it be necessary for there to be multiple image files? Marissa On Wed, Sep 14, 2016 at 9:54 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Marissa - You have to specify as many b-values and gradient vectors as > there are volumes in your DWI data file. This means that, if you combine > the AP and PA volumes, you also have to concatenate the bvals from the two > into one file, and do the same with the bvecs. Make sure that the order in > which the AP and PA volumes are combined is the same as the order in which > the corresponding bvals and bvecs are combined. > > Hope this helps, > > a.y > > > On Wed, 14 Sep 2016, Marissa Pifer wrote: > > Hello freesurfer experts, >> I am trying to run tracula on subjects that have separate AP/PA direction >> DTI files. We combined the data >> into one using topup, and would now like to run tracula on the subject. >> The problem is, the combined file >> doesn't have a bvals/bvecs file. When I try to use the original bval/bvec >> files, I get the error that the >> bvals and bvecs don't match up. I have tried combining the files into >> one, and then running a dicom to >> nifty conversion to get a combined bvals/bvecs output, but that results >> again in two separate bvals/bvecs >> files as well. I then tried just have two specified bvals and bvecs. This >> did not give us an error >> message, but trac-prep took only a few seconds and did not complete the >> steps it was supposed to to create >> the directories for trac-bedp to complete. I have attached our >> dmrirc.example file and the log for the >> trac-prep step for your reference. >> >> The questions then are; is there a way to get one bvals/bvecs file that >> has the correct parameters for the >> AP and PA combined file. Or, if not, is there a way to run tracula with >> two sets of bvals and bvecs (one >> for the AP and one for the PA direction)? >> >> In case you need this information, the process is being run with >> freesurfer 5.3, on a macbook pro OS X >> version 10.9.5. >> >> Thank you in advance, >> >> Marissa >> >> > ___ > 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 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] Getting combined bvals/bvecs
Hi Marissa - You have to specify as many b-values and gradient vectors as there are volumes in your DWI data file. This means that, if you combine the AP and PA volumes, you also have to concatenate the bvals from the two into one file, and do the same with the bvecs. Make sure that the order in which the AP and PA volumes are combined is the same as the order in which the corresponding bvals and bvecs are combined. Hope this helps, a.y On Wed, 14 Sep 2016, Marissa Pifer wrote: Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa ___ 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.
