[Freesurfer] recon-all head motion
Dear experts, I was wondering if there is an output from the recon-all procedure that quantifies the motion/ motion correction. I am thinking it may be the talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt file, but am not sure how to interpret this. I tried to review the list serv, but couldn't find anything that exactly answered the question. Thanks for your help, Allison ___ 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] Longitudinal processing
Hello, I am using the longitudinal processing stream to analyze a data set. I have two questions: 1: We are expecting there to be significant changes in the volume of certain structures and gray matter between time point 1 and 2. We wanted to make sure the longitudinal stream is still appropriate. 2: If some subjects do not have both time points, should we process them as individual time points or should we use a template brain in order to use the longitudinal stream? Thank you very much, Allison ___ 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] Tracula preprocessing step error
Dear Freesurfer experts, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. Selection from log: mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 Please let me know if this is not enough information. Thank you for your help. Allison ___ 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] Tracula preprocessing step error
Hi Anastasia, Thanks so much for your help. I was able to correct this problem in my configuration file. I have now run into another error- "bvecs and bvals don't have the same number of entries." I have read other postings about this error and can see that my bvec file is not formatted correctly when I import into Excel. However, I am not sure how to correctly fix this formatting. I know that I have 28 bval entries and 84 bvec entries, so the overall number is correct. I am just unclear on how to fix the formatting of the bvec file so that it corresponds correctly to the ordering in the bval file (which order the bvec entries should appear in within the three columns). Do you have any resources on this? Thank you again for your help, Allison Quoting Anastasia Yendiki : > > Hi Allison - The mri_convert command at the top of your log file is > trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to > a nifti file. From the name of that nifti file, it looks like it's > expecting to find a field map and not finding it. > > Hope this helps, > a.y > > On Tue, 8 Jan 2013, Allison Gruber wrote: > >> Dear Freesurfer experts, >> >> I have encountered the following error while running the tracula >> pre-processing command and was hoping you could help me understand how >> to correct this. >> >> Selection from log: >> >> mri_convert /Users/Desktop/Tracula/diffusion_DTI/ >> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz >> mri_convert /Users/Desktop/Tracula/diffusion_DTI/ >> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz >> corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> reading from /Users/Desktop/Tracula/diffusion_DTI/... >> Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr >> 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 >> >> Please let me know if this is not enough information. Thank you for >> your help. >> >> Allison >> ___ >> 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
[Freesurfer] Head motion question
Dear Freesurfer, I was wondering if there is any output from Tracula that quantifies head motion (or the head motion correction performed). If so, is there any standard in the field about an acceptable level or a cut-off point? Thank you for your help, Allison Gruber ___ 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.
