Hi Katherine - The dlabel/ directory is created during the -prep step, when the structural segmentation gets mapped from T1 to diffusion space. However bedpost may still run fine without the dlabel/ directory. It seems that the problem is fairly early in the -prep step. Any errors there?
Best,
a.y
On Wed, 23 Mar 2016, Katherine Damme wrote:
Hey Anastasia,
Although the bedpost appears to complete properly the dlabel/diff is not being created during the bedp step. I am not sure how or why this error is occurring. That would, it appears, definitely be the cause of the failure. However, I am not getting an error during the prep or the bedpost stage, and so I am still completely lost any advice would be deeply appreciated!
Thank you,
KD
On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Katherine - Do the freesurfer segmentations look ok? What about the registration from structural to diffusion? You can inspect those quickly with: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3 Hope this helps, a.y On Sun, 3 Jan 2016, Katherine Damme wrote: First I should note that using the same scripts I completed 52 participants successfully and am currently trying to batch process the newest 42 participants that are only failing at the path level. Upon Visual Inspection they all appear normal (with the exception of the one attached). After carefully comparing a random sample of 5 from each group images from the files that failed versus the files that were successful, I found: 1. The range of values in the mean_ph1samples in the successful ( i.e. -3.00 to 87.30 ) differed from the failures (i.e. -2 to 17) (the successful samples varied on their high end from 50-114 but the failures were on the 5-24 range) 2. The range of values in the mean_th1samples in the successful ( -0.02 to 19.12) differed from the failures (-0.00267 to 7.176) (the successful samples varied on their high end from 19-17 but the failures were on the 3-10 range) 3. Some, but not all (2/5), mean_S0samples, had a abnormal range in successful (0 to 19998.4) compared to the unsuccessful (0 to 709.96) However, I understand that the diffusion units are likely arbitrary and not sure these patterns will hold in a larger sample. I know this is a lot of confusing information and so in response to your question. After an initial inspection there are two types of output: 1. data that appears visually normal with a slightly altered range. Should I be concerned about the range if all other data looks fine? 2. data that appears visually normal with a normal range and bizarre merged files. What do you think could be a cause of these odd merged files? On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote: Hi Katherine - Have you looked at any of the intermediate images? Do they look normal? a.y On Mon, 21 Dec 2015, Katherine Damme wrote: Hello Everyone! It looks as though my prep and bedp stages completed properly, but the prep stage ends in a segmentation errror. See attached and let me know your thoughts. I would prefer not to have to redo all steps if possible! Thank you! 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.