Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - Good to know things worked out! a.y On Tue, 19 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > I thought I should let you know that this issue has now been resolved. We > specified the base ID's/ subject ID's incorrectly in the config file! Sorry > for the confusion. Now our group output looks correct. > > Thanks for your help, > Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner > [dpis...@psychiatry.arizona.edu] > Sent: Tuesday, July 12, 2016 5:06 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Anastasia, > > All subjects had both time-points (for DWI and T1-weighted recons). The > recons were run following the standard longitudinal pipeline for FS. > > Would it matter that I ran the pipeline piecemeal (i.e. separate > configuration files for each subject--see attached example)? In case you are > wondering, I did it this way in order to run the pipeline in parallel (i.e. > by subject) on our cluster... > > Another consideration is that we did preprocessing outside of TRACULA (i.e. > using FSL's tools directly so that we could apply a fieldmap, use new EDDY > with TOPUP, as well as apply a denoising algorithm). We then setup the folder > structure and filenames to begin TRACULA at the trac-all -intra stage, which > we have done successfully in the past when not using the longitudinal > pipeline (i.e. single-subject analyses) > > Still, I have a feeling that none of these customizations should have made > any difference as our merged outputs look excellent for both timepoints, for > all subjects... Any other thoughts about what might be causing this? > > Kind regards, > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 12, 2016 1:45 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't > been able to replicate the problem in our own longitudinal data. Did you > by any chance have any subjects that had only a single time point? > > a.y > > On Thu, 7 Jul 2016, Derek Pisner wrote: > >> Sure thing. fmajor mean.txt file is attached. >> >> >> Thanks a bunch, >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Thursday, July 07, 2016 4:48 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - this is strange. The dev and 5.3 version of freeview should >> display them differently. Can you send me one of those mean.txt files? >> >> a.y >> >> On Wed, 6 Jul 2016, Derek Pisner wrote: >> >>> Hi Anastasia, >>> >>> This occurs for me on both stable and dev versions of freview and trac-all >>> -stat >>> >>> -Derek >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: Monday, July 04, 2016 12:47 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA group stats visualization >>> >>> Hi Derek - Are you by any chance using the dev version of freeview? >>> >>> a.y >>> >>> On Fri, 1 Jul 2016, Derek Pisner wrote: >>> >>>> Dear Anastasia, >>>> I am running into an issue with the trac-all -stat option on our >>>> longitudinal TRACULA data. >>>> >>>> Everything runs smoothly through all earlier stages, and I checked >>>> individual subjects' merged outputs in freeview with -tv mode. Everything >>>> looks fine. >>>> >>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>>> without error. >>>> >>>> But then when I open the results with the command: >>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>>> >>>> I get the image seen in the attached .png file. Any idea what migh
Re: [Freesurfer] TRACULA group stats visualization
Hi Anastasia, I thought I should let you know that this issue has now been resolved. We specified the base ID's/ subject ID's incorrectly in the config file! Sorry for the confusion. Now our group output looks correct. Thanks for your help, Derek From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner [dpis...@psychiatry.arizona.edu] Sent: Tuesday, July 12, 2016 5:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA group stats visualization Hi Anastasia, All subjects had both time-points (for DWI and T1-weighted recons). The recons were run following the standard longitudinal pipeline for FS. Would it matter that I ran the pipeline piecemeal (i.e. separate configuration files for each subject--see attached example)? In case you are wondering, I did it this way in order to run the pipeline in parallel (i.e. by subject) on our cluster... Another consideration is that we did preprocessing outside of TRACULA (i.e. using FSL's tools directly so that we could apply a fieldmap, use new EDDY with TOPUP, as well as apply a denoising algorithm). We then setup the folder structure and filenames to begin TRACULA at the trac-all -intra stage, which we have done successfully in the past when not using the longitudinal pipeline (i.e. single-subject analyses) Still, I have a feeling that none of these customizations should have made any difference as our merged outputs look excellent for both timepoints, for all subjects... Any other thoughts about what might be causing this? Kind regards, -Derek From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, July 12, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA group stats visualization Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't been able to replicate the problem in our own longitudinal data. Did you by any chance have any subjects that had only a single time point? a.y On Thu, 7 Jul 2016, Derek Pisner wrote: > Sure thing. fmajor mean.txt file is attached. > > > Thanks a bunch, > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Thursday, July 07, 2016 4:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - this is strange. The dev and 5.3 version of freeview should > display them differently. Can you send me one of those mean.txt files? > > a.y > > On Wed, 6 Jul 2016, Derek Pisner wrote: > >> Hi Anastasia, >> >> This occurs for me on both stable and dev versions of freview and trac-all >> -stat >> >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, July 04, 2016 12:47 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - Are you by any chance using the dev version of freeview? >> >> a.y >> >> On Fri, 1 Jul 2016, Derek Pisner wrote: >> >>> Dear Anastasia, >>> I am running into an issue with the trac-all -stat option on our >>> longitudinal TRACULA data. >>> >>> Everything runs smoothly through all earlier stages, and I checked >>> individual subjects' merged outputs in freeview with -tv mode. Everything >>> looks fine. >>> >>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>> without error. >>> >>> But then when I open the results with the command: >>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>> >>> I get the image seen in the attached .png file. Any idea what might be >>> causing this? >>> >>> Many thanks in advance for you help. >>> >>> Best, >>> Derek >>> >>> >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harv
Re: [Freesurfer] TRACULA group stats visualization
Hi Anastasia, All subjects had both time-points (for DWI and T1-weighted recons). The recons were run following the standard longitudinal pipeline for FS. Would it matter that I ran the pipeline piecemeal (i.e. separate configuration files for each subject--see attached example)? In case you are wondering, I did it this way in order to run the pipeline in parallel (i.e. by subject) on our cluster... Another consideration is that we did preprocessing outside of TRACULA (i.e. using FSL's tools directly so that we could apply a fieldmap, use new EDDY with TOPUP, as well as apply a denoising algorithm). We then setup the folder structure and filenames to begin TRACULA at the trac-all -intra stage, which we have done successfully in the past when not using the longitudinal pipeline (i.e. single-subject analyses) Still, I have a feeling that none of these customizations should have made any difference as our merged outputs look excellent for both timepoints, for all subjects... Any other thoughts about what might be causing this? Kind regards, -Derek From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, July 12, 2016 1:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA group stats visualization Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't been able to replicate the problem in our own longitudinal data. Did you by any chance have any subjects that had only a single time point? a.y On Thu, 7 Jul 2016, Derek Pisner wrote: > Sure thing. fmajor mean.txt file is attached. > > > Thanks a bunch, > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Thursday, July 07, 2016 4:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - this is strange. The dev and 5.3 version of freeview should > display them differently. Can you send me one of those mean.txt files? > > a.y > > On Wed, 6 Jul 2016, Derek Pisner wrote: > >> Hi Anastasia, >> >> This occurs for me on both stable and dev versions of freview and trac-all >> -stat >> >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, July 04, 2016 12:47 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - Are you by any chance using the dev version of freeview? >> >> a.y >> >> On Fri, 1 Jul 2016, Derek Pisner wrote: >> >>> Dear Anastasia, >>> I am running into an issue with the trac-all -stat option on our >>> longitudinal TRACULA data. >>> >>> Everything runs smoothly through all earlier stages, and I checked >>> individual subjects' merged outputs in freeview with -tv mode. Everything >>> looks fine. >>> >>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>> without error. >>> >>> But then when I open the results with the command: >>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>> >>> I get the image seen in the attached .png file. Any idea what might be >>> causing this? >>> >>> Many thanks in advance for you help. >>> >>> Best, >>> Derek >>> >>> >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > 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 group stats visualization
Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't been able to replicate the problem in our own longitudinal data. Did you by any chance have any subjects that had only a single time point? a.y On Thu, 7 Jul 2016, Derek Pisner wrote: > Sure thing. fmajor mean.txt file is attached. > > > Thanks a bunch, > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Thursday, July 07, 2016 4:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - this is strange. The dev and 5.3 version of freeview should > display them differently. Can you send me one of those mean.txt files? > > a.y > > On Wed, 6 Jul 2016, Derek Pisner wrote: > >> Hi Anastasia, >> >> This occurs for me on both stable and dev versions of freview and trac-all >> -stat >> >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, July 04, 2016 12:47 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - Are you by any chance using the dev version of freeview? >> >> a.y >> >> On Fri, 1 Jul 2016, Derek Pisner wrote: >> >>> Dear Anastasia, >>> I am running into an issue with the trac-all -stat option on our >>> longitudinal TRACULA data. >>> >>> Everything runs smoothly through all earlier stages, and I checked >>> individual subjects' merged outputs in freeview with -tv mode. Everything >>> looks fine. >>> >>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>> without error. >>> >>> But then when I open the results with the command: >>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>> >>> I get the image seen in the attached .png file. Any idea what might be >>> causing this? >>> >>> Many thanks in advance for you help. >>> >>> Best, >>> Derek >>> >>> >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > 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
Re: [Freesurfer] TRACULA group stats visualization
Sure thing. fmajor mean.txt file is attached. Thanks a bunch, -Derek From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Thursday, July 07, 2016 4:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA group stats visualization Hi Derek - this is strange. The dev and 5.3 version of freeview should display them differently. Can you send me one of those mean.txt files? a.y On Wed, 6 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > This occurs for me on both stable and dev versions of freview and trac-all > -stat > > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, July 04, 2016 12:47 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Are you by any chance using the dev version of freeview? > > a.y > > On Fri, 1 Jul 2016, Derek Pisner wrote: > >> Dear Anastasia, >> I am running into an issue with the trac-all -stat option on our >> longitudinal TRACULA data. >> >> Everything runs smoothly through all earlier stages, and I checked >> individual subjects' merged outputs in freeview with -tv mode. Everything >> looks fine. >> >> Also, then when I run trac-all -c dmric_config -stat, everything finishes >> without error. >> >> But then when I open the results with the command: >> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >> >> I get the image seen in the attached .png file. Any idea what might be >> causing this? >> >> Many thanks in advance for you help. >> >> Best, >> Derek >> >> >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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. #!ascii label 273 1 54.9828 -112.501 134.663 0 2 54.8962 -112.723 134.277 0 3 54.0067 -113.333 135.846 0 4 53.8695 -113.932 136.691 0 5 53.488 -114.202 136.28 0 6 53.4998 -114.438 135.639 0 7 53.632 -112.881 136.864 0 8 53.3387 -112.84 136.552 0 9 53.0535 -113.161 136.031 0 10 52.9872 -113.197 135.736 0 11 52.8514 -113.258 135.182 0 12 52.4076 -113.371 134.821 0 13 52.2039 -113.531 134.275 0 14 52.1372 -113.697 133.98 0 15 52.0764 -113.804 133.217 0 16 51.8519 -113.722 132.737 0 17 51.7159 -113.81 132.038 0 18 51.6539 -113.897 131.42 0 19 51.5181 -113.984 131.109 0 20 51.3017 -113.883 130.785 0 21 51.3861 -114.038 130.187 0 22 51.1757 -114.051 129.486 0 23 51.1854 -114.098 129.097 0 24 51.191 -114.043 128.46 0 25 51.2034 -114.111 127.835 0 26 51.4293 -114.06 127.592 0 27 51.3601 -114.142 126.947 0 28 51.37 -114.23 126.088 0 29 51.4519 -114.289 125.551 0 30 51.6811 -114.268 125.169 0 31 51.835 -114.279 124.435 0 32 51.9185 -114.331 123.889 0 33 52.2176 -114.398 123.35 0 34 52.5197 -114.503 122.581 0 35 52.524 -114.463 122.161 0 36 53.0479 -114.374 121.687 0 37 53.114 -114.364 121.276 0 38 53.3473 -114.501 120.582 0 39 53.8011 -114.525 120.43 0 40 53.8766 -114.583 119.812 0 41 54.3976 -114.613 119.485 0 42 54.7717 -114.673 119.028 0 43 54.9236 -114.726 118.395 0 44 55.2803 -113.186 120.859 0 45 55.7019 -113.144 120.469 0 46 55.9703 -113.171 120.184 0 47 56.4664 -113.232 119.667 0 48 56.6804 -113.292 119.236 0 49 56.789 -112.336 121.61 0 50 57.1244 -112.444 121.202 0 51 57.468 -111.296 123.863 0 52 57.5774 -110.19 126.032 0 53 57.7526 -110.28 125.502 0 54 58.1686 -110.318 124.941 0 55 58.5142 -110.392 124.715 0 56 58.8735 -110.535 124.181 0 57 59.051 -110.578 124.062 0 58 59.3363 -110.624 123.756 0 59 59.6364 -110.645 123.25 0 60 60.1 -110.692 123.017 0 61 60.5096 -110.734 122.772 0 62 60.9678 -110.682 122.446 0 63 61.3771 -110.716 122.329 0 64 61.6718 -110.668 122.256 0 65 61.9056 -109.866 123.949 0 66 62.063 -108.816 126.077 0 67 62.3246 -108.75 126.048 0 68 62.896 -108.687 126.098 0 69 63.1635 -108.724 125.928 0 70 63.4838 -108.704 125.751 0 71 63.740
Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - this is strange. The dev and 5.3 version of freeview should display them differently. Can you send me one of those mean.txt files? a.y On Wed, 6 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > This occurs for me on both stable and dev versions of freview and trac-all > -stat > > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, July 04, 2016 12:47 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Are you by any chance using the dev version of freeview? > > a.y > > On Fri, 1 Jul 2016, Derek Pisner wrote: > >> Dear Anastasia, >> I am running into an issue with the trac-all -stat option on our >> longitudinal TRACULA data. >> >> Everything runs smoothly through all earlier stages, and I checked >> individual subjects' merged outputs in freeview with -tv mode. Everything >> looks fine. >> >> Also, then when I run trac-all -c dmric_config -stat, everything finishes >> without error. >> >> But then when I open the results with the command: >> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >> >> I get the image seen in the attached .png file. Any idea what might be >> causing this? >> >> Many thanks in advance for you help. >> >> Best, >> Derek >> >> >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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 group stats visualization
Hi Anastasia, This occurs for me on both stable and dev versions of freview and trac-all -stat -Derek From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Monday, July 04, 2016 12:47 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA group stats visualization Hi Derek - Are you by any chance using the dev version of freeview? a.y On Fri, 1 Jul 2016, Derek Pisner wrote: > Dear Anastasia, > I am running into an issue with the trac-all -stat option on our longitudinal > TRACULA data. > > Everything runs smoothly through all earlier stages, and I checked individual > subjects' merged outputs in freeview with -tv mode. Everything looks fine. > > Also, then when I run trac-all -c dmric_config -stat, everything finishes > without error. > > But then when I open the results with the command: > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w > /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt > > I get the image seen in the attached .png file. Any idea what might be > causing this? > > Many thanks in advance for you help. > > Best, > Derek > > > > ___ 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 group stats visualization
Hi Derek - Are you by any chance using the dev version of freeview? a.y On Fri, 1 Jul 2016, Derek Pisner wrote: Dear Anastasia, I am running into an issue with the trac-all -stat option on our longitudinal TRACULA data. Everything runs smoothly through all earlier stages, and I checked individual subjects' merged outputs in freeview with -tv mode. Everything looks fine. Also, then when I run trac-all -c dmric_config -stat, everything finishes without error. But then when I open the results with the command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt I get the image seen in the attached .png file. Any idea what might be causing this? Many thanks in advance for you help. Best, Derek ___ 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.
