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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Derek Pisner [dpisner@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@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