Interesting – I never did any editing directly on the original brain.finalsurfs.mgz.  I only did cerebellar edits on the brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz.  Looks like those edits copied over somehow.

 

Regardless, it sounds like this will be easy to correct.  Where can I find an unedited copy of brain.finalsurfs.mgz and when/how would I reintegrate that into the processing stream?

 

Thanks,

Laura

 

 

 

It looks like someone edited the brain.finalsurfs.mgz. In the attached is the image of the brain.final... You can see where the brain is missing. The white surface (green line) stops at that edge. When I used the unedited brain, the surfaces went to the right place (yellow surface)

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Thanks Douglas.  I could send other problem data sets too if it would help.  Just let me know.

 

Thanks,

Laura

 

 

From: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 19, 2020 at 6:10 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Stream Problem

 

OK, I have it now and am able to verify the problem. It's really strange -- I don't know why it is behaving like this. It may take me a few days to dig into.

On 6/18/2020 11:39 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

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Sorry I’m not sure why it didn’t upload.  I just tried it again.  danielianall.tar.gz  - Should include all parts.  EM2 is the cross-sectional.  EM is the base.  EM2.long.EM is the long.  I also tried sending just the base again.  danielianbase.tar.gz.

 

Thanks,

 

Laura

 

From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, June 18, 2020 at 9:12 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Stream Problem

 

I have not seen that file appear. Can you re-upload it?

On 6/16/2020 10:19 AM, Danielian, Laura (NIH/NINDS) [E] wrote:

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Hi Douglas,

 

OK I just uploaded the base separately.  danielianbase.tar.gz  I thought it was part of the original bundle.  Sorry!

 

Laura

 

 

From: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, June 16, 2020 at 10:10 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Stream Problem

 

I have your data, but it does not have the base image. Can you upload that as well?

On 6/15/2020 5:15 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

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Hi Douglas,

 

I just upload the files as danielian.tar.gz.  I didn’t notice any damage or artifact on this particular brain or the others that had this same problem.  This subject is a healthy control and most of the subjects (3 of 4) that are having this problem are healthy.  For each we used 2 T1s for the original cross-sectional input.  The cross was reconstructed fine as was the base and the 2 other longitudinal timepoints for this same subject.  The same is the case with the others I’m having trouble with – all of the their other timepoints are fine for the cross/base/longitudinal surfaces.  The warped surfaces are always lower posterior (cerebellum adjacent) and sometimes also temporal.  Upper cortical and frontal regions are unaffected.

 

Thanks for your help!

 

Laura 

 

 

 

From: "Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 12, 2020 at 10:35 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal Stream Problem

 

Hard to tell from just that view. Was there a lot of brain change with that time point? Or was there an MRI artifact? If no to both, then you can upload all the cross, the base, and that one long. Follow instructions below (you can make one tarball for all subjects)

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subjects.tar.gz ./subject1 ./subject2
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subjects.tar.gz
Send an email that the file has been and the name of the file.

On 6/9/2020 6:32 PM, Danielian, Laura (NIH/NINDS) [E] wrote:

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Hi, I’ve finished processing a data set that included longitudinal data and I’m having a problem with a small percentage of the longitudinal timepoints.  To review what I’ve done, I edited all of the individual (cross-sectional) timepoints until the wm and pial surfaces were correct, then created the base and edited that until it looked good, and then created the longitudinal files for each cross-sectional timepoint.  Most of these did not need editing and some needed slight edits to either wm or brainmask which corrected the longitudinal surfaces. 

 

However, in a small handful of cases, the wm/pial surfaces were so distorted that editing would not fix the problem.  In these cases, longitudinal surfaces were very different from both the original cross-section and base.  I’ve tried to attach a file that shows an example – it might only affect a small portion of the brain but in these cases I don’t think I could edit it to improve the surfaces.  In the example I attached, red/blue are from the long file and pink/lt blue are from the base.

 

Do you have any suggestions for why this might be happening and how to fix it?  I’m running v6.0.

 

Thanks!

Laura Danielian

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