External Email - Use Caution
Thanks Douglas. I could send other problem data sets too if it would help.
Just let me know.
Thanks,
Laura
From: "Douglas N. Greve" <dgr...@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:
External Email - Use Caution
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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, June 18, 2020 at 9:12 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, June 16, 2020 at 10:10 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 12, 2020 at 10:35 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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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