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>
*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:
* 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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