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>
*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:
* 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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