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>
*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:
* 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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