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)
On 6/22/2020 9:21 AM, Danielian, Laura (NIH/NINDS) [E] wrote:
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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" <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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