If you run this, it will create a new brain.finalsurfs and rerun just
what you need to rerun
recon-all -s subject -autorecon2 -nogcareg -nocalabel -nonormalization2
-autorecon3
On 6/22/2020 1:20 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
Interesting – I never did any editing directly on the original
brain.finalsurfs.mgz. I only did cerebellar edits on the
brain.finalsurfs.manedit.mgz copy of brain.finalsurfs.mgz. Looks like
those edits copied over somehow.
Regardless, it sounds like this will be easy to correct. Where can I
find an unedited copy of brain.finalsurfs.mgz and when/how would I
reintegrate that into the processing stream?
Thanks,
Laura
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, June 22, 2020 at 12:13 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Longitudinal Stream Problem
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:
* 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>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, June 19, 2020 at 6:10 PM
*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
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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