Hi Laura, it looks like there is a bug in v6 that does not transfer the
edits correctly. This is fixed in v7, but I'm looking into getting you a
version of mri_mask that will work in v6.
doug
On 6/23/2020 1:49 PM, Danielian, Laura (NIH/NINDS) [E] wrote:
External Email - Use Caution
OK thanks. Do you recommend that I re-run this for every subject that
I did these cerebellar edits on since it ended up editing
brain.finalsurfs.mgz? I have a handful of other data sets where it
didn’t affect the longitudinal surfaces, but upon further inspection
it’s clear that those cross-sectional edits within the cerebellum
carried over to brain.finalsurfs.mgz in the longitudinal data sets.
Also, I’m still not sure how the edits I made on the
brain.finalsurfs.manedit.mgz volumes got transferred over to the
original. Do you have any suggestions for how this happened and how
to avoid doing this in the future?
Thanks,
Laura
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, June 23, 2020 at 10:18 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Longitudinal Stream Problem
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>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, June 22, 2020 at 12:13 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
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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