Oh, yes, sorry. The problem was that you are using FS 5.1 segmentations and
things have changed since then in a way that makes it incompatable with gtmseg.
One possibility is to run gtmseg with --ctab
$FRESURFER_HOME_51/FreeSurferColorLUT.txt
If that does not work, you may need to reanalyze your
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Dear Douglas,
Did you get the subjects? I hope I loaded them correctly.
Best regards,
Marina.
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Dear Douglas,
I put the subjects yesterday. They are: qsm_04_yr3 (it is the first subject
with problems and we have another copy that is solved) and mci13_hsp (it is
the new subject with problems).
Thank you very much for your attention.
Marina.
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Dear Douglas,
Thank you very much for the help. We could solve the problem with that
subject but now we have a similar problem with another subject. In the
previous case, we have only one problematic voxel in the skull, but now the
label 75 (it shoul
Can you upload one of your problematic subjects? Follow these instructions
From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: us
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Dear Douglas,
Thank you very much for the help. We could solve the problem with that
subject but now we have a similar problem with another subject. In the
previous case, we have only one problematic voxel in the skull, but now the
label 75 (it shouldn
Probably the easiest thing is just to edit that voxel to be one of the
neighboring segments. First, load the aseg and find that voxel. See which
segment(s) are around that voxel and get the segmentation id. Then run
mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o
aparc+aseg.m
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I run the command that you told me (mri_binarize --i aseg.presurf.mgz
--match 229 --o bin229.mgz) and I get a mask with one voxel.
How can I do to solve it?
Thank you.
Marina.
El lun., 7 oct. 2019 a las 23:19, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.h
We'll have to figure out where those 229s are coming from. Try this
mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz
It should print out whether there were any voxels that matched. If so, you can
load bin229.mgz with the norm.mgz and the aseg.presurf.mgz and see where they
are. If the
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Dear Douglas,
Sorry! This is the previous information:
> Dear Douglas,
>
> Thank you for the replay.
>
> I think so, I can't find the code 229 in any subject.
>
> I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels
have the normal
Sorry, can you include the previous correspondence so that I know the context?
On 10/7/2019 11:45 AM, Marina Fernández wrote:
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Dear Douglas,
Thank you for the replay.
I think so, I can't find the code 229 in any subject.
I can't see anything strange in the
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Dear Douglas,
Thank you for the replay.
I think so, I can't find the code 229 in any subject.
I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels
have the normal segmentation and labels. Could it be a problem with the
extracerebra
That is kind of weird. It says it has found a segmentation with number 229, but
we don't have that code in our system. Can you find the 229 voxels in the
aparc+aseg.mgz?
On 10/4/2019 6:28 PM, Marina Fernández wrote:
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Dear experts,
The following error occurs
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Dear experts,
The following error occurs with one subject when I am running gtmseg
command:
*Computing colortable*
*ERROR: cannot find match for subcortical segid 229*
*ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas
apas+head.mgz --no
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