searched the email archive and found this thread:
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22=newest=1
> My problem seems identical to the one described by initial poster.
> The suggestion was
+Error\%3A+indices+out+of+bounds%22=newest=1
My problem seems identical to the one described by initial poster.
The suggestion was to try the following command:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
$mir/nu.mgz
When I tried
Hello Edgar,
We think we were able to isolate the problem. Version 5.1 is failing to
apply the talairach transform to the nu.mgz. It gets computed and
applied to the orig.mgz but then not transferred during the next step.
When mri_normalize tries to run without this information, it fails,
Hello Edgar,
I am going to be looking at your case and seeing if I can replicate the
error. I have your .nii file and will run it through our processing
stream here, but could you send me your subject folder so that I can
look through your files/logs to give me some more information?
You
Hello Bruce,
I just wanted to touch base regarding the Indices_oob.nii subject I had
sent to MGH. Were you by any chance able to detect the issue with running
recon-all on this subject. Thanks in advance for taking a look at this.
Best regards,
Edgar Busovaca
Hello Edgar,
Could you upload the whole subject folder? I could try to run it through
recon all here and see if I can reproduce the error. It would also allow
me to look through your log files to see if I can spot anything that
could be causing this issue.
You can use FileDrop2.0 if the
Hello Bruce,
I took a look at the file with freeview and I can't identify anything
peculiar about the data. The file is named Indices_oob.nii and has been
uploaded to /transfer/incoming on the FTP file exchange server. Thank you
for your swift reply and in advance for your time.
Best regards,
Hi Edgar
the LINE SEARCH thing is not a real problem. I've never seen indices out
of bounds before though. Is there anything strange about your dataset?
Does freeview display it properly (that is, are what freeview thinks the
RAS dirs the correct anatomical ones)? If you upload the dataset
Dear Freesurfer users,
I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).
During skullstripping the following warning appears twice:
IFLAG= -1 LINE
Dear Freesurfer users,
I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).
During skullstripping the following warning appears twice:
IFLAG= -1 LINE SEARCH FAILED. SEE
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