Hi,
Do I need to run laleb2label and label2annot to get once again the BA.thresh?
Or is it enough to just extract the stats?
I already extracted the aseg stats and one of the subjects came out
with slightly different values this time, while the other presented
the same values. Was this
Hi Andreia
I haven't been following this whole thread, but the matlab warning is not
a problem
cheers
Bruce
On Tue, 20 May 2014, _andre...@sapo.pt wrote:
Hi,
Do I need to run laleb2label and label2annot to get once again the BA.thresh?
Or is it enough to just extract the stats?
I
Hi Bruce,
Thank you!
Andreia
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Andreia
I haven't been following this whole thread, but the matlab warning is not
a problem
cheers
Bruce
On Tue, 20 May 2014, _andre...@sapo.pt wrote:
Hi,
Do I need to run laleb2label and label2annot
If you ran with -autorecon3, then you do not need to redo the labels. As
for the aseg, it depends on what you ran and what edits you made. If
you ran with -autorecon2 and you had added control points, then it
would change slightly.
You can ignore that matlab warning (it is only saying that
I think it is still out of synch. Try running
vno_match_check subject lh
doug
On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote:
Hello,
Only after sending the email below I noticed that now the stats file
generated give only 0,00 were the LGI values should be, even though
they appear in
Hello again,
Sorry for not waiting for your reply, but I realized that I get the
same warning with another different subject when trying to get
destrieux lgi and this happens only for the left hemisphere:
[user@localhost Freesurfer]# mris_anatomical_stats -a
aparc.a2009s.annot -t pial_lgi
Hi Doug,
I just ran that command on the first subject I referred and the output is:
[user@localhost Freesurfer]$ vno_match_check subj lh
Checking subj/surf/lh.orig...
Checking subj/surf/lh.white...
Checking subj/surf/lh.pial...
Checking subj/surf/lh.inflated...
Checking subj/surf/lh.smoothwm...
On 05/19/2014 02:32 PM, _andre...@sapo.pt wrote:
Sorry for all the emails..
Now I ran that same command on the second subject in which I only
detected a problem for the left hemisphere when trying to get
Destrieux lgi, and got this error but for both hemispheres:
ERROR: subj2/surf/rh.orig
Sorry for all the emails..
Now I ran that same command on the second subject in which I only
detected a problem for the left hemisphere when trying to get
Destrieux lgi, and got this error but for both hemispheres:
ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere
has
Hi Doug,
That's really bad news. So I'll check all my subjects to track the
ones who give the error. Then I'll have to run each one from scratch?
I don't quite understand what went wrong with only a few subjects
since I did (as far as I'm aware) everything in the same way for all
of them.
I just ran vno_match_check for all my subjects and the scenario is:
S_UBJ1_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
subj1/stats/lh.BA_lgi.stats subj1 lh
the warning appears: MRISREADANNOTATIONINTOARRAY: vertex index out of
range: 120389 i=0014C8B5, in_array_size=120388
ONLY FOR
If the subject is out of synch, then running mris_preproc or recon-all
-qcache should have failed too (as would have anything that tried to map
the subject to a group space). This usually happens when you make edits
to a subject but don't re-run the analysis all the way through (or the
On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:
I just ran vno_match_check for all my subjects and the scenario is:
*S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f
subj1/stats/lh.BA_lgi.stats subj1 lh
the warning appears: *MRISreadAnnotationIntoArray*: vertex index out
of
BA.annot I think that was created before any problem because I had no
error (at least I didn't see any) untill I extracted aparcstats2table
of those values. But I just checked my notes and these two subjects
were the only ones that gave aberrantly high LGI values when running
-localGI. I
Hi Andreia,
Then I would guess that your error comes from the fact that you didn't rerun
the autorecon3 at that stage for these 2 subjects. As the randomness flag
changes the number of vertices when recreating the surfaces, that explains the
error. So for your subjects, just rerun autorecon3
Hi Marie,
Thanks for the input! Actually, from the recon-all log I can see that
autorecon3 was caled in the terminal, and comparing it to a subject
without any error they look the same to me. Also, qcache gave no error.
Anyway, I'll rerun -autorecon3 for these 2 subjects and all the
Hi Doug,
I tried to load the annotation and it gave an error. I look in the
archives and I found someone with the same problem and the advice was
to run:
recon-all -s subject -sd subjects dir -make all
I did that and tried to run again mris_anatomical_stats as previously
and still have
Hello,
Only after sending the email below I noticed that now the stats file
generated give only 0,00 were the LGI values should be, even though
they appear in the terminal.
How can I solve this issue? And, again, are all the measures (cortical
thickness, surface area, aseg) invalidated? As
Hi Andreia,
You probably have lGI values that correspond to earlier versions of your
surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces
and reprocessed them, but forgot to recalculate lGI for this new surfaces).
If you simply reprocess lGI now, that should solve the
That probably means that the subject is out of synch. Try viewing the
subject's surface tksurfer or freeview and load the annotation.
doug
On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
Hello all,
I generated the lgi.stats file for all my subjects and in one of them
I got this warning:
20 matches
Mail list logo
