What happens if you don't include --segno ?
On 10/13/2020 8:11 AM, Rovai Antonin wrote:
> External Email - Use Caution
>
> Hello,
>
> when using asegstats2table with the two flags --etiv and --no-vol-
> extras, I get the following error:
>
> ERROR: --etiv, cannot find EstimatedTotalIntraC
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Hello,
when using asegstats2table with the two flags --etiv and --no-vol-
extras, I get the following error:
ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list
It seems computing the ratio of volumes to etiv needs etiv to be
included in
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Dear Freesurfer experts,
I did find another message with the same error (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40379.html)
where you ask if the versions are the same. They are for me. I had also
already run this command, but
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Dear Freesurfer experts,
We had just reprocessed our subjects with the -long flag fr the
longitudinal processing, and when extracting volumes with asegstats2table I
have the following error:
WARN: SUBJ229_ses-1.long.SUBJ229_tmpl nmeasures = 63, expec
Hi,
This is a bug introduced by python3, you must run this script with python2 by
either modifying the first line to say:
#!/usr/bin/env python2
or by running:
python2 $FREESURFER_HOME/bin/asegstats2table --subjects baseline 12m 24m 36m
--meas volume --tablefile aseg_stats.txt
best,
Andrew
O
Hi, I'm getting the following error when trying to use the asegstats2table
command, I can't see anything similar from previous emails, any ideas what
the issue is? Thanks v much in advance.
asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile
aseg_stats.txt
File "/Applicati
Not sure what the problem is, but it might be something specific to your
site (looks like it cannot find the proper libraries to import). Can you
run it at all. Eg, if just run the script without any arguments, do you
get the same thing? What about if you run it with -h ?
On 07/06/2017 03:33 A
Dear experts,
I have completed recon-all with no errors. Now I would like to use the
'asegstats2table' command but I've received the error below. I would
appreciate any help in solving this problem. I am using FreeSurfer v6.0.0
on a Linux CentOS machine.
[TLA@CogmobCentOS MCI]$ asegstats2table --
actually, you are right, they should have 45. Which one had 66? What was
your command line?
On 03/03/2014 04:22 PM, sabin khadka wrote:
> All aseg.stats seems to have volume of 45 ROIs with some
> hypointensities value =0. Also, I checked aseg.mgz and looks fine with
> these subjects. I extracte
All aseg.stats seems to have volume of 45 ROIs with some hypointensities value
=0. Also, I checked aseg.mgz and looks fine with these subjects. I extracted
values with asegstats2table with --all-seg flag. I hope that is okay?
On Sunday, March 2, 2014 11:28 AM, Douglas Greve
wrote:
That m
That means that it was expecting to find 66 segmentations but only found
55. Sometimes there are some segmentations in one subject that are not
in another (usually hypointensities). But 11 is too many. Have you
looked at the aseg to see if it looks right? You can also compare the
aseg.stats f
Hi all,
While using asegstats2table, I got following error for few subjects,
WARN SUBID: nmeasure 66, expecting 55
It let me extract cortical thickness and surface area using aparcstats2table
though.
Any suggestions?
-SABIN___
Freesurfer mailing list
Fr
Hello,
This morning I tried to get the segmentation measurement in table formate, but
I got the following error message
asegstats2table --subjects AB197.T0b AB232.T0a AD721.T0 --skip --meas volume
--tablefile asegstats1.txt
Error message :SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the .sta
Hi Doug,
yes. and i narrowed it down:
asegstats2table can deal with non-subjects (fsaverage, qdec), unless it is the
*first item* in the list. If they are somewhere in between, they are just
skipped, with a meaningful message.
Anyway, my bad for not sanitizing the list, it previously (v5.1) wo
Hi Andreas, fsaverage does not have stats files so should cause it to
crash. Are you saying that if you sort it in a certain way, you can get
it to run with fsaverage?
doug
On 04/24/2013 09:51 AM, Andreas Berger wrote:
> Hi Surfers,
>
> as of version 5.2, i'm getting an error using asegstats2t
Hi Surfers,
as of version 5.2, i'm getting an error using asegstats2table, depending on
how i sort the subjects:
andreas@psy058:~$ asegstats2table --subjects $(ls $SUBJECTS_DIR | sort -t _ -k
1 -nk 2) -t segstats.csv --skip -d comma
SUBJECTS_DIR : /mnt/raid/freesurfer/subjects
Parsing the .sta
Do those files exist? Do they have content in them?
doug
On 05/15/2012 05:51 PM, Rashmi Singh wrote:
> Hello,
> I am trying to get the asegmentation information after the recon-all
> run in the table form, but I am continuously getting the following error
>
> asegstats2table --subjects AA262.G1
Hello,
I am trying to get the asegmentation information after the recon-all run in
the table form, but I am continuously getting the following error
asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile
asegstats.txt
SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the
Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile
aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "
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