Re: [Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

[Douglas N. Greve]

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 EstimatedTotalIntraCranialVol in list
>
> It seems computing the ratio of volumes to etiv needs etiv to be
> included in the list (which by the way is not very useful because it is
> 100% by definition), but is there a way to get the ratios without
> including all the "extra" volumes?
>
> For instance using
>
> asegstats2table --tablefile "output.txt" --no-vol-extras --etiv --segno
> 225
>
> I would expect to get the volume of CC_Anterior in % of etiv.
>
> Thanks for your help
>
> Antonin
>
> Hôpital Erasme - ULB
> Cliniques universitaires de Bruxelles
> Route de Lennik 808 - B - 1070 Bruxelles
> S www.erasme.ulb.ac.be
>
> Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
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[Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

[Rovai Antonin]

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 EstimatedTotalIntraCranialVol in list

It seems computing the ratio of volumes to etiv needs etiv to be
included in the list (which by the way is not very useful because it is
100% by definition), but is there a way to get the ratios without
including all the "extra" volumes?

For instance using

asegstats2table --tablefile "output.txt" --no-vol-extras --etiv --segno
225

I would expect to get the volume of CC_Anterior in % of etiv.

Thanks for your help

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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Re: [Freesurfer] asegstats2table error - measure 63 expected 66

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

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 it is the first time I get this error message
for all of my subjects. Do you have any suggestion on what to do?


Thank you very much in advance,

Fernanda


Em sex, 9 de ago de 2019 às 17:51, Fernanda Hansen P. de Moraes <
fernandahmor...@gmail.com> escreveu:

> 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, expecting 66 for all
> our subjects on the list.
>
> I just found this older message about the same error (
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036502.html 
> ),
> and I am now looking for the subject with 66 ROIs. However, for now, all of
> then present 45 ROIs.
>
> Is there any suggestion on how can we trespass this error?
>
>
> Regards,
> --
> Fernanda Hansen P. de Moraes
>
> fernandahmor...@gmail.com
> Física Médica | Rede D'Or São Luiz
> Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
>


-- 
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Física Médica | Rede D'Or São Luiz
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
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[Freesurfer] asegstats2table error - measure 63 expected 66

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

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, expecting 66 for all
our subjects on the list.

I just found this older message about the same error (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036502.html
),
and I am now looking for the subject with 66 ROIs. However, for now, all of
then present 45 ROIs.

Is there any suggestion on how can we trespass this error?


Regards,
-- 
Fernanda Hansen P. de Moraes

fernandahmor...@gmail.com
Física Médica | Rede D'Or São Luiz
Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
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Re: [Freesurfer] asegstats2table error message

[Hoopes, Andrew]

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


On Jan 6, 2018, at 1:22 PM, Hugh Pemberton 
> wrote:

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 "/Applications/freesurfer/bin/asegstats2table", line 195

  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'

SyntaxError: invalid syntax
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[Freesurfer] asegstats2table error message

[Hugh Pemberton]

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 "/Applications/freesurfer/bin/asegstats2table", line 195

  print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'

SyntaxError: invalid syntax
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Re: [Freesurfer] asegstats2table error

[Douglas N Greve]

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 AM, Elizabeth Dao wrote:
> 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 --subjects 201.MR1 202.MR1 
> 203.MR1 --meas volume --tablefile aseg_stats_all.txt
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
>   File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 
> 4, in 
> import os
>   File "/usr/local/lib/python2.7/os.py", line 398, in 
> import UserDict
>   File "/usr/local/lib/python2.7/UserDict.py", line 84, in 
> _abcoll.MutableMapping.register(IterableUserDict)
>   File "/usr/local/lib/python2.7/abc.py", line 109, in register
> if issubclass(subclass, cls):
>   File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__
> cls._abc_negative_cache.add(subclass)
>   File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add
> self.data.add(ref(item, self._remove))
> TypeError: cannot create weak reference to 'classobj' object
>
> Thank you in advance for your help!
>
> Liz
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] asegstats2table error

[Elizabeth Dao]

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 --subjects 201.MR1 202.MR1 203.MR1
--meas volume --tablefile aseg_stats_all.txt
'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 4, in

import os
  File "/usr/local/lib/python2.7/os.py", line 398, in 
import UserDict
  File "/usr/local/lib/python2.7/UserDict.py", line 84, in 
_abcoll.MutableMapping.register(IterableUserDict)
  File "/usr/local/lib/python2.7/abc.py", line 109, in register
if issubclass(subclass, cls):
  File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__
cls._abc_negative_cache.add(subclass)
  File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add
self.data.add(ref(item, self._remove))
TypeError: cannot create weak reference to 'classobj' object

Thank you in advance for your help!

Liz
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Re: [Freesurfer] asegstats2table error

[Douglas N Greve]

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 extracted values with asegstats2table with --all-seg 
 flag. I hope that is okay?


 On Sunday, March 2, 2014 11:28 AM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu wrote:

 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 file to see which segs are missing.
 doug


 On 3/2/14 9:46 AM, sabin khadka wrote:
 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


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 e-mail
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] asegstats2table error

[sabin khadka]

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 gr...@nmr.mgh.harvard.edu 
wrote:
 

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 file to see which segs are missing.
doug



On 3/2/14 9:46 AM, sabin khadka wrote:

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


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[Freesurfer] asegstats2table error

[sabin khadka]

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___
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Re: [Freesurfer] asegstats2table error

[Douglas Greve]

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 file to see which segs are missing.

doug


On 3/2/14 9:46 AM, sabin khadka wrote:

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


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[Freesurfer] asegstats2table error

[Rashmi Singh]

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 .stats files
Skipping /opt/freesurfer/subjects/AB197.T0b/stats/aseg.stats
Skipping /opt/freesurfer/subjects/AB232.T0a/stats/aseg.stats
Skipping /opt/freesurfer/subjects/AD721.T0/stats/aseg.stats
Building the table..
Traceback (most recent call last):
  File /opt/freesurfer/bin/asegstats2table, line 513, in module
rows, columns, table = sanitize_table(options, pretable)
  File /opt/freesurfer/bin/asegstats2table, line 412, in sanitize_table
_specs, _id_name_map, _measl = _t[0]
IndexError: list index out of range

 Then tried asegstat2table for individual subjects but for each subject the 
computer gave following error message

Example:
asegstats2table --subjects AB232.T0a --meas volume --tablefile asegstats1.txt
SUBJECTS_DIR : /opt/freesurfer/subjects
Parsing the .stats files
ERROR: The stats file /opt/freesurfer/subjects/AB232.T0a/stats/aseg.stats is 
not found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files

I looked into each subjects' segmetation file (attached). It looked fine to me 
and had all the information.
Please advise why I got error message.
Thanks,
Rashmi


aseg.stats
Description: aseg.stats
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Re: [Freesurfer] asegstats2table error depending on subject sorting

[Andreas Berger]

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) worked, so i 
never noticed.


Andreas

On Wednesday, April 24, 2013 17:52:32 Douglas N Greve wrote:
 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 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 .stats files
  Skipping /mnt/raid/freesurfer/subjects/fsaverage/stats/aseg.stats
  Skipping /mnt/raid/freesurfer/subjects/lh.EC_average/stats/aseg.stats
  Skipping /mnt/raid/freesurfer/subjects/qdec/stats/aseg.stats
  Skipping /mnt/raid/freesurfer/subjects/rh.EC_average/stats/aseg.stats
  
  Traceback (most recent call last):
 File /usr/local/freesurfer/bin/asegstats2table, line 553, in
 module
 
   if(nmeasures != nmeasures0 and not options.common_flag and not
  
  options.all_flag):
  NameError: name 'nmeasures0' is not defined
  
  
  i don't get that error if i either:
  1) remove the non-subjects (fsaverage, qdec, etc..) from the list, or:
  2) do not sort the list like i do
  
  
  the subjects list is attached, sorted the way it produces the error
  
  
  greetings,
  Andreas
  
  
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[Freesurfer] asegstats2table error depending on subject sorting

[Andreas Berger]

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 .stats files
Skipping /mnt/raid/freesurfer/subjects/fsaverage/stats/aseg.stats
Skipping /mnt/raid/freesurfer/subjects/lh.EC_average/stats/aseg.stats
Skipping /mnt/raid/freesurfer/subjects/qdec/stats/aseg.stats
Skipping /mnt/raid/freesurfer/subjects/rh.EC_average/stats/aseg.stats
Traceback (most recent call last):
  File /usr/local/freesurfer/bin/asegstats2table, line 553, in module
if(nmeasures != nmeasures0 and not options.common_flag and not 
options.all_flag):
NameError: name 'nmeasures0' is not defined


i don't get that error if i either:
1) remove the non-subjects (fsaverage, qdec, etc..) from the list, or:
2) do not sort the list like i do


the subjects list is attached, sorted the way it produces the error


greetings,
Andreas
fsaverage
lh.EC_average
qdec
rh.EC_average
H458_1Md
H458_2F
H458_2Fd
H458_3F
H458_4F
H458_4Fd
H458_5Fd
H458_5M
H458_6M
H458_6Md
H458_7F
H458_7Fd
H458_8Fd
H458_8M
H458_9F
H458_10Fd
H458_10M
H458_11Fd
H458_12F
H458_12Fd
H458_13M
H458_14Fd
P458_14M
H458_15F
H458_15Fd
H458_16M
H458_16Md
H458_17Md
H458_18M
P458_19F
H458_20F
H458_20Md
H458_21F
H458_21Md
H458_22M
H458_22Md
H458_23M
H458_23Md
H458_24M
H458_24Md
H458_25M
H458_25Md
P458_26M
P458_26Md
H458_27M
P458_27Md
P458_28F
P458_28Fd
H458_29M
P458_29Fd
H458_30F
P458_30Md
P458_31F
P458_31Md
H458_32F
P458_32Fd
P458_33Md
H458_34M
P458_34Fd
H458_35F
P458_35Md
P458_36F
P458_36Fd
P458_37Fd
P458_37M
P458_38Fd
P458_38M
P458_39F
P458_39Md
P458_40F
P458_40Fd
P458_41M
P458_41Md
P458_42Fd
P458_42M
P458_43F
P458_43Fd
P458_44Fd
P458_45F
P458_45Fd
P458_46M
H458_47M
P458_48F
P458_49M
P458_50F
H458_51Fd
P458_51F
H458_52F
H458_52Fd
H458_53Md
P458_53M
H458_54Fd
H458_55Md
P458_55M
H458_56M
H458_56Md
H458_57Fd
P458_57M
H458_58Fd
P458_58F
H458_59M
P458_60F
H458_61F
H458_61Fd
H458_62Fd
H458_62M
P458_64F
H458_65M
P458_65M
H458_66F
H458_67M
H458_68F
H458_69F
H458_70M
H458_71F
P458_72F
H458_73F
H458_74F
H458_75F
H458_76F
H458_77F
H458_78F
H458_79F
H458_81F
H458_82F
H458_84M
H458_86M
P458_87F
P458_88F
P458_90F
H458_91F
P458_92F
P458_93F
P458_94M
H458_95M
P458_96M
P458_97M
P458_98F
P458_99M
P458_100F
P458_101M
H458_102F
P458_105F
H458_107M
H458_108M
P458_109M
H458_110M
P458_111M
H458_112F
P458_113F
H458_114M
P458_115F
P458_116M
P458_117F
H458_118F
H458_119F
H458_120F
P458_121F
H458_122F
P458_123F
H458_127F
P458_129M
H458_130F
H458_131F
H458_132M
H458_133F
P458_134F
H458_135F
H458_137M
H458_138F
H458_139F
H458_141M
H458_142M
H458_143F
H458_144F
H458_145F
H458_146F
H458_147F
H458_148M
P458_149M
H458_151F
P458_152M
P458_153F
P458_155F
P458_156M
P458_157F
P458_158F
P458_159F
P458_161F
P458_162M
P458_163F
H458_164M
P458_165M
P458_166F
H458_167F
H458_168F
H458_171F
H458_172F
P458_173F
P458_175F
P458_176F
P458_177F
P458_178F
H458_180M
P458_181M
P458_183F
P458_184F
P458_185F
P458_186F
P458_187M
P458_188F
H458_189F
H458_190M
P458_191M
P458_192F
H458_193M
P458_194F
P458_195M
P458_196M
H458_197F
H458_198F
H458_199M
H458_200F
P458_201M
H458_202M
P458_203M
P458_204M
P458_205F
H458_206F
P458_207M
H458_208M
P458_210F
H458_211F
P458_212F
H458_214F
P458_215F
P458_216F
P458_217F
H458_218M
P458_219F
P458_220F
P458_221F
H458_224M
H458_225F
H458_226M
P458_227F
H458_228M
H458_229M
P458_230F
H458_232M
P458_233F
H458_234F
P458_235F
H458_236M
H458_238F
H458_240M
P458_244M
H458_245M
H458_250M
H458_251M
P458_253F
H458_254M
H458_256F
H458_257F
H458_258M
H458_260F
H458_261F
P458_262F
P458_263F
H458_264M
H458_265F
P458_266M
P458_267M
P458_268F
H458_269F
P458_270F
H458_271F
P458_272F
H458_274F
H458_275F
H458_276F
P458_277M
H458_279M
H458_280M
P458_281F
H458_282M
H458_283M
H458_284M
H458_285M
H458_286M
H458_287F
H458_288M
H458_289M
H458_290F
H458_291M
H458_292M
H458_293F
H458_294F
H458_295F
H458_296F
H458_297M
P458_298F
P458_299M
P458_300F
P458_301M
P458_302F
H458_304F
P458_305M
H458_306M
H458_307M
P458_308F
P458_309F
H458_310F
H458_311M
H458_312M
H458_313M
H458_314F
P458_315M
H458_316F
H458_317M
P458_318F
H458_319F
H458_320M
P458_321M
H458_322F
H458_324F
H458_325M
H458_327M
H458_328F
P458_329M
H458_330M
H458_331F
P458_332F
H458_333M
H458_334F
H458_335F
H458_336F
H458_338F
H458_339F
H458_340M
H458_341F
H458_342M
H458_343F
H458_344M
H458_345M
H458_346M
P458_347M
P458_348F
H458_349F
H458_350F
P458_351M
H458_352M
139_01F
139_02M
139_03M
139_04F
139_05F
139_07M
139_08M
139_09F
139_11M
139_12M
139_13M
139_14F
139_15F
139_16F
139_17F
139_18M
139_19F
139_20F
139_21M
139_22F
139_23M
139_24M
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Re: [Freesurfer] asegstats2table error depending on subject sorting

[Douglas N Greve]

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 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 .stats files
 Skipping /mnt/raid/freesurfer/subjects/fsaverage/stats/aseg.stats
 Skipping /mnt/raid/freesurfer/subjects/lh.EC_average/stats/aseg.stats
 Skipping /mnt/raid/freesurfer/subjects/qdec/stats/aseg.stats
 Skipping /mnt/raid/freesurfer/subjects/rh.EC_average/stats/aseg.stats
 Traceback (most recent call last):
File /usr/local/freesurfer/bin/asegstats2table, line 553, in module
  if(nmeasures != nmeasures0 and not options.common_flag and not
 options.all_flag):
 NameError: name 'nmeasures0' is not defined


 i don't get that error if i either:
 1) remove the non-subjects (fsaverage, qdec, etc..) from the list, or:
 2) do not sort the list like i do


 the subjects list is attached, sorted the way it produces the error


 greetings,
 Andreas


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] asegstats2table error

[Rashmi Singh]

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 .stats files
ERROR: The stats file /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not 
found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files

I did try to use the skip option , but then , it skips all the files giving the 
same error.
When I individually open the aseg files from the stats folder, those look fine 
to me.

Please advise.

Rashmi.




This document may contain information covered under the Privacy Act, 5 USC 
552(a), and/or the Health Insurance Portability and Accountability Act (PL 
104-191) and its various implementing regulations and must be protected in 
accordance with those provisions. Healthcare information is personal and 
sensitive and must be treated accordingly. If this correspondence contains 
healthcare information it is being provided to you after appropriate 
authorization from the patient or under circumstances that don't require 
patient authorization. You, the recipient, are obligated to maintain it in a 
safe, secure and confidential manner. Redisclosure without additional patient 
consent or as permitted by law is prohibited. Unauthorized redisclosure or 
failure to maintain confidentiality subjects you to application of appropriate 
sanction. If you have received this correspondence in error, please notify the 
sender at once and destroy any copies you have made.
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] asegstats2table error

[Douglas N Greve]

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 AA267.G2 AA304.G1 --meas volume 
 --tablefile asegstats.txt
 SUBJECTS_DIR : /opt/freesurfer/subjects
 Parsing the .stats files
 ERROR: The stats file 
 /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is 
 too small to be a valid statsfile
 Use --skip flag to automatically skip bad stats files

 I did try to use the skip option , but then , it skips all the files 
 giving the same error.
 When I individually open the aseg files from the stats folder, those 
 look fine to me.

 Please advise.

 Rashmi.


 

 This document may contain information covered under the Privacy Act, 5 
 USC 552(a), and/or the Health Insurance Portability and Accountability 
 Act (PL 104-191) and its various implementing regulations and must be 
 protected in accordance with those provisions. Healthcare information 
 is personal and sensitive and must be treated accordingly. If this 
 correspondence contains healthcare information it is being provided to 
 you after appropriate authorization from the patient or under 
 circumstances that don't require patient authorization. You, the 
 recipient, are obligated to maintain it in a safe, secure and 
 confidential manner. Redisclosure without additional patient consent 
 or as permitted by law is prohibited. Unauthorized redisclosure or 
 failure to maintain confidentiality subjects you to application of 
 appropriate sanction. If you have received this correspondence in 
 error, please notify the sender at once and destroy any copies you 
 have made.


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 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] asegstats2table error

[Jesse Bledsoe]

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 /usr/local/freesurfer/bin/asegstats2table, line 4, in ?
import os;
ImportError: No module named os


I am on Linux-centos4-stable-pub-v4.2.0

Any suggestions are much appreciated,
Jesse
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