Re: [Freesurfer] aparcstats2table - append option

[Horn, Mitchell Jacob]

Wow that was fast! Thanks!
-Mitch

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Monday, December 18, 2023 2:18:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] aparcstats2table - append option


'--append' option is added to aparcstats2table and asegstats2table. It should 
be available tomorrow in Freesurfer dev version.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Monday, December 18, 2023 9:06 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] aparcstats2table - append option



Exactly.



My understanding (and correct me if I’m wrong) is that both commands 
create/overwrite the specified --tablefile each time it’s run.



Best,

Mitch





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Monday, December 18, 2023 8:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table - append option



I would like to confirm that this is what you have in mind:

  1.  the new ‘—append’ flag will work with ‘--tablefile=OUTPUTFILE’
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] aparcstats2table - append option



Hi FS Devs,



Would it be possible to add an “append” flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.



Thanks,

Mitch
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Re: [Freesurfer] aparcstats2table - append option

[Huang, Yujing]

'--append' option is added to aparcstats2table and asegstats2table. It should 
be available tomorrow in Freesurfer dev version.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Monday, December 18, 2023 9:06 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] aparcstats2table - append option

Exactly.

My understanding (and correct me if I'm wrong) is that both commands 
create/overwrite the specified --tablefile each time it's run.

Best,
Mitch


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Monday, December 18, 2023 8:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table - append option

I would like to confirm that this is what you have in mind:

  1.  the new '-append' flag will work with '--tablefile=OUTPUTFILE'
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] aparcstats2table - append option

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Re: [Freesurfer] aparcstats2table - append option

[Siegel-Ramsay, Jennifer]

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Horn, Mitchell Jacob 

Sent: Tuesday, December 12, 2023 9:10:22 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] aparcstats2table - append option


Hi FS Devs,



Would it be possible to add an “append” flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.



Thanks,

Mitch
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Re: [Freesurfer] aparcstats2table - append option

[Horn, Mitchell Jacob]

Exactly.

My understanding (and correct me if I'm wrong) is that both commands 
create/overwrite the specified --tablefile each time it's run.

Best,
Mitch


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Monday, December 18, 2023 8:55 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] aparcstats2table - append option

I would like to confirm that this is what you have in mind:

  1.  the new '-append' flag will work with '--tablefile=OUTPUTFILE'
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] aparcstats2table - append option

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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<https://www.massgeneralbrigham.org/complianceline> .

Re: [Freesurfer] aparcstats2table - append option

[Huang, Yujing]

I would like to confirm that this is what you have in mind:

  1.  the new '-append' flag will work with '--tablefile=OUTPUTFILE'
  2.  when same OUTPUTFILE is specified, new stats output will be appended to 
the end of file

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Horn, Mitchell Jacob
Sent: Tuesday, December 12, 2023 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparcstats2table - append option

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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<https://www.massgeneralbrigham.org/complianceline> .

Re: [Freesurfer] aparcstats2table - IndexError

[Huang, Yujing]

Can you check if you have any extra empty lines after your last ‘Input’?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Laura Willers de Souza
Sent: Thursday, December 14, 2023 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparcstats2table - IndexError


External Email - Use Caution
Hello FreeSurfer Developers,
I'm trying to get the cortical thickness values for a list of subjects using 
aparcstats2table and I'm encountering this error:

aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh 
--common-parcs --tablefile lh.aparc.thickness.table
SUBJECTS_DIR : /mnt/wsl/PHYSICALDRIVE1/FS_OUTPUTS
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 376, 
in 
subj_listoftuples = assemble_inputs(options)
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 273, 
in assemble_inputs
if splitline[0].upper() == 'INPUT':
IndexError: list index out of range

The fsgd file only contains the list of subjects, as illustrated below:
GroupDescriptorFile 1   
Title subjects.test1 
Input 002_S_0295_S13408
Input 002_S_0413_S13893
Input 002_S_0559_S14875

I have successfully executed the same command for an individual subject.
For other measurements (surface area, volume) this error also occurs.

It's worth noting that the images and files for the subjects and recon-all are 
stored on an external hard drive that I have mounted on Linux, emulated on 
Windows. Could this be the source of the problem?

I appreciate any assistance you can provide with resolving this issue.

Thanks in advance!

Laura Willers de Souza

PhD Student in Pharmacology and Therapeutics

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil
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[Freesurfer] aparcstats2table - IndexError

[Laura Willers de Souza]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm trying to get the cortical thickness values for a list of subjects using 
aparcstats2table and I'm encountering this error:

aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh 
--common-parcs --tablefile lh.aparc.thickness.table
SUBJECTS_DIR : /mnt/wsl/PHYSICALDRIVE1/FS_OUTPUTS
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 376, 
in 
subj_listoftuples = assemble_inputs(options)
  File "/usr/local/freesurfer/7.4.1/python/scripts/aparcstats2table", line 273, 
in assemble_inputs
if splitline[0].upper() == 'INPUT':
IndexError: list index out of range

The fsgd file only contains the list of subjects, as illustrated below:
GroupDescriptorFile 1   
Title subjects.test1 
Input 002_S_0295_S13408
Input 002_S_0413_S13893
Input 002_S_0559_S14875

I have successfully executed the same command for an individual subject.
For other measurements (surface area, volume) this error also occurs.

It's worth noting that the images and files for the subjects and recon-all are 
stored on an external hard drive that I have mounted on Linux, emulated on 
Windows. Could this be the source of the problem?

I appreciate any assistance you can provide with resolving this issue.

Thanks in advance!

Laura Willers de Souza

PhD Student in Pharmacology and Therapeutics

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil
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[Freesurfer] aparcstats2table - append option

[Horn, Mitchell Jacob]

Hi FS Devs,

Would it be possible to add an "append" flag for use with aparcstats2table and 
asegstats2table? If I understand their usage correctly, each time one of them 
are run they will create (or overwrite) a new file. Not urgent but would be 
useful.

Thanks,
Mitch
___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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 .

Re: [Freesurfer] aparcstats2table segmentation fault error

[fsbuild]

External Email - Use Caution

You don’t need to manually set MINC_BIN_DIR or the MINC_LIB_DIR variables as 
those should get set when you source the freesurfer setup script.
Try manually running the bash shell, set FREESURFER_HOME, and check you can see 
that directory,
$ bash$ export 
FREESURFER_HOME=/home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0$
 ls $FREESURFER_HOME … output deleted but you should see the top of the 
tree including theSetUpFreeSurfer.sh script you are going to source … 
Then source the setup script,
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted … 
Then try running the command in debug mode and see if you get the help output. 
If you see the help output, then the command ran.
$ bash -x `which aparcstats2table` --help
+ '[' '!' -e 
/home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0']'+ 
exec /homes/1/rd521/freesurfer/dev/bin/fspython 
/homes/1/rd521/freesurfer/dev/python/scripts/aparcstats2table —help … help 
output deleted ... 
- R.
On Nov 15, 2022, at 22:07, fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionDifficult to enlarge 
your screenshots and read the text, but it looks like even though the output 
from the setup script displays the path to FREESSURFER_HOME, the script wrapper 
for the shell cannot verify that path actually exists.  And it looks like 
you are using a “dot” directory named “.local” in your path for FREESURFER_HOME 
which is usually reserved for hidden subdirs in the shell. I would not 
name any subdirectory to begin with a "dot" for normal use with the shell, so 
try$ mv .local local… reset FREESURFER_HOME, source the setup script again, and 
see if running the command works.- R.On Nov 15, 2022, at 19:59, Eric Yin 
eric@mail.utoronto.ca 
wrote:External Email - Use 
CautionHello!I’m trying 
to run the aparcstats2table function on a single participant and I cannot seem 
to get rid of the following segmentation fault error. I checked the forums and 
did not find anyone with the same 
problem.9ECE8F5D2E7645A5962B55E842687C47.pngI have tried a 
few different options. First, I read that aparcstats2table requires PATH to 
lead to python2, but this call would throw the error that freesurfer has not 
been sourced properly even though I sourced it manually. Please find my 
Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 
(Core).4E289904EB384B21861CA9E16B7DD234.pngThen I thought 
that it might be because freesurfer/7.2.0 requires a newer version of python, 
but it also did not work for python3 or 
python3.6.64B17BE84D1E4AFBBF7FFCE28ED15CD7.pngPlease let me 
know if I’m doing something wrong, or if anyone has run into a similar 
issue.Thank you for your 
time.___Freesurfer mailing 
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attempt from "secure-web.cisco.com" claiming to 
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Re: [Freesurfer] aparcstats2table segmentation fault error

[Eric Yin]

External Email - Use Caution

Thanks for your response. I tried moving the .local directory and rerunning the 
command but it still gave me the same error despite the fact that I manually 
corrected all the directories. I attached a screenshot so hopefully the image 
quality is better.

From: fsbuild<mailto:fsbu...@contbay.com>
Sent: November 15, 2022 10:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: Eric Yin<mailto:eric@mail.utoronto.ca>
Subject: Re: [Freesurfer] aparcstats2table segmentation fault error

You don't often get email from fsbu...@contbay.com. Learn why this is 
important<https://secure-web.cisco.com/1lRk6KkAxnHXMoVnv5Yfy7p33mx-_tDw1IO8xyeW-Sc4s2WsE5CIR5wOkEAoipJHfMToVsBCOIzXkR6ueDU-far7wue8zxZ9dXGMmdEIhbP_v0UdSHiu6vvzdkb0wNtE--EEcUFKNEufPcNDV0JzoR24L43466nSyFIhZpOLVio-3KuQ-G9ysIQkUAke4GU6WTSXNiNLLnVhAhuuhKH3THBwYwxCzdmmQBwr1EAszdPM1bHWrsd6TNVfR1PaZr67SI4V3ZEdcz3TrdnhrX06diA6JOq7_K_xu_fTaqYe2EacPmgwugLx0HM7t27Gnx6RnYv3Gwj3koLZrXZRfCq47wA/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification>
Difficult to enlarge your screenshots and read the text, but it looks like even 
though the output from the setup script displays the path to FREESSURFER_HOME, 
the script wrapper for the shell cannot verify that path actually exists.   And 
it looks like you are using a “dot” directory named “.local” in your path for 
FREESURFER_HOME which is usually reserved for hidden subdirs in the shell.  I 
would not name any subdirectory to begin with a "dot" for normal use with the 
shell, so try


$ mv .local local

… reset FREESURFER_HOME, source the setup script again, and see if running the 
command works.

- R.


On Nov 15, 2022, at 19:59, Eric Yin  wrote:

External Email - Use Caution

Hello!

I’m trying to run the aparcstats2table function on a single participant and I 
cannot seem to get rid of the following segmentation fault error. I checked the 
forums and did not find anyone with the same problem.

<9ECE8F5D2E7645A5962B55E842687C47.png>

I have tried a few different options. First, I read that aparcstats2table 
requires PATH to lead to python2, but this call would throw the error that 
freesurfer has not been sourced properly even though I sourced it manually. 
Please find my Freesurfer version in the screenshot as well. I’m running on 
CentOS Linux v7 (Core).

<4E289904EB384B21861CA9E16B7DD234.png>

Then I thought that it might be because freesurfer/7.2.0 requires a newer 
version of python, but it also did not work for python3 or python3.6.

<64B17BE84D1E4AFBBF7FFCE28ED15CD7.png>

Please let me know if I’m doing something wrong, or if anyone has run into a 
similar issue.

Thank you for your time.
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] aparcstats2table segmentation fault error

[fsbuild]

External Email - Use Caution

Difficult to enlarge your screenshots and read the text, but it looks like even 
though the output from the setup script displays the path to FREESSURFER_HOME, 
the script wrapper for the shell cannot verify that path actually exists. 
 And it looks like you are using a “dot” directory named “.local” in your 
path for FREESURFER_HOME which is usually reserved for hidden subdirs in the 
shell. I would not name any subdirectory to begin with a "dot" for normal 
use with the shell, so try

$ mv .local local
… reset FREESURFER_HOME, source the setup script again, and see if running the 
command works.
- R.
On Nov 15, 2022, at 19:59, Eric Yin eric@mail.utoronto.ca 
wrote:External Email - Use 
CautionHello!I’m trying 
to run the aparcstats2table function on a single participant and I cannot seem 
to get rid of the following segmentation fault error. I checked the forums and 
did not find anyone with the same 
problem.9ECE8F5D2E7645A5962B55E842687C47.pngI have tried a 
few different options. First, I read that aparcstats2table requires PATH to 
lead to python2, but this call would throw the error that freesurfer has not 
been sourced properly even though I sourced it manually. Please find my 
Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 
(Core).4E289904EB384B21861CA9E16B7DD234.pngThen I thought 
that it might be because freesurfer/7.2.0 requires a newer version of python, 
but it also did not work for python3 or 
python3.6.64B17BE84D1E4AFBBF7FFCE28ED15CD7..pngPlease let 
me know if I’m doing something wrong, or if anyone has run into a similar 
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Re: [Freesurfer] aparcstats2table command

[Douglas N. Greve]

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
instead of listing all the subjects on the command line, put all the 
subjects names in a file and use --subjectsfile=SUBJECTSFILE



On 10/20/2022 12:03 PM, eso wrote:


External Email - Use Caution

Hi Freesurfer experts,

I am new to the Freesurfer world !

My question is how to use aparcstats2table to extract data for a large 
number of subjects (approximately 700 subjects).


I have tried to paste the folder path that included all the 
pre-processed images, but it has not worked.


Anything will help

Thanks

Esraa


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[Freesurfer] aparcstats2table command

[eso]

External Email - Use Caution

Hi Freesurfer experts,



I am new to the Freesurfer world !

My question is how to use aparcstats2table to extract data for a large
number of subjects (approximately 700 subjects).

I have tried to paste the folder path that included all the pre-processed
images, but it has not worked.

Anything will help









Thanks

Esraa
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[Freesurfer] aparcstats2table

[Saman Fouladi]

External Email - Use Caution

 hi

I run in linux command:
"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats
--parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats
.txt
"""
but show below error an i can not solve it nix:

"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
"""

I changed the code several times, but in all cases there is this error.
This error also happens to asegstats2table.

please help me
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Re: [Freesurfer] aparcstats2table {Disarmed}

[Kiyotaka Nemoto]

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Hi,

Suppose the fsid of your subj10 is subj10 and you set SUBJECTS_DIR
correctly to /home/team33/MRI4,

the command should be

aparcstats2table --hemi lh --subjects subj10 --parc aparc.a2009s  --meas
meancurv --tablefile /home/team33/aparcstats.txt

I noticed that there is a space between team33/ and aparcstats.txt, which
will cause another problem.

Hope this helps,

Kiyotaka



2020/11/5 0:24 saman fouladi :

> External Email - Use Caution
>
> hi
>
> I run in linux command:
> """
> aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats
> --parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats
> .txt
> """
> but show below error an i can not solve it nix:
>
> """
>  File "/usr/local/freesurfer/bin/aparcstats2table", line 156
> print 'ERROR: atleast 1 subject must be provided'
> """
>
> I changed the code several times, but in all cases there is this error.
> This error also happens to asegstats2table.
>
> please help me
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyot...@nemotos.net
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[Freesurfer] aparcstats2table

[saman fouladi]

External Email - Use Caution

hi
 I run in linux command:"""
aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats --parc 
aparc.a2009s  --meas meancurv --tablefile /home/team33/ 
aparcstats.txt"""
but show below error an i can not solve it nix:
"""
 File "/usr/local/freesurfer/bin/aparcstats2table", line 156
    print 'ERROR: atleast 1 subject must be provided'
"""
I changed the code several times, but in all cases there is this error.
 This error also happens to asegstats2table. 

please help me
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Re: [Freesurfer] aparcstats2table error

[Rovai Antonin]

External Email - Use Caution

Hi Devika,
I ran into the same issue and in case you don’t want to change your PATH (like 
me), another option is to edit aparcstats2table script and simply replace the 
shebang from “#!/usr/bin/env python” to e.g. “#!/usr/bin/env python2” (please 
make sure “which python2” returns something in a terminal).
Cheers
Antonin

On 19 Jan 2020, at 20:35, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must 
be run with python2. Your error implies that the python in your PATH points to 
python3. You should make sure python points to a python2 version before running 
freesurfer. Sorry for the inconvenience.
Andrew


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Devika K mailto:devikakutt...@gmail.com>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, January 19, 2020 at 9:09 AM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] aparcstats2table error


External Email - Use Caution

I tried doing cortical parcellation using Destrieux atlas.  I ran the 
aparcstats2table command from the SUBJECTS_DIR directory containing all of the 
output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running 
aparcstats2table command, I would be grateful if anyone could  help me to 
resolve this issue.

Many thanks in advance.
[Image removed by sender.]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu<mailto:k_dev...@cb.students.amrita.edu>
Amrita Vishwa Vidyapeetham
Coimbatore, India


[Hôpital Erasme]

Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer>

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Re: [Freesurfer] aparcstats2table

[Douglas N. Greve]

yes

On 2/25/20 2:05 AM, Devika K wrote:
>
> External Email - Use Caution
>
> Hi,
>
> Can I use the below command to extract the cortical thickness using 
> Destrieux Atlas from longitudinally preprocessed subjects?
> aparcstats2table --hemi lh \
>--subjects 004 021 040 067 080 092 \
>--meas thickness \
>--parc aparc.a2009s \
>--tablefile lh.aparc.a2009.thickness.table
> Regards
> Devika K
>
>
>
>
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Re: [Freesurfer] aparcstats2table

[Devika K]

External Email - Use Caution

Hi,

Can I use the below command to extract the cortical thickness using
Destrieux Atlas from longitudinally preprocessed subjects?

aparcstats2table --hemi lh \
  --subjects 004 021 040 067 080 092 \
  --meas thickness \
  --parc aparc.a2009s \
  --tablefile lh.aparc.a2009.thickness.table

Regards
Devika K
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Re: [Freesurfer] aparcstats2table error

[Hoopes, Andrew]

Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must 
be run with python2. Your error implies that the python in your PATH points to 
python3. You should make sure python points to a python2 version before running 
freesurfer. Sorry for the inconvenience.
Andrew


From:  on behalf of Devika K 

Reply-To: FS Help 
Date: Sunday, January 19, 2020 at 9:09 AM
To: FS Help 
Subject: Re: [Freesurfer] aparcstats2table error


External Email - Use Caution
I tried doing cortical parcellation using Destrieux atlas.  I ran the 
aparcstats2table command from the SUBJECTS_DIR directory containing all of the 
output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running 
aparcstats2table command, I would be grateful if anyone could  help me to 
resolve this issue.

Many thanks in advance.
[Image removed by sender.]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu<mailto:k_dev...@cb.students.amrita.edu>
Amrita Vishwa Vidyapeetham
Coimbatore, India

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Re: [Freesurfer] aparcstats2table error

[Bruce Fischl]

Hi Devika

In the future can you include the text of the command and the output in 
your email instead of a screenshot? That will make our job easier.


Try specifying which subjects you want processed explicitly with 
--subjects


cheers
Bruce

On Sun, 19 Jan 
2020, Devika K wrote:




External Email - Use Caution

I tried doing cortical parcellation using Destrieux atlas.  I ran the
aparcstats2table command from the SUBJECTS_DIR directory containing all of
the output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running
aparcstats2table command, I would be grateful if anyone could  help me to
resolve this issue.

Many thanks in advance.[cleardot.gif]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India


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Re: [Freesurfer] aparcstats2table

[Greve, Douglas N.,Ph.D.]

I can't replicate the error (even when using the same subject name), so 
I'm not sure what to say. The only think I can think of is that it is 
something in your environment that is causing the strangeness. Can 
someone you work with run the command to see if the same error happens?

On 5/14/19 5:05 PM, Alan Francis wrote:
>
> External Email - Use Caution
>
> Hi Doug:
>
> I used the following command:
>
> [airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table 
> --subjects 100610 --hemi rh --meas thickness --tablefile aparc_stats.txt
>
> However, I got an error message:
>
>   File "/usr/local/freesurfer/stable6/bin/aparcstats2table", line 156
>     print 'ERROR: atleast 1 subject must be provided'
> ^
> SyntaxError: Missing parentheses in call to 'print'. Did you mean 
> print('ERROR: atleast 1 subject must be provided')?
>
> I have used this command on several occasions without any problems, so 
> this is quite puzzling.
>
> Could you please help.
>
> Thanks,
>
> Alan
>
> -- 
> /|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|/
> /*
> *Alan N. Francis PhD
> Instructor in Psychiatry
> Harvard Medical School
> /
> /
> Louis V. Gerstner III scholar
> Martinos Center for Biomedical Imaging
> /
> /Massachusetts General Hospital
> /
> /149, 13th street, Charlestown, MA
> /
> /al...@bwh.harvard.edu 
> /
> /afran...@mclean.harvard.edu /
>
>
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[Freesurfer] aparcstats2table

[Alan Francis]

External Email - Use Caution

Hi Doug:

I used the following command:

[airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects
100610 --hemi rh --meas thickness --tablefile aparc_stats.txt

However, I got an error message:

  File "/usr/local/freesurfer/stable6/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean
print('ERROR: atleast 1 subject must be provided')?

I have used this command on several occasions without any problems, so this
is quite puzzling.

Could you please help.

Thanks,

Alan

-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*




*Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School*



*Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging*

*Massachusetts General Hospital*

*149, 13th street, Charlestown, MA*

*al...@bwh.harvard.edu  *
*afran...@mclean.harvard.edu *
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Re: [Freesurfer] aparcstats2table --parcs-from-file trouble

[Greve, Douglas N.,Ph.D.]

If you are using output froom mri_segstats, then you need to use 
asegstats2table, not aparcstats2table. It can be confusing ...

On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote:
>
> Hi,
>
>
> I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg 
> --> mri_segstats .
>
> Now I am trying to extract the summary table using aparcstats2table 
> --parcs-from-file , but every time an error message pops up:
>
>
> ERROR: cannot read 
>
>
> The stats files generated by the mri_segstats look correct (similar 
> with the other files in the directory) and I can read the volumes of 
> each individual.
>
>
> The last command that has an error is:
>
>
> aparcstats2table --qdec-long qdec.txt --hemi lh --meas volume 
> --parcs-from-file  --tablefile volumes.txt
>
>
> I really appreciate any help!
>
> Thanks!
>
> Gabriela
>
>
>
>
>
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[Freesurfer] aparcstats2table --parcs-from-file trouble

[Figueiro Longo, Maria Gabriela]

Hi,


I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg --> 
mri_segstats .

Now I am trying to extract the summary table using aparcstats2table 
--parcs-from-file , but every time an error message pops up:


ERROR: cannot read 


The stats files generated by the mri_segstats look correct (similar with the 
other files in the directory) and I can read the volumes of each individual.


The last command that has an error is:


aparcstats2table --qdec-long qdec.txt --hemi lh --meas volume --parcs-from-file 
 --tablefile volumes.txt


I really appreciate any help!

Thanks!

Gabriela


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Re: [Freesurfer] aparcstats2table for white surface total area

[Douglas N. Greve]

If you just run aparcstats2table it should be in the table. I don't 
think there is a way to only get that value


On 04/26/2018 11:20 AM, Sian Emma Davies wrote:
>
> External Email - Use Caution
>
> Hello,
>
> Forgive me, I’m new to FreeSurfer. I wish to collate values of white 
> surface total area from all my subjects into a single table, so that I 
> can control for this in my analyses. I understand this value is in the 
> aparc.stats files for each participant and hemisphere, so I have tried:
>
> aparcstats2table –subjectfile sublist –hemi lh –meas WhiteSurfArea 
> –tablefile aparc_stats_lh.wsa.table
>
> but WhiteSurfArea isn’t an option for –meas. Please let me know if you 
> can help,
>
> Many thanks,
>
> Emma Davies
>
> PhD Student
>
> Department of Psychiatry
>
> University of Cambridge
>
> Douglas House
>
> 18b Trumpington Road
>
> Cambridge
>
> CB2 8AH
>
>
>
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[Freesurfer] aparcstats2table for white surface total area

[Sian Emma Davies]

External Email - Use Caution

Hello,

Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface 
total area from all my subjects into a single table, so that I can control for 
this in my analyses. I understand this value is in the aparc.stats files for 
each participant and hemisphere, so I have tried:

aparcstats2table -subjectfile sublist -hemi lh -meas WhiteSurfArea -tablefile 
aparc_stats_lh.wsa.table

but WhiteSurfArea isn't an option for -meas. Please let me know if you can help,

Many thanks,

Emma Davies
PhD Student

Department of Psychiatry
University of Cambridge
Douglas House
18b Trumpington Road
Cambridge
CB2 8AH

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Re: [Freesurfer] aparcstats2table subject space?

[Douglas N Greve]

Yes, it is in native subject space


On 02/07/2018 07:35 AM, Kasper Jessen wrote:
>
> Dear FreeSurfer,
>
> When you extract e.g. thickness from the command aparcstats2table – is 
> the data extracted from subject space?
>
> We need to know whether or not, we need to covariate for total brain 
> volume.
>
> Bw
>
> Kasper
>
> Kasper Jessen,
>
> MD, PhD student
> Center for Neuropsychiatric Schizophrenia Research (CNSR)
>
> Mental Health Centre Glostrup
>
> Nordre Ringvej 29-67
>
> 2600 Glostrup
> Tlf.: 24430136
> E-mail: kasper.jes...@regionh.dk 
>
>
> 
>
>
> Denne e-mail indeholder fortrolig information. Hvis du ikke er den 
> rette modtager af denne e-mail eller hvis du modtager den ved en 
> fejltagelse, beder vi dig venligst informere afsender om fejlen ved at 
> bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme 
> uden at videresende eller kopiere den.
>
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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
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[Freesurfer] aparcstats2table subject space?

[Kasper Jessen]

Dear FreeSurfer,

When you extract e.g. thickness from the command aparcstats2table - is the data 
extracted from subject space?

We need to know whether or not, we need to covariate for total brain volume.

Bw
Kasper

Kasper Jessen,
MD, PhD student
Center for Neuropsychiatric Schizophrenia Research (CNSR)
Mental Health Centre Glostrup
Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kasper.jes...@regionh.dk





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Re: [Freesurfer] aparcstats2table

[Douglas Greve]

Why don't you just create a fake directory structure. Should be pretty 
easy to script (if you know how to script:)



On 1/15/18 3:44 AM, Stephanos Leandrou wrote:


Dear Freesurfer Developers,

I want to use the asegstats2table and aparcstats2table for my 
research. First of all, my subjects (several hundreds) are not in the 
Freesurfer/Subjects directory and for each one I have run the 
recon-all command.


For the asegstats2table command we know that the subjects list can be 
specified in one of four ways:


 1. Specify each subject after -s
  * -s subject1 -s subject2 ..
 2. specify all subjects after --subjects.
  * --subjects does not have to be the last argument. Eg:
  o --subjects subject1 subject2 ...
 3. Specify each input file after -i
  * -i subject1/stats/aseg.stats -i subject2/stat/aseg.stats ..
 4. Specify all the input stat files after --inputs. --inputs does not
have
  * to be the last argument. Eg:
  o --inputs subject1/stats/aseg.stats
subject2/stats/aseg.stats ...

The first two methods assume the freesurfer directory structure. 
The last two are general and can be used with any file produced 
by mri_segstats regardless of whether it was created with recon-all or 
not…..


According to 3 and 4 by changing –subjects to –i I was able to run the 
asegstats2table command for my subjects that are not in the Freesurfer 
directory structure with success.


However, (and here comes my question) I cannot do the same for the 
aparcstats2table because there is no option (if I am not mistaken) to 
run the command for subjects outside the Freesurfer directory 
structure? In the aparcstats2table webpage mentions that the subjects 
list can be specified on either of two ways:


 1. Specify each subject after a -s flag
  * -s subject1 -s subject2 ... --hemi lh
 2. Specify all subjects after --subjects flag. --subjects does not have
  * to be the last argument. Eg:
  o --subject subject1 subject2 ... --hemi lh

However, when I run the command (in the path of my subjects directory 
where the stats folder is) it comes with an error which says that it 
cannot find the stats file in the Freesurfer/directory which is 
expected…as my subjects are not in that directory.


Thank you for your help !!

Stephanos



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[Freesurfer] aparcstats2table

[Stephanos Leandrou]

Dear Freesurfer Developers,

I want to use the asegstats2table and aparcstats2table for my research. First 
of all, my subjects (several hundreds) are not in the Freesurfer/Subjects 
directory and for each one I have run the recon-all command.

For the asegstats2table command we know that the subjects list can be specified 
in one of four ways:

  1.  Specify each subject after -s
 *   -s subject1 -s subject2 ..
  2.  specify all subjects after --subjects.
 *   --subjects does not have to be the last argument. Eg:
*   --subjects subject1 subject2 ...
  3.  Specify each input file after -i
 *   -i subject1/stats/aseg.stats -i subject2/stat/aseg.stats ..
  4.  Specify all the input stat files after --inputs. --inputs does not have
 *   to be the last argument. Eg:
*   --inputs subject1/stats/aseg.stats subject2/stats/aseg.stats ...
The first two methods assume the freesurfer directory structure. The last two 
are general and can be used with any file produced by mri_segstats regardless 
of whether it was created with recon-all or not.
According to 3 and 4 by changing -subjects to -i I was able to run the 
asegstats2table command for my subjects that are not in the Freesurfer 
directory structure with success.

However, (and here comes my question) I cannot do the same for the 
aparcstats2table because there is no option (if I am not mistaken) to run the 
command for subjects outside the Freesurfer directory structure? In the 
aparcstats2table webpage mentions that the subjects list can be specified on 
either of two ways:

  1.  Specify each subject after a -s flag
 *   -s subject1 -s subject2 ... --hemi lh
  2.  Specify all subjects after --subjects flag. --subjects does not have
 *   to be the last argument. Eg:
*   --subject subject1 subject2 ... --hemi lh
However, when I run the command (in the path of my subjects directory where the 
stats folder is) it comes with an error which says that it cannot find the 
stats file in the Freesurfer/directory which is expected...as my subjects are 
not in that directory.

Thank you for your help !!

Stephanos

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Re: [Freesurfer] aparcstats2table surface area

[Douglas Greve]

On 10/24/17 2:37 AM, Kasper Jessen wrote:


Hi FreeSurfer,


We have extracted the surface area using aparcstats2table.

1.The ROIs extracted are by default the White Surface Area, correct?


Correct.


2.Why does the WhiteSurfArea (default average) have decimals but not 
the surface area of the different ROIs? When taking the SUM of all the 
ROIs, it does not equal the WhiteSurfArea and I am thinking this must 
be due to the decimals?


No real reason. Whoever wrote the program that printed them out 
deliberately set it to have no decimal places. It is not clear why


Best Regards

Kasper





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[Freesurfer] aparcstats2table surface area

[Kasper Jessen]

Hi FreeSurfer,

We have extracted the surface area using aparcstats2table.


1.The ROIs extracted are by default the White Surface Area, correct?


2.Why does the WhiteSurfArea (default average) have decimals but not the 
surface area of the different ROIs? When taking the SUM of all the ROIs, it 
does not equal the WhiteSurfArea and I am thinking this must be due to the 
decimals?


Best Regards
Kasper





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Re: [Freesurfer] aparcstats2table

[Douglas N Greve]

This appears to be broken in 5.3. You can do 2 things: (1) specify the 
subjects in a different way, or (2) use the aparcstats2table below. I'm 
not 100% sure it will work in the 5.3 env, so make a backup of your 
aparcstats2table file.

https://gate.nmr.mgh.harvard.edu/safelinks/greve/aparcstats2table

For your other questions

a) average across what? Subject? You can use mri_glmfit --table ..., or 
you can load it into matlab with fast_ldtable and do your averages there

b) Are what in fsaverage space? When you run aparcstats2table you get 
averages in the parcellations of the individual, fsaverage does not come 
into it

c) We don't have anything that will do this easily (a harder problem 
than you might think). I would do it in matlab, loading the annotation 
using read_annotation.m, create a vector of values (one item per 
vertex), then assign all the vertices in a given parcellation the value 
for that parcellation from your average, then write it out as an mgh 
file  using MRIwrite.m




On 11/09/2016 08:27 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> Please find the attached qdec file, along with diagnosis file which I 
> used in QDEC, and this is the same qdec file I trying to use for 
> the aparcstats2table command.
>
> Thanks.
>
> PS: I was also wondering (a) how can I average thickness stats (b) are 
> these in fsaverage (standard) space and (c) how can I display it on 
> standard fsaverage for publications purpose?
>
> On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve 
> > wrote:
>
> can you send the qdec file with variables?
>
>
> On 11/09/2016 11:51 AM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > Somehow even after adding variables, it's not working, although same
> > qdec file works fine when I perform GLM in qdec.
> > So I replaced the flag with subjectsfile and provided subject
> list.txt
> > file. So in that way, it's working fine now.
> >
> > I was also wondering (a) how can I average these thickness stats (b)
> > are these in fsaverage (standard) space and (c) how can I display it
> > on standard fsaverage for publications purpose?
> >
> > Thanks a lot.
> >
> > On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve
> > 
>  >> wrote:
> >
> > Appears to be having problems reading the qdec table. It
> might be
> > expecting the qdec table to actually variables in it. Can
> you try
> > adding variables? Also, try it without the --qdec flag instead
> > specifying the subjects with --subjects HC003_1 HC004_1 ...
> >
> >
> > On 11/8/16 8:09 PM, Martin Juneja wrote:
> >> Hi everyone,
> >>
> >> I am trying to use following command to save stats from a
> set of
> >> subjects in a table format:
> >>
> >> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t
> >> zzz.txt
> >>
> >> But after I run this, I get following error:
> >>
> >> Traceback (most recent call last):
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line
> 353, in
> >> 
> >>
> >> subj_listoftuples = assemble_inputs(options)
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line
> 228, in
> >> assemble_inputs
> >>
> >> fsid=row['fsid'].strip()
> >>
> >> KeyError: 'fsid'
> >>
> >> My qdec.dat file looks like below:
> >>
> >> fsidHC003_1
> >> HC004_1
> >> HC006_1
> >> HC015_1
> >>
> >> This command works fine if I use subject IDs individually
> here e.g.
> >> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1
> >> HC015_1 --hemi lh --meas thickness -t zzz.txt
> >>
> >> Another question I have here is: How can I average these
> >> thickness stats and display it on standard fsaverage?
> >>
> >> Any help would be really appreciated.
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> 
> >>  >
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >>  >
> > ___ Freesurfer
> mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> 
>   

Re: [Freesurfer] aparcstats2table

[Martin Juneja]

Hi Dr. Greve,

Please find the attached qdec file, along with diagnosis file which I used
in QDEC, and this is the same qdec file I trying to use for
the aparcstats2table command.

Thanks.

PS: I was also wondering (a) how can I average thickness stats (b) are
these in fsaverage (standard) space and (c) how can I display it on
standard fsaverage for publications purpose?

On Wed, Nov 9, 2016 at 10:52 AM, Douglas N Greve 
wrote:

> can you send the qdec file with variables?
>
>
> On 11/09/2016 11:51 AM, Martin Juneja wrote:
> > Hi Dr. Greve,
> >
> > Somehow even after adding variables, it's not working, although same
> > qdec file works fine when I perform GLM in qdec.
> > So I replaced the flag with subjectsfile and provided subject list.txt
> > file. So in that way, it's working fine now.
> >
> > I was also wondering (a) how can I average these thickness stats (b)
> > are these in fsaverage (standard) space and (c) how can I display it
> > on standard fsaverage for publications purpose?
> >
> > Thanks a lot.
> >
> > On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve
> > > wrote:
> >
> > Appears to be having problems reading the qdec table. It might be
> > expecting the qdec table to actually variables in it. Can you try
> > adding variables? Also, try it without the --qdec flag instead
> > specifying the subjects with --subjects HC003_1 HC004_1 ...
> >
> >
> > On 11/8/16 8:09 PM, Martin Juneja wrote:
> >> Hi everyone,
> >>
> >> I am trying to use following command to save stats from a set of
> >> subjects in a table format:
> >>
> >> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t
> >> zzz.txt
> >>
> >> But after I run this, I get following error:
> >>
> >> Traceback (most recent call last):
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in
> >> 
> >>
> >> subj_listoftuples = assemble_inputs(options)
> >>
> >>   File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
> >> assemble_inputs
> >>
> >> fsid=row['fsid'].strip()
> >>
> >> KeyError: 'fsid'
> >>
> >> My qdec.dat file looks like below:
> >>
> >> fsidHC003_1
> >> HC004_1
> >> HC006_1
> >> HC015_1
> >>
> >> This command works fine if I use subject IDs individually here e.g.
> >> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1
> >> HC015_1 --hemi lh --meas thickness -t zzz.txt
> >>
> >> Another question I have here is: How can I average these
> >> thickness stats and display it on standard fsaverage?
> >>
> >> Any help would be really appreciated.
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> 
> > ___ Freesurfer mailing
> > list Freesurfer@nmr.mgh.harvard.edu
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >  The
> > information in this e-mail is intended only for the person to whom
> > it is addressed. If you believe this e-mail was sent to you in
> > error and the e-mail contains patient information, please contact
> > the Partners Compliance HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was sent
> > to you in error but does not contain patient information, please
> > contact the sender and properly dispose of the e-mail.
> >
> > ___
> > 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


Diagnosis_HC_PRE
Description: Binary data


qdec.HC.dat
Description: Binary data
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Re: [Freesurfer] aparcstats2table

[Douglas N Greve]

can you send the qdec file with variables?


On 11/09/2016 11:51 AM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> Somehow even after adding variables, it's not working, although same 
> qdec file works fine when I perform GLM in qdec.
> So I replaced the flag with subjectsfile and provided subject list.txt 
> file. So in that way, it's working fine now.
>
> I was also wondering (a) how can I average these thickness stats (b) 
> are these in fsaverage (standard) space and (c) how can I display it 
> on standard fsaverage for publications purpose?
>
> Thanks a lot.
>
> On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve 
> > wrote:
>
> Appears to be having problems reading the qdec table. It might be
> expecting the qdec table to actually variables in it. Can you try
> adding variables? Also, try it without the --qdec flag instead
> specifying the subjects with --subjects HC003_1 HC004_1 ...
>
>
> On 11/8/16 8:09 PM, Martin Juneja wrote:
>> Hi everyone,
>>
>> I am trying to use following command to save stats from a set of
>> subjects in a table format:
>>
>> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t
>> zzz.txt
>>
>> But after I run this, I get following error:
>>
>> Traceback (most recent call last):
>>
>>   File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in
>> 
>>
>> subj_listoftuples = assemble_inputs(options)
>>
>>   File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
>> assemble_inputs
>>
>> fsid=row['fsid'].strip()
>>
>> KeyError: 'fsid'
>>
>> My qdec.dat file looks like below:
>>
>> fsidHC003_1
>> HC004_1
>> HC006_1
>> HC015_1
>>
>> This command works fine if I use subject IDs individually here e.g.
>> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1
>> HC015_1 --hemi lh --meas thickness -t zzz.txt
>>
>> Another question I have here is: How can I average these
>> thickness stats and display it on standard fsaverage?
>>
>> Any help would be really appreciated.
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
> ___ Freesurfer mailing
> list Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  The
> information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in
> error and the e-mail contains patient information, please contact
> the Partners Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in error but does not contain patient information, please
> contact the sender and properly dispose of the e-mail. 
>
> ___
> 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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Re: [Freesurfer] aparcstats2table

[Martin Juneja]

Hi Dr. Greve,

Somehow even after adding variables, it's not working, although same qdec
file works fine when I perform GLM in qdec.
So I replaced the flag with subjectsfile and provided subject list.txt
file. So in that way, it's working fine now.

I was also wondering (a) how can I average these thickness stats (b) are
these in fsaverage (standard) space and (c) how can I display it on
standard fsaverage for publications purpose?

Thanks a lot.

On Wed, Nov 9, 2016 at 7:39 AM, Douglas Greve 
wrote:

> Appears to be having problems reading the qdec table. It might be
> expecting the qdec table to actually variables in it. Can you try adding
> variables? Also, try it without the --qdec flag instead specifying the
> subjects with --subjects HC003_1 HC004_1 ...
>
> On 11/8/16 8:09 PM, Martin Juneja wrote:
>
> Hi everyone,
>
> I am trying to use following command to save stats from a set of subjects
> in a table format:
>
> aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt
>
> But after I run this, I get following error:
>
> Traceback (most recent call last):
>
>   File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in 
>
> subj_listoftuples = assemble_inputs(options)
>
>   File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
> assemble_inputs
>
> fsid=row['fsid'].strip()
>
> KeyError: 'fsid'
>
> My qdec.dat file looks like below:
>
> fsid HC003_1
> HC004_1
> HC006_1
> HC015_1
>
> This command works fine if I use subject IDs individually here e.g.
> aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1
> --hemi lh --meas thickness -t zzz.txt
>
> Another question I have here is: How can I average these thickness stats
> and display it on standard fsaverage?
>
> Any help would be really appreciated.
>
>
>
>
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> e-mail
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Re: [Freesurfer] aparcstats2table

[Douglas Greve]

Appears to be having problems reading the qdec table. It might be 
expecting the qdec table to actually variables in it. Can you try adding 
variables? Also, try it without the --qdec flag instead specifying the 
subjects with --subjects HC003_1 HC004_1 ...



On 11/8/16 8:09 PM, Martin Juneja wrote:

Hi everyone,

I am trying to use following command to save stats from a set of 
subjects in a table format:


aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt

But after I run this, I get following error:

Traceback (most recent call last):

  File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in 

subj_listoftuples = assemble_inputs(options)

  File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in 
assemble_inputs


fsid=row['fsid'].strip()

KeyError: 'fsid'

My qdec.dat file looks like below:

fsidHC003_1
HC004_1
HC006_1
HC015_1

This command works fine if I use subject IDs individually here e.g.
aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1 
--hemi lh --meas thickness -t zzz.txt


Another question I have here is: How can I average these thickness 
stats and display it on standard fsaverage?


Any help would be really appreciated.




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[Freesurfer] aparcstats2table

[Martin Juneja]

Hi everyone,

I am trying to use following command to save stats from a set of subjects
in a table format:

aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt

But after I run this, I get following error:

Traceback (most recent call last):

  File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in 

subj_listoftuples = assemble_inputs(options)

  File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in
assemble_inputs

fsid=row['fsid'].strip()

KeyError: 'fsid'

My qdec.dat file looks like below:

fsid
HC003_1
HC004_1
HC006_1
HC015_1

This command works fine if I use subject IDs individually here e.g.
aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1
--hemi lh --meas thickness -t zzz.txt

Another question I have here is: How can I average these thickness stats
and display it on standard fsaverage?

Any help would be really appreciated.
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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

Hi Doug, 

I get the following error when I use 'foldind' in this command >> 
aparcstats2table --hemi lh --subjectsfile 
$SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc rostralmiddlefrontal.label 
--meas foldind --tablefile 
$SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt

aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose 
from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')

Isn't it an option for aparcstats2table yet? Should I make a matlab or python 
script to extract it?

Thanks!
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 13, 2015 6:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures

Use foldind


On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
> Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
> allows to make a table with the folding index measure? If so, what variable 
> should I use in the flag -meas?
>
> Best,
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, November 12, 2015 11:26 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>
> you have to run it separately
>
> On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
>> Dear experts,
>>
>> I am using aparcstats2table to extract values on a number of measures
>> like thickness, curvature, folding index, and surface area for
>> specific ROIs. Is it possible to create a table (using
>> aparcstats2table)  with all these measures included or do I have to
>> run it separately and create a separate table for each measure?
>> Passing --meas flag multiple items did not work.
>>
>> Thanks for your help!
>> Hamdi
>>
>>
>>
>>
>>
>>
>> ___
>> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Douglas N Greve]

what version of FS are you using? When I run

aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat

it runs fine


On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> I get the following error when I use 'foldind' in this command >> 
> aparcstats2table --hemi lh --subjectsfile 
> $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc 
> rostralmiddlefrontal.label --meas foldind --tablefile 
> $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt
>
> aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose 
> from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
>
> Isn't it an option for aparcstats2table yet? Should I make a matlab or python 
> script to extract it?
>
> Thanks!
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, November 13, 2015 6:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>
> Use foldind
>
>
> On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
>> Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
>> allows to make a table with the folding index measure? If so, what variable 
>> should I use in the flag -meas?
>>
>> Best,
>> Hamdi
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, November 12, 2015 11:26 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>>
>> you have to run it separately
>>
>> On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
>>> Dear experts,
>>>
>>> I am using aparcstats2table to extract values on a number of measures
>>> like thickness, curvature, folding index, and surface area for
>>> specific ROIs. Is it possible to create a table (using
>>> aparcstats2table)  with all these measures included or do I have to
>>> run it separately and create a separate table for each measure?
>>> Passing --meas flag multiple items did not work.
>>>
>>> Thanks for your help!
>>> Hamdi
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

I'm using 5.0. It's a version issue then. Thanks Doug! 



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, November 16, 2015 12:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures

what version of FS are you using? When I run

aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat

it runs fine


On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> I get the following error when I use 'foldind' in this command >> 
> aparcstats2table --hemi lh --subjectsfile 
> $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc 
> rostralmiddlefrontal.label --meas foldind --tablefile 
> $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt
>
> aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose 
> from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
>
> Isn't it an option for aparcstats2table yet? Should I make a matlab or python 
> script to extract it?
>
> Thanks!
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, November 13, 2015 6:27 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>
> Use foldind
>
>
> On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
>> Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
>> allows to make a table with the folding index measure? If so, what variable 
>> should I use in the flag -meas?
>>
>> Best,
>> Hamdi
>>
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, November 12, 2015 11:26 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>>
>> you have to run it separately
>>
>> On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
>>> Dear experts,
>>>
>>> I am using aparcstats2table to extract values on a number of measures
>>> like thickness, curvature, folding index, and surface area for
>>> specific ROIs. Is it possible to create a table (using
>>> aparcstats2table)  with all these measures included or do I have to
>>> run it separately and create a separate table for each measure?
>>> Passing --meas flag multiple items did not work.
>>>
>>> Thanks for your help!
>>> Hamdi
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Douglas Greve]

Use foldind


On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
> Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
> allows to make a table with the folding index measure? If so, what variable 
> should I use in the flag -meas?
>
> Best,
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, November 12, 2015 11:26 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
>
> you have to run it separately
>
> On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
>> Dear experts,
>>
>> I am using aparcstats2table to extract values on a number of measures
>> like thickness, curvature, folding index, and surface area for
>> specific ROIs. Is it possible to create a table (using
>> aparcstats2table)  with all these measures included or do I have to
>> run it separately and create a separate table for each measure?
>> Passing --meas flag multiple items did not work.
>>
>> Thanks for your help!
>> Hamdi
>>
>>
>>
>>
>>
>>
>> ___
>> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
allows to make a table with the folding index measure? If so, what variable 
should I use in the flag -meas? 

Best,
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, November 12, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures

you have to run it separately

On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
> Dear experts,
>
> I am using aparcstats2table to extract values on a number of measures
> like thickness, curvature, folding index, and surface area for
> specific ROIs. Is it possible to create a table (using
> aparcstats2table)  with all these measures included or do I have to
> run it separately and create a separate table for each measure?
> Passing --meas flag multiple items did not work.
>
> Thanks for your help!
> Hamdi
>
>
>
>
>
>
> ___
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[Douglas N Greve]

you have to run it separately

On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
> Dear experts,
>
> I am using aparcstats2table to extract values on a number of measures 
> like thickness, curvature, folding index, and surface area for 
> specific ROIs. Is it possible to create a table (using 
> aparcstats2table)  with all these measures included or do I have to 
> run it separately and create a separate table for each measure? 
> Passing --meas flag multiple items did not work.
>
> Thanks for your help!
> Hamdi
>
>
>
>
>
>
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[Freesurfer] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

Dear experts,

I am using aparcstats2table to extract values on a number of measures like 
thickness, curvature, folding index, and surface area for specific ROIs. Is it 
possible to create a table (using aparcstats2table)  with all these measures 
included or do I have to run it separately and create a separate table for each 
measure? Passing --meas flag multiple items did not work.

Thanks for your help!
Hamdi




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Re: [Freesurfer] aparcstats2table

[Douglas N Greve]

white

On 11/05/2015 04:18 PM, Yang, Daniel wrote:
> Dear FreeSurfer Experts,
>
> When I perform aparcstats2table —meas area, does it get it pial.area 
> or white area?
>
> I believe it is the pial.area, but this is not documented. If yes, 
> what can I obtain white area via aparcstats2table?
>
> Thanks,
> Daniel
>
> -- 
> Daniel Yang, Ph.D.
> Yale Child Study Center
> E-mail: daniel.yj.y...@yale.edu
>
>
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[Freesurfer] aparcstats2table

[Yang, Daniel]

Dear FreeSurfer Experts,

When I perform aparcstats2table —meas area, does it get it pial.area or white 
area?

I believe it is the pial.area, but this is not documented. If yes, what can I 
obtain white area via aparcstats2table?

Thanks,
Daniel

--
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Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] Aparcstats2table Insula Thickness is Zero

[Douglas Greve]

Can you send the command and terminal output?

On 9/24/15 2:23 PM, Popal, Haroon (NIH/NIMH) [F] wrote:

Hello,

When I use aparcstats2table to pull thickness values of the Desikan 
atlas, I get a value of zero for two of my subject’s insula thickness 
in both hemispheres. For these two subjects, I also get values for 
“lh_unknown_thickness” and “lh_corpuscallosum_thickness”, while all of 
the other subjects have zeros for those two extra columns.


Can anyone help me with this issue?

Haroon S. Popal
Postbaccalaureate Research Fellow
Laboratory of Brain and Cognition
NIMH, NIH



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[Freesurfer] Aparcstats2table Insula Thickness is Zero

[Popal, Haroon (NIH/NIMH) [F]]

Hello,

When I use aparcstats2table to pull thickness values of the Desikan atlas, I 
get a value of zero for two of my subject’s insula thickness in both 
hemispheres. For these two subjects, I also get values for 
“lh_unknown_thickness” and “lh_corpuscallosum_thickness”, while all of the 
other subjects have zeros for those two extra columns.

Can anyone help me with this issue?

Haroon S. Popal
Postbaccalaureate Research Fellow
Laboratory of Brain and Cognition
NIMH, NIH

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Re: [Freesurfer] aparcstats2table for functional overlay

[Douglas N Greve]

You can use mri_segstats to create a stats file which averages the data 
over an ROI (you can pass it an annotation). If you do this for each 
individual, you then run asegstats2table passing it each of the 
individual tables (don't be fooled by the name of asegstats2table, it is 
just the program that converts the output of mri_segstats into a table 
and does not really have anything to do with aseg)

doug


On 05/18/2014 06:09 PM, Jonathan DuBois wrote:
 Hi all,

 I was wondering if there was a script like aparcstats2table that would 
 accept a functional overlay file that has been sampled to the surface 
 as a measure instead of the available options for structural measures?

 In tksurfer there is a manual way to average over an ROI using the 
 sig.mgh and the y.fsgd file, marking the label and exporting the 
 average graph. I would like to do something similar. Is there anything 
 like this avaiable?

 Thanks,
 Jonathan


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[Freesurfer] aparcstats2table for functional overlay

[Jonathan DuBois]

Hi all,

I was wondering if there was a script like aparcstats2table that would
accept a functional overlay file that has been sampled to the surface as a
measure instead of the available options for structural measures?

In tksurfer there is a manual way to average over an ROI using the sig.mgh
and the y.fsgd file, marking the label and exporting the average graph. I
would like to do something similar. Is there anything like this avaiable?

Thanks,
Jonathan
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[Freesurfer] aparcstats2table question

[Jonathan Holt]

Hi FS experts,

I’m about to run aparcstats2table for a longitudinal study, and I’m wondering 
seeing as I’ve already written a longitudinal qdec table that includes subject 
IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3 
… etc AND the qdec to aparcstats2table or should I just pass the qdec?

I only ask as the tutorial says -subjects is required, but it seems redundant 
and I wanted to verify.

jon
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Re: [Freesurfer] aparcstats2table question

[Douglas Greve]

I think you just need the qdec table.
doug


On 11/11/13 11:27 AM, Jonathan Holt wrote:
 Hi FS experts,

 I’m about to run aparcstats2table for a longitudinal study, and I’m wondering 
 seeing as I’ve already written a longitudinal qdec table that includes 
 subject IDs under the fsid column, is it necessary to pass -subjects subj1 
 subj2 subj3 … etc AND the qdec to aparcstats2table or should I just pass the 
 qdec?

 I only ask as the tutorial says -subjects is required, but it seems redundant 
 and I wanted to verify.

 jon
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Re: [Freesurfer] aparcstats2table for multiple labels

[Douglas Greve]

The only way to do what you want is to combine the labels into an 
annotation file (mris_label2annot), then run mris_anatomical_stats on 
the annot, then you can run aparcstats2table on the output of that. This 
may or may not be easier than doing what you are already doing.
doug.


On 11/10/13 3:58 PM, Chung, Yoonho wrote:
 Dear fs experts,

 I have created 5 customized labels that I want to extract mean thickness from 
 each subject. Is there a way to generate a text file for all the labels I 
 made?
 For example, aparcstats2table --parc option only allows to read one label at 
 a time. I am wondering if there is a way for this function to take all 5 
 labels I created so that I will have all the measures in one text file. Right 
 now I have to do them independently for each label and manually combine them 
 together into one text file.

 Thanks!
 Yoon




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[Freesurfer] aparcstats2table for multiple labels

[Chung, Yoonho]

Dear fs experts,

I have created 5 customized labels that I want to extract mean thickness from 
each subject. Is there a way to generate a text file for all the labels I made?
For example, aparcstats2table --parc option only allows to read one label at a 
time. I am wondering if there is a way for this function to take all 5 labels I 
created so that I will have all the measures in one text file. Right now I have 
to do them independently for each label and manually combine them together into 
one text file.

Thanks!
Yoon




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[Freesurfer] aparcstats2table error

[Corinna Bauer]

Hi;
I want to put cortical thickness in a table format and am getting an error.
command:

aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas
thickness --tablefile symm_aparc_stats_rh.txt

error:
ERROR: The stats file
/media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.stats is not
found or is too small to be a valid statsfile


The statsfile is there and is not empty.
Subject names are all in this format ABC_12345678

Any suggestions?

Thanks

Corinna
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Re: [Freesurfer] aparcstats2table error

[Douglas Greve]

Hi Corinna, is it just that subject or does it happen on more? Can you 
send me the stats file?

doug


On 10/17/13 3:55 PM, Corinna Bauer wrote:

Hi;
I want to put cortical thickness in a table format and am getting an 
error.

command:

aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas 
thickness --tablefile symm_aparc_stats_rh.txt


error:
ERROR: The stats file 
/media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.stats is 
not found or is too small to be a valid statsfile



The statsfile is there and is not empty.
Subject names are all in this format ABC_12345678

Any suggestions?

Thanks

Corinna


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[Freesurfer] aparcstats2table for manually drawn ROIs

[Jackie Lam]

Hi there,

So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn 
my ROIs, used mris_anatomical_stats to create a .stats files for each subject 
from my hand drawn ROIs and now I want to use aparcstats2table to gather the 
thicknesses from all my subjects Is there an option to gather stats from a 
particular .stats file rather than from just the two parcellation atlases? I 
think there is something similar in asegstats2table (--stats=lh.xxx.stats), but 
is there something like that for aparcstats2table?

Many thanks,

Jack
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Re: [Freesurfer] aparcstats2table for manually drawn ROIs

[Tara Ann Miskovich]

Hi Jack,

You can specify the .stats file created. Here is an example from the script I 
use.

Anyone, correct me if this is wrong!

Tara

mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f 
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial

aparcstats2table --hemi lh \
--subjects sub1 sub2 sub3 \
   --meas thickness \
   --parc lh_frontal_surface \
   --tablefile lh.frontal_thickness.stats.txt


- Original Message -
From: Jackie Lam jackie@mail.mcgill.ca
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 3, 2013 12:51:21 PM
Subject: [Freesurfer] aparcstats2table for manually drawn ROIs

Hi there,

So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn 
my ROIs, used mris_anatomical_stats to create a .stats files for each subject 
from my hand drawn ROIs and now I want to use aparcstats2table to gather the 
thicknesses from all my subjects Is there an option to gather stats from a 
particular .stats file rather than from just the two parcellation atlases? I 
think there is something similar in asegstats2table (--stats=lh.xxx.stats), but 
is there something like that for aparcstats2table?

Many thanks,

Jack
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Re: [Freesurfer] aparcstats2table for manually drawn ROIs

[Jackie Lam]

Hi Tara,

Brilliant, that's exactly what I need. For some reason I was under the 
impression that the --parc flag was restricted to either the Killiany/Desikan 
atlas or the Destrieux atlas. Thanks again!

Jack

On 2013-10-03, at 2:03 PM, Tara Ann Miskovich misko...@uwm.edu
 wrote:

 Hi Jack,
 
 You can specify the .stats file created. Here is an example from the script I 
 use.
 
 Anyone, correct me if this is wrong!
 
 Tara
 
 mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f 
 ${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
 
 aparcstats2table --hemi lh \
 --subjects sub1 sub2 sub3 \
   --meas thickness \
   --parc lh_frontal_surface \
   --tablefile lh.frontal_thickness.stats.txt
 
 
 - Original Message -
 From: Jackie Lam jackie@mail.mcgill.ca
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, October 3, 2013 12:51:21 PM
 Subject: [Freesurfer] aparcstats2table for manually drawn ROIs
 
 Hi there,
 
 So I've run recon-all on my group of subjects, ran them in QDEC, manually 
 drawn my ROIs, used mris_anatomical_stats to create a .stats files for each 
 subject from my hand drawn ROIs and now I want to use aparcstats2table to 
 gather the thicknesses from all my subjects Is there an option to gather 
 stats from a particular .stats file rather than from just the two 
 parcellation atlases? I think there is something similar in asegstats2table 
 (--stats=lh.xxx.stats), but is there something like that for aparcstats2table?
 
 Many thanks,
 
 Jack
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 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
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 properly
 dispose of the e-mail.
 


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Re: [Freesurfer] aparcstats2table error

[Alex Hanganu]

Thank you for your quick answer.

Chris - 
it's /stats/ in the address.

Doug - 
Thanks, mris_anatomical_stats works. For this it was also necessary to copy the 
.label file in each subjects - /label/ directory


Alex

--- En date de : Jeu 24.2.11, Chris Hyatt chy...@harthosp.org a écrit :

De: Chris Hyatt chy...@harthosp.org
Objet: Re: [Freesurfer] aparcstats2table error
À: FS Mailing List Freesurfer@nmr.mgh.harvard.edu, Alex Hanganu 
hanganu.alexan...@yahoo.de
Date: Jeudi 24 février 2011,
 18h48


 
You have /stat/ rather than /stats/ in the address. Have you checked that?

 Alex Hanganu hanganu.alexan...@yahoo.de 2/24/2011 12:22 PM 




Dear Chris, Doug,

We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness.

The cmd used:
aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas 
thickness --t ROI.txt

ERROR: cannot find 
.../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

Can you please tell us what might be the problem ?

Sincerely,
Alex.





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Re: [Freesurfer] aparcstats2table error

[Douglas N Greve]

You probably don't want to just copy it. You probably need to transform 
it from what ever space it's in to the individual anat space. Use 
mri_surf2surf.

doug

Alex Hanganu wrote:
 Thank you for your quick answer.

 Chris -
 it's /stats/ in the address.

 Doug -
 Thanks, mris_anatomical_stats works. For this it was also necessary to 
 copy the .label file in each subjects - /label/ directory


 Alex

 --- En date de : *Jeu 24.2.11, Chris Hyatt /chy...@harthosp.org/* a 
 écrit :


 De: Chris Hyatt chy...@harthosp.org
 Objet: Re: [Freesurfer] aparcstats2table error
 À: FS Mailing List Freesurfer@nmr.mgh.harvard.edu, Alex
 Hanganu hanganu.alexan...@yahoo.de
 Date: Jeudi 24 février 2011, 18h48

 You have /stat/ rather than /stats/ in the address. Have you
 checked that?

  Alex Hanganu hanganu.alexan...@yahoo.de 2/24/2011 12:22 PM 
 Dear Chris, Doug,

 We created a ROI in qdec (EXMPL.label) and tried to measure it's
 thickness.

 The cmd used:
 aparcstats2table --hemi ?h --subjects 1 2 3 --parc
 .../DIR/EXMPL.label --meas thickness --t ROI.txt

 ERROR: cannot find
 .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

 Can you please tell us what might be the problem ?

 Sincerely,
 Alex.




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[Freesurfer] aparcstats2table error

[Alex Hanganu]

Dear Chris, Doug,

We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness.

The cmd used:
aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas 
thickness --t ROI.txt

ERROR: cannot find 
.../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

Can you please tell us what might be the problem ?

Sincerely,
Alex.




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Re: [Freesurfer] aparcstats2table error

[Douglas N Greve]

Use mris_anatomical_stats. aparcstats2table is used for combining 
several outputs of mris_anatomical_stats.

Alex Hanganu wrote:
 Dear Chris, Doug,

 We created a ROI in qdec (EXMPL.label) and tried to measure it's 
 thickness.

 The cmd used:
 aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label 
 --meas thickness --t ROI.txt

 ERROR: cannot find 
 .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

 Can you please tell us what might be the problem ?

 Sincerely,
 Alex.


 

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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] aparcstats2table error

[Chris Hyatt]

You have /stat/ rather than /stats/ in the address. Have you checked that?

 Alex Hanganu hanganu.alexan...@yahoo.de 2/24/2011 12:22 PM 

Dear Chris, Doug,

We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness.

The cmd used:
aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas 
thickness --t ROI.txt

ERROR: cannot find 
.../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

Can you please tell us what might be the problem ?

Sincerely,
Alex.


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[Freesurfer] aparcstats2table for std dev associated with av thickness

[Ritobrato Datta]

Hi all

Is there a way to create a multi subject table of the std dev associated with 
av thickness using aparcstats2table or for that matter any way to create a 
table similar to the outout of aparcstats2table ?

Thanks

Ri
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Re: [Freesurfer] aparcstats2table for std dev associated with av thickness

[Douglas N Greve]

I've modified aparc2stats2table to accept a -meas thicknessstd option. 
This will output the spatial standard deviation of the thickness for 
each subject. You can get it from here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table

doug

Ritobrato Datta wrote:
 Hi all

 Is there a way to create a multi subject table of the std dev associated with 
 av thickness using aparcstats2table or for that matter any way to create a 
 table similar to the outout of aparcstats2table ?

 Thanks

 Ri
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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[Freesurfer] aparcstats2table

[Falk Lüsebrink]

Hi Freesurfers,

 

I tried using aparcstats2table today and encountered following error
message:

 

Trackback (most recent call last):

  File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in module

Import fsutils

ImportError: No module named fsutils

 

Is anyone able to offer some help? I am using v4.3.0 and it didn’t matter if
I used any flags or not.

 

Thanks in advance,

Falk

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Re: [Freesurfer] aparcstats2table

[Krish Subramaniam]

Hi Falk

fsutils is one of the 4 helper scripts missing from the distribution.

Please get the 4 scripts from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/misc.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/subject_info.py

And put them in your $FREESURFER_HOME/bin directory.

Sorry for the trouble.
Krish


On Apr 14, 2009, at 10:36 AM, Falk Lüsebrink wrote:


Hi Freesurfers,

I tried using aparcstats2table today and encountered following error  
message:


Trackback (most recent call last):
  File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in  
module

Import fsutils
ImportError: No module named fsutils

Is anyone able to offer some help? I am using v4.3.0 and it didn’t  
matter if I used any flags or not.


Thanks in advance,
Falk
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RE: [Freesurfer] aparcstats2table

[Falk Lüsebrink]

Hi Krish,

Thanks for your help.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Krish
Subramaniam
Sent: Tuesday, April 14, 2009 5:03 PM
To: Falk Lüsebrink
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table

Hi Falk

fsutils is one of the 4 helper scripts missing from the distribution.

Please get the 4 scripts from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils.
py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/misc.py
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/subject_info.py

And put them in your $FREESURFER_HOME/bin directory.

Sorry for the trouble.
Krish


On Apr 14, 2009, at 10:36 AM, Falk Lüsebrink wrote:

 Hi Freesurfers,

 I tried using aparcstats2table today and encountered following error  
 message:

 Trackback (most recent call last):
   File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in  
 module
 Import fsutils
 ImportError: No module named fsutils

 Is anyone able to offer some help? I am using v4.3.0 and it didn’t  
 matter if I used any flags or not.

 Thanks in advance,
 Falk
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Re: [Freesurfer] aparcstats2table new version (-parc)

[Pratap Kunwar]

Hi Diana,

Make sure you name stats file as ?h.aparc.a2005s_300.stats not just
aparc.a2005s_300.stats.

then --parc aparc.a2005s_300

this should work otherwise if you post your commands, that will help.

thanks
pratap

 Hi Krish

 Thanks again for your quick help! I tried out the new version, it seams to
 work fine.

 Nevertheless, I created a new  parcellation with  mris_anatomical_stats
 getting a .stat file I called aparc.a2005s_300. Only now I get the
 following
 error message  (Which was not the case in the former version):

 aparcstats2table: error: option --parc: invalid choice: 'aparc.a2005s_300'
 (choose from 'aparc', 'aparc.a2005s')

 How can I force the -parc option to read my own parcellations?

 Diana
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Re: [Freesurfer] aparcstats2table new version (-parc)

[Diana Wotruba]

Dear Pratap

The file is called ?h.aparc.a2005s_300.stats as you suggested. The commands 
I used are the following:


mris_divide_parcellation fsaverage_fineparc ?h aparc.a2005s.annot 300 
?h.aparc.a2005s_300.annot


mri_surf2surf --srcsubject fsaverage_fineparc --sval-annot 
aparc.a2005s_300.annot --trgsubject 001--tval aparc.a2005s_300.annot --hemi 
?h


mris_anatomical_stats -a aparc.a2005s_300.annot -t ?h.thickness -b -f 
001/stats/?h.aparc.a2005s_300.stats 001 ?h


aparcstats2table --subjects 001 002 003 --hemi ?h --parc aparc.a2005s_300 
--meas thickness -t ?h_aparc.a2005s_300_stat.txt



Thanks for your help
Diana
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[Freesurfer] aparcstats2table new version (-parc)

[Diana Wotruba]

Hi Krish

Thanks again for your quick help! I tried out the new version, it seams to 
work fine.


Nevertheless, I created a new  parcellation with  mris_anatomical_stats 
getting a .stat file I called aparc.a2005s_300. Only now I get the following 
error message  (Which was not the case in the former version):


aparcstats2table: error: option --parc: invalid choice: 'aparc.a2005s_300' 
(choose from 'aparc', 'aparc.a2005s')


How can I force the -parc option to read my own parcellations?
 
Diana

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Re: [Freesurfer] aparcstats2table bug

[Krish Subramaniam]

We have done a rewrite of both aparcstats2table and asegstats2table,  
although it needs a little a bit of testing, still. I'll put the new  
version online and send you the link soon. It will be great if you can  
test i) the bug in question and ii) aparcstats2table in general.


Both will definitely be in our next release.

-Krish

On Feb 5, 2009, at 9:24 AM, Diana Wotruba wrote:



Dear experts

If some of the subjects in a group have missing values of a certain  
label, aparcstats2table fails to designate a 0 for them. According  
to the freesurfers website, this bug will be fixed in the next  
release.   Is it already known when this can be expected?


Thanks in advance
Diana
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Re: [Freesurfer] aparcstats2table bug

[Douglas N Greve]

Krish actually has a new version and is looking for alpha testers  
Krish, do you want to give Diana a copy?


doug

Diana Wotruba wrote:


Dear experts

If some of the subjects in a group have missing values of a certain 
label, aparcstats2table fails to designate a 0 for them. According to 
the freesurfers website, this bug will be fixed in the next release.   
Is it already known when this can be expected?


Thanks in advance
Diana
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Re: [Freesurfer] aparcstats2table bug

[Krish Subramaniam]

Hi Diana

I've put it here.

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/stats2table_alpha.tar.gz

To install

cp stats2table_alpha.tar.gz $FREESURFER_HOME/bin/
cd $FREESURFER_HOME/bin
tar zvxf stats2table_alpha.tar.gz

The binary is named aparcstats2table_re ( _re for rewrite which will  
be changed to aparcstats2table during the release ) and it will also  
install a directory called fsutils/ which contains a few Python helper  
scripts.


To view the usage, just type
aparcstats2table_re -h

which should give you an overview of options. There are a few changes  
( that means your old aparcstats2table command line *may not* work  
fine ) as well as a few feature additions.


* changes - the subject specification is now the same if you use -s  
and --subjects ( in accordance with GNU style )
For example, in the prev version, to specify multiple subjects you  
could give

aparcstats2table -s sub1 -s sub2

That option is no longer valid. The only way to specify subjects is

aparcstats2table_re --subjects sub1 sub2 ( or )
aparcstats2table_re -s sub1 sub2

the extra features:

* The ROI bug is no longer there. The default behaviour is it finds  
the union of all ROIs and displays 0.0 to the ROIs which are not  
present in that particular subject.
This behavior can be altered with the --common-parcs switch which  
only outputs the common ROIs to all the subjects.

To illustrate,
Suppose out of subjects 004, 007, 011... only 004 and 007 have  
unknown and all 3 have caudate. The default behavior now is

lh.aparc.meas caudate unknown
004 3.4 4.3
007 2.8 6.7
011 1.3 0.0

Using common-parcs, we get
lh.aparc.meas caudate
004 3.4
007 2.8
011 1.3

* there is an option --report-rois which gives information as to
- what ROIs current subject has and no other subject has and
- what ROI current subject is missing which at-least one other subject  
has

The display is still raw and needs work.

* --transpose option switches the order. Usually the subjects are in  
the rows and ROIs in the columns. This option transposes. ( looks good  
for display )


* --delimiter tab ( or comma or semicolon or space ) .. The  
delimiter between the measures in the table file.



You can let me know in case of any errors

Krish



On Feb 5, 2009, at 11:29 AM, Douglas N Greve wrote:



Krish actually has a new version and is looking for alpha  
testers  Krish, do you want to give Diana a copy?


doug

Diana Wotruba wrote:


Dear experts

If some of the subjects in a group have missing values of a certain  
label, aparcstats2table fails to designate a 0 for them. According  
to the freesurfers website, this bug will be fixed in the next  
release.   Is it already known when this can be expected?


Thanks in advance
Diana
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Re: [Freesurfer] aparcstats2table bug

[Krish Subramaniam]

Hi Diana

I have put the latest rewrite ( more fixes and updates ) of both the  
aparcstats2table and asegstats2table here. If you still haven't tried  
with the previous one we sent you, use this version instead.


ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/stats2table.tar.gz

Extract it in your FREESURFER_HOME/bin directory ( this will overwrite  
the a*stats2table files )


This version honors both the type of inputs for the subjects. For  
example, you can specify subjects with


-s sub1 -s sub2 ...

as well as

--subjects sub1 sub2 ..

~Krish

On Feb 5, 2009, at 11:29 AM, Douglas N Greve wrote:



Krish actually has a new version and is looking for alpha  
testers  Krish, do you want to give Diana a copy?


doug

Diana Wotruba wrote:


Dear experts

If some of the subjects in a group have missing values of a certain  
label, aparcstats2table fails to designate a 0 for them. According  
to the freesurfers website, this bug will be fixed in the next  
release.   Is it already known when this can be expected?


Thanks in advance
Diana
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