Hi Doug,

I am using version 5.3 and the terminal output does not state an error (below) and the file is created (attached) but as you will see, it is the area measurements which are output.

dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 CON_004 CON_006 CON_007 CON_008 CON_009 CON_010 CON_011 CON_013 CON_014 CON_015 CON_016 CON_017 CON_018 CON_019 CON_021 CON_022 CON_025 CON_026 CON_027 CON_028 CON_029 CON_030 CON_032 CON_033 CON_034 CON_035 CON_036 CON_038 CON_039 CON_040 CON_041 CON_042 CON_045 CON_049 CON_054 CON_055 CON_057 CON_063 OXCON_005 OXCON_009 OXCON_012 OXCON_025 OXCON_026 OXCON_028 OXCON_029 OXCON_031 OXCON_040 OXCON_042 OXCON_052 OXCON_053 OXCON_054 OXCON_055 OXCON_058 OXCON_059 OXCON_060 OXCON_061 OXCON_062 OXCON_064 OXCON_065 OXCON_066 OXCON_067 --hemi rh –meas volume --tablefile aparc_stats_volume_rh.txt --skip SUBJECTS_DIR : /Users/clare/Desktop/MAP/Volumetrics/FreeSurfer/CONTROLS/ Parsing the .stats files Building the table.. Writing the table to aparc_stats_volume_rh.txt

Since posting the original message, it does seem that the correct measurement can be acquired when I aparcstat2table on subjects individually. Although often it will state error that the rh.aparc.stats is not found or is too small to be a valid stats file. This is not the case as they are all there and full of measurements.

Many thanks,

Clare

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 15 March 2016 16:55 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc stats volume outputting area instead

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:

Hi,

I am trying to pull out the volumes from the aparc stats file but when I input the following (below) it produces a file identical to the area instead:

aparcstats2table --subjects 001 002 003 --hemi rh --meas volume --tablefile aparc_stats_volume_rh.txt

It works fine for thickness and area as well aseg_stats.

I would appreciate any help with this.

Thank you!

Clare

---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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

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.

Hi Doug,

Many thanks indeed: everything working fine now.

BW

clare ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: 16 March 2016 14:53 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc stats volume outputting area instead

There is not actually a "-meas" option. It should be either " -m volume" or " --measure=volume". Strange, it should have exited with an error but some reason it did not and used area as the default.

On 3/16/16 10:27 AM, Clare Loane wrote:

Hi Doug,

I am using version 5.3 and the terminal output does not state an error (below) and the file is created (attached) but as you will see, it is the area measurements which are output.

dcnmac75:Freesurfer clare$ aparcstats2table --subjects CON_001 CON_002 CON_003 CON_004 CON_006 CON_007 CON_008 CON_009 CON_010 CON_011 CON_013 CON_014 CON_015 CON_016 CON_017 CON_018 CON_019 CON_021 CON_022 CON_025 CON_026 CON_027 CON_028 CON_029 CON_030 CON_032 CON_033 CON_034 CON_035 CON_036 CON_038 CON_039 CON_040 CON_041 CON_042 CON_045 CON_049 CON_054 CON_055 CON_057 CON_063 OXCON_005 OXCON_009 OXCON_012 OXCON_025 OXCON_026 OXCON_028 OXCON_029 OXCON_031 OXCON_040 OXCON_042 OXCON_052 OXCON_053 OXCON_054 OXCON_055 OXCON_058 OXCON_059 OXCON_060 OXCON_061 OXCON_062 OXCON_064 OXCON_065 OXCON_066 OXCON_067 --hemi rh –meas volume --tablefile aparc_stats_volume_rh.txt --skip SUBJECTS_DIR : /Users/clare/Desktop/MAP/Volumetrics/FreeSurfer/CONTROLS/ Parsing the .stats files Building the table.. Writing the table to aparc_stats_volume_rh.txt

Since posting the original message, it does seem that the correct measurement can be acquired when I aparcstat2table on subjects individually. Although often it will state error that the rh.aparc.stats is not found or is too small to be a valid stats file. This is not the case as they are all there and full of measurements.

Many thanks,

Clare

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Sent: 15 March 2016 16:55 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparc stats volume outputting area instead

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:

Hi,

I am trying to pull out the volumes from the aparc stats file but when I input the following (below) it produces a file identical to the area instead:

aparcstats2table --subjects 001 002 003 --hemi rh --meas volume --tablefile aparc_stats_volume_rh.txt

It works fine for thickness and area as well aseg_stats.

I would appreciate any help with this.

Thank you!

Clare

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@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.htmlhttp://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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer