So, I ran the follwing for two subjects:
[user@localhost stats]$ cd /home/user/visao/Freesurfer/subjid/stats [user@localhost stats]$ mris_anatomical_stats -l /home/user/visao/Freesurfer/subjid/label/lh.cortex.label -log lh.total.stats subjid lh white
which created the file with the values in aparc, so far so good.
But when trying to get the table with
[user@localhost Freesurfer]$ aparcstats2table --hemi lh --subjects ANTONIOMARCOS SUSANAFERREIRA --parc lh.total.stats --meas thickness -t lh.cortex.thickness.test.txt Number of subjects : 2 Building the table.. ERROR: cannot find /home/user/visao/Freesurfer/subj1/stats/lh.lh.total.stats.stats Use --skip flag if you want to continue in such cases
What am I missing?
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
The name is arbitrary. You can specify it on the aparcstats2table command line doug
On 08/15/2013 12:10 PM, _andreia_@sapo.pt wrote:
Hi Doug,
It created an indidual .txt file, however I think I need a .stats file so to extract all the values from all subjects in a table using aparcstats2table.
Or can I do that from several .txt?
Thank you! Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
If mris_anatomical_stats created the correct values, what's the problem? doug
On 08/15/2013 10:05 AM, _andreia_@sapo.pt wrote:
With mris_anatomical_stats using -log a .txt was created with the correct values. I'm trying mri_segstats now but I'm not getting the .stats file...
Waiting for Nick or Doug advice now.
Thank you Bruce!
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
oh, I see. mris_anatomical_stats can write to a file with -log <file name>, but Doug or Nick can probably point you at a better way to do it with mri_segstats.
cheers Bruce On Thu, 15 Aug 2013, _andreia_@sapo.pt wrote:
Hi Bruce,
The values are displayed in the terminal but how can I create a .stats file with those measures to get a table with aparcstats2table?
I did manage do create such file from ?h.cortex.label but the values do not match the ones in aparc.
Andreia
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
> Hi Andreia > > mris_anatomical_stats -l <path to ?h.cortex.label> should do the trick. > > cheers > Bruce > On Thu, 15 Aug 2013, _andreia_@sapo.pt wrote: > >> How can I get the thickness and surface area values per hemisphere? >> >> Should I use the ones from cortex.label or the ones in aparc? How can >> I get the aparc ones? >> >> Thank you in advance! >> >> Andreia >> >> >> Quoting _andreia_@sapo.pt: >> >>> Sorry, the measures are only thickness and surface area, since I can >>> get the volumes from aseg. >>> >>> Andreia >>> >>> >>> Quoting _andreia_@sapo.pt: >>> >>>> Dear list, >>>> >>>> To obtain the thickness, surface area and volume values for each >>>> hemisphere I ran the command line in the subjdir: >>>> >>>> mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats >>>> subjid lh white >>>> >>>> And did that with the pial surface too. However, the values >>>> I get from >>>> the generated cortex.stats do not match the ones in aparc.stats >>>> >>>> How can I get the referred measures, which are in the >>>> aparc.stats but >>>> do not appear in the table when using aparcstats2table? >>>> >>>> Thank you! >>>> >>>> Andreia >>>> >>>> _______________________________________________ >>>> 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 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>
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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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