It worked!
Thank you very much!
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
try this
mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b subject lh white
On 08/15/2013 01:37 PM, _andreia_@sapo.pt wrote:
The message that appear is
[user@localhost Freesurfer]$ aparcstats2table --hemi lh --subjects subj1 subj2 --parc 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.total.stats.stats Use --skip flag if you want to continue in such cases
Thus I specifyed only total since I realized that it is duplication lh and stats and now I get:
[user@localhost Freesurfer]$ aparcstats2table --hemi lh --subjects subj1 subj2 --parc total --meas thickness -t lh.cortex.thickness.test.txtNumber of subjects : 2 Building the table.. Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 291, in ? (rows, cols, table) = build_table(options) File "/usr/local/freesurfer/bin/aparcstats2table", line 202, in build_table val = float(strlist[measure_field_map[o.meas]]) ValueError: invalid literal for float(): <gray
Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Spec total.stats not lh.total.stats
On 08/15/2013 01:24 PM, _andreia_@sapo.pt wrote:
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 >>>>>> >>>>>> >>>>>> >>>> >> _______________________________________________ >> 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 > 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
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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/
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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/
-- 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/