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
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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/