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
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
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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.
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
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
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
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
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
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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.
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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/
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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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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
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
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
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
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
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
-- 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/
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
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
-- 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/
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/
freesurfer@nmr.mgh.harvard.edu
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_andreia_＠sapo.pt -
Bruce Fischl -
Douglas N Greve