After running the mri_label2label and mris_label2annot a new rh.BA.annot file was created (I had to remove the old one since it doesn't overwritte) but when running
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white It says that can't read annotation file: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory I only tried with rh, but I don't think that's a problem is it? Thank you! Andreia Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > In the "BA label" section there are: > - Several mri_label2label commands that map each label from > fsaverage space to your indidvidual's space > - One mris_label2annot command that combines the mapped label into > an annotation file. > - One mris_anatomical_stats command that gets stats for that annotation. > > For each of these commands you can run them with --help to see what > the inputs and outputs are, or look them up on the wiki. > > On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: > >> Nevermind the last email... If I change the output (wich is the second >> place where BAxx.label appears, right?) file name and give the subjs >> id this won't be a problem... Anyway, what are these files for? Will I >> need to use them somehow? >> >> Thanks >> Andreia >> >> >> Quoting _andre...@sapo.pt: >> >>> Addicionaly, this approach is creating an individual file for each >>> BAxxx.thresh.label (see atchment) and I think that if I run these >>> commands for another subject these outputs will be replaced since >>> the name of the files has no info relating to the subject who it >>> belongs. >>> >>> I'm kind of lost here... >>> >>> >>> >>> >>> >>> Quoting _andre...@sapo.pt: >>> >>>> Hi, >>>> >>>> I run the command for each BA labels of the right hemisphere and then run: >>>> >>>> [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f >>>> ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab >>>> SUBJECT rh white >>>> >>>> Which resulted in: >>>> >>>> INFO: assuming MGZ format for volumes. >>>> computing statistics for each annotation in ./rh.BA.annot. >>>> reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... >>>> reading input surface >>>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... >>>> reading input pial surface >>>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... >>>> reading input white surface >>>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... >>>> could not read annot file ./rh.BA.annot >>>> No such file or directory >>>> mris_anatomical_stats: could not read annotation file ./rh.BA.annot >>>> No such file or directory >>>> >>>> What is wrong? Is there a way to run everything that is needed to >>>> get the BA stats at once using the BAxxx.thresh.label? >>>> >>>> Thank you, >>>> Andreia >>>> >>>> Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >>>> >>>>> If you replace *every* occurence of BAxxx.label with >>>>> BAxxx.thresh.label, this will keep things simple and you won't >>>>> have to worry about which one is input and which one is output. >>>>> >>>>> Run *all* the commands from the "BA labels" section, all the way >>>>> to the end of that section, this will get you to the stats. >>>>> >>>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: >>>>> >>>>>> Ok. So the first is the input and the second is the output, >>>>>> correct? So I'll have a different file for each out put? Is it >>>>>> possible to have a table with the different measures after the >>>>>> threshold? >>>>>> >>>>>> Thank you very much and I apologize for the naive questions... >>>>>> >>>>>> Andreia >>>>>> >>>>>> >>>>>> Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >>>>>> >>>>>>> What you call the output label is up to you. What you call the >>>>>>> input label is more important - it has to be a file that >>>>>>> actually exists. >>>>>>> >>>>>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: >>>>>>> >>>>>>>> Ah ok! Sorry... In both places? >>>>>>>>>> Quoting Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>> It's .thresh.label, not .threshold.label. >>>>>>>>>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>> Hi Anastasia! >>>>>>>>>>> The command in the recon-all.log is this one: >>>>>>>>>>> mri_label2label --srcsubject fsaverage --srclabel > > > > >>>>>>>>>>> /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label >>>>>>>>>> --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi >>>>>>>>>> rh > > > > --regmethod surface >>>>>>>>>>> And I tried substituing BAxxx.label by BAxxx.thresh.label >>>>>>>>>> like > > > > this: >>>>>>>>>>> mri_label2label --srcsubject fsaverage --srclabel >>>>>>>>>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label > >>>>>>>>>>>>> --trgsubject SUSANAFERREIRA --trglabel >>>>>>>>>> ./lh.BA1.thresolh.label --hemi lh --regmethod surface >>>>>>>>>>> gave an error : >>>>>>>>>>> SUBJECTS_DIR /home/user/visao/Freesurfer/ >>>>>>>>>> FREESURFER_HOME /usr/local/freesurfer >>>>>>>>>> Loading source label. >>>>>>>>>> No such file or directory >>>>>>>>>> mri_label2label: could not open label file > > > > >>>>>>>>>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >>>>>>>>>> Illegal seek >>>>>>>>>> ERROR reading > > > > >>>>>>>>>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >>>>>>>>>>> Thus, I substitued only in the second BAxxx.label and it >>>>>>>>>> worked. I > > > > > thought that was it, but then the values >>>>>>>>>> were the same. I'm sorry, I'm not sure what is missing. >>>>>>>>>>> Thank you! >>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>> Quoting Anastasia Yendiki > > > > > > > >>>>>>>>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>>>> Hi Andreia - What you're rerunning is using BAxxx.label >>>>>>>>>> instead > > > > > of >>>>>>>>>>> BAxxx.thresh.label. So of course the results will be the >>>>>>>>>> same as > > > > before >>>>>>>>>>> you copied over the BAxxx.thresh.label files, b/c these >>>>>>>>>> new files > > > > > > aren't >>>>>>>>>>> being used in 5.0. >>>>>>>>>>>>> You'll need to find the "BA labels" section in >>>>>>>>>> recon-all.log > > > > > > and rerun >>>>>>>>>>> those commands yourself, changing every BAxxx.label to > > >>>>>>>>>>>>>> BAxxx.thresh.label. >>>>>>>>>>>>> Hope this helps, >>>>>>>>>>> a.y >>>>>>>>>>>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>>> Hello list! >>>>>>>>>>>>>>> Any suggestions on what I may be doing wrong? >>>>>>>>>>>>>>> Thanks! >>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>> ----- Mensagem encaminhada de > > > > >>>>>>>>>>>>>>>>>>>> _andre...@sapo.pt ----- >>>>>>>>>>>> Data: Sun, 24 Mar 2013 19:11:13 +0000 >>>>>>>>>>>> De: _andre...@sapo.pt >>>>>>>>>>>> Assunto: Re: [Freesurfer] Brodmann area thickness, >>>>>>>>>> surface area > > > > > and > > > volume >>>>>>>>>>>> Para: Anastasia Yendiki >>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>, > > > > > > > > freesurfer >>>>>>>>>>>> <freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>>> Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>> Hi all, >>>>>>>>>>>>>>> I want to study Brodmann Areas cortical thickness, >>>>>>>>>> surface > > > > > > > > area and >>>>>>>>>>>> volume. I've added the 5.2 BAxxx.threshold.label to my >>>>>>>>>> 5.0 > > > > > fsaverage >>>>>>>>>>>> and run the recon-all BA labels command. Now I run > > > >>>>>>>>>>>> aparcstats2table >>>>>>>>>>>> and get a table with the values but they are the same as before >>>>>>>>>>>> running the BAxxx.threshold.label. >>>>>>>>>>>>>>> So, everything is working but the values haven't >>>>>>>>>> changed. > > > > > > > > Am I > > > missing >>>>>>>>>>>> something? Do I need to run any other command so to the >>>>>>>>>>>>>>> threshold > > > have >>>>>>>>>>>> effect? >>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>> Quoting Anastasia Yendiki > > > > > > > > > >>>>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>> Sounds like centos4 is probably the safest bet >>>>>>>>>> for you, > > > > > > > > > although > > > > you >>>>>>>>>>>>> should ask the list this question. >>>>>>>>>>>>>>>>> Sorry, I don't know what values you want to >>>>>>>>>> get in a > > > > > > > > > > table. >>>>>>>>>>>>>>>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>> Ah ok! Anyway, I'm thinking of working with >>>>>>>>>> 5.2, > > > > > > > > > > > should I > > > > > download >>>>>>>>>>>>>> the version for centOS 4 then? >>>>>>>>>>>>>>>>>>> After running the new BAxxx.thresh.label >>>>>>>>>> files how > > > > > > > > > > > > can I get the >>>>>>>>>>>>>> values in a table? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Quoting >>>>>>>>>> Anastasia > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>> Yendiki > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>> It doesn't matter. You just need to use >>>>>>>>>> those > > > > > > > > > > > > > .label files from >>>>>>>>>>>>>>> the fsaverage directory in the 5.2 distritbution. >>>>>>>>>> You > > > > > > > > don't > > > > > > need >>>>>>>>>>>>>>> to run any of the executables from the 5.2 distribution. >>>>>>>>>>>>>>>>>>>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>> I'm using Centos5, which file should >>>>>>>>>> I > > > > > > > > > > > > > > > download? The one for >>>>>>>>>>>>>>>> CentOS 6 or > 4? >>>>>>>>>>>>>>>>>> Quoting Anastasia Yendiki > > > > > > > > > >>>>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>> You'll need to go to the section of >>>>>>>>>> recon-all.log > > > > > > > > > > > under > > > > > > > > > >>>>>>>>>> the >>>>>>>>>>>>>>>>> heading "BA > > labels". You'll need to rerun >>>>>>>>>> the > > > > > > > > > > commands > > > > > > > > in >>>>>>>>>>>>>>>>> that section, but instead > > of using the >>>>>>>>>> BAxxx.label > > > > > > > > > > > > > > > > > > files, us >>>>>>>>>>>>>>>>> the BAxxx.thresh.label files, which > > you'll >>>>>>>>>> find in > > > > > > > > > > the >>>>>>>>>>>>>>>>> fsaverage subject dir in the 5.2 distribution. >>>>>>>>>>>>>>>>>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>> Hello Anastasia, >>>>>>>>>>>>>>>>>>> How should I proceed to get the >>>>>>>>>> different BAs > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>> measures >>>>>>>>>>>>>>>>> output with > > > > FS > 5.0? >>>>>>>>>>>>>>>>>>> Thank you very much! >>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>> Quoting Anastasia Yendiki > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> <ayend...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>> The thresholded labels are in the 5.2 >>>>>>>>>> version > > > > > > > > > > > > > of >>>>>>>>>>>>>>>>> fsaverage > > > > > under: >>>>>>>>>>>>>>>>>>> > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>> $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label >>>>>>>>>>>>>>>>>>>>> On Sat, 23 Mar 2013, Bruce Fischl wrote: >>>>>>>>>>>>>>>>>>>>>> Anastasia? >>>>>>>>>>>>>>>>>>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>> Ok, that was my guess... I am >>>>>>>>>> running > > > > > > > > > > > > > > > against > > > > > > > >>>>>>>>>>>>>>>> a >>>>>>>>>>>>>>>>> deadline, > > > > > > > any > > > > > news on >>>>>>>>>>>>>>>>>>>>> automatically computing the correct >>>>>>>>>>>>>>>>>>>>>>>> threshold > > > > > > > > > > > >>>>>>>>>>> script? >>>>>>>>>>>>>>>>> Will I > > > > > > be > > > > able to >>>>>>>>>>>>>>>>>>>>> use it in 5.0? >>>>>>>>>>>>>>>>>>>>>>> Thanks you! >>>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>>>>> Quoting Bruce Fischl > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>>>>>> yes. Surface area will be >>>>>>>>>> the > > > > > > > > > > > > > > > > > affected > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> much >>>>>>>>>>>>>>>>> more than > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>> thickness > > > > > > > > (and > >>>>>>>>>>>>>>>>>>>> volume of > > > > > > > > > course >>>>>>>>>> scales > > > > > > > > > > > > > with > > > > > > > > > > > >>>>>>>>>> area) >>>>>>>>>>>>>>>>>>>>>>> On Fri, 22 Mar 2013, > > > > >>>>>>>>>>>>>>>>>>>>>> _andre...@sapo.pt > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>>>>>>>>>>>>> Thank you for the quick response! >>>>>>>>>>>>>>>>>>>>>>>>> In the meanwhile, does >>>>>>>>>> that also > > > > > > > > > > > > > > > > > > apply > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> cortical > > > > > > > > > > > > > > > > >>>>>>>>>>>> > > > > > > > > > > > cortical > > > > > > > > > > > >>>>>>>>>>>>>>>> cortical > > > > > > > > > > > cortical > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cortical > > >>>>>>>>>>>>>>>>>> thickness > >>>>>>>>>>>>>>>>>>>>>> and > > > > > > > > > > > > volume? >>>>>>>>>>>>>>>>>>>>>>>>> Thank you! >>>>>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>>>>> Quoting Bruce Fischl > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Andreia >>>>>>>>>>>>>>>>>>>>>>>>>>> the issue is that the >>>>>>>>>> BA > > > > > > > > > > > > > > > > > > > > labels > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> contain >>>>>>>>>>>>>>>>> every > > > > > > > > > > > > point > > > >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> that > > > > > > > > > > > > > > > > > > > >>>>>>>>>> > has > > > > > > > > > > any > > > > > > > > > > > >>>>>>>>>>>>>>>>> non-zero >>>>>>>>>>>>>>>>>>>>>>>> probability (no matter how >>>>>>>>>> small!) > > > > > > > > > > > > > > > > > of > > > > > > > > >>>>>>>>>>>>>>>>> being > > > > > > > > > > > > > > > > > in >>>>>>>>>>>>>>>>> that > > > > > > > > > label. > > > > > > >>>>>>>>>>> So > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> the > > > > > > > > > > > > total >>>>>>>>>>>>>>>>>>>>>>>> label area is almost >>>>>>>>>> certainly > > > > > > > > > > > > > > > > > always > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bigger >>>>>>>>>>>>>>>>> than the > > > > > > > > > > > > > > > > >>>>>>>>>> actual > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> BA. > > > > > > > > > > > > Anastasia >>>>>>>>>>>>>>>>>>>>>>>> has some scripts for >>>>>>>>>> automatically > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>> computing >>>>>>>>>>>>>>>>> the > > > > > > > > > correct > > > > > > >>>>>>>>>>>> > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> threshold, > > > > > > > > > > > > and I >>>>>>>>>>>>>>>>>>>>>>>> believe she and Nick >>>>>>>>>> integrated > > > > > > > > > > > > > > > > > them > > > > > >>>>>>>>>>>>>>>>>>>> into > > > > > > > > > > > > > > > > > 5.2 >>>>>>>>>>>>>>>>> so that > > > > > > > > > the > > > > > > >>>>>>>>>>> > > > > > > > > > > stats > > > > > > > > > > > > >>>>>>>>>>>>>>>>>> are >>>>>>>>>>>>>>>>>>>>>>>> computed both thresholded >>>>>>>>>> and > > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>> unthresholded, > >>>>>>>>>>>>>>>>>>>>>>>>> hopefully > > > > > > > >>>>>>>>>> they > > > > > > > > > > > > > > > > > > can > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>> comment. >>>>>>>>>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, >>>>>>>>>> 22 Mar > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>> 2013, > > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _andre...@sapo.pt >>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi all, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm using FS 5.0 >>>>>>>>>> and some > > > > > > > > > > > > > > > > > > > > > > time > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> ago I >>>>>>>>>>>>>>>>> was > > > > > > > > > > > > > > told by > >>>>>>>>>>>>>>>>>>>>>>>> was > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was > > > > > > > > > >>>>>>>>>>>>>>> was > > > > > > > > > > > > > > > > > > > was > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>> >>>>>>>>>>>>>>>>> Bruce that I had > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>> > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>> threshold the BA in order >>>>>>>>>> to have > > > > > > > > > > > > > > > > > > an >>>>>>>>>>>>>>>>> approximate > > > > > > > > > > area > > >>>>>>>>>>>>>>>>>>>>>>>> approximate > > > > > > > > > > >>>>>>>>>>>> > > > > > > > > > > > > > > > > > > approximate > > > > >>>>>>>>>>>>>>>> approximate > > > > > > > > > > > > > > > >>>>>>>>>> approximate > > > > > > > > > > > > > > > when >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> overlaying >>>>>>>>>>>>>>>>>>>>>>>>> in the inflated surface. >>>>>>>>>> To get > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> surface > > > > > > > > > > > > > > > > > > area >>>>>>>>>>>>>>>>> values > > > > > > > > > > I > > > > > > >>>>>>>>>>>> > > > > > > > > > > values > > > > > > > > > > also > >>>>>>>>>>>>>>>>>>>>>>>>>>>> values > > > > > > > > > >>>>>>>>>>> values > > > > > > > > > > > > > > > > > > > > values > > >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> need to > > > > > > > > > > > > > > use >>>>>>>>>>>>>>>>>>>>>>>>> the label_area and put a >>>>>>>>>>>>>>>>>>>>>>>>>>>> threshold >>>>>>>>>>>>>>>>>>>>>>>>> having the possibility to >>>>>>>>>> choose > > > > > > > > > > > > > > > > > > the > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface >>>>>>>>>>>>>>>>> that I > > > > > > > > > > > > > > > > > >>>>>>>>>>> > > > > > > > > > > want, > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>> either > > > > > > > > > > > > > > white >>>>>>>>>>>>>>>>>>>>>>>>> or pial. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> But I can also >>>>>>>>>> get the BA > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> stats in a >>>>>>>>>>>>>>>>> table > > > > > > > > > > > > > > for > > >>>>>>>>>>>>>>>>>>>>>>>> table > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table > > > > > > > >>>>>>>>>>>>>>>>> table > > > > > > > > > > > > > > > > > table >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> all > > > > > > > > > > > > > > > > > > >>>>>>>>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> subjects and > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>> > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>> areas >>>>>>>>>>>>>>>>>>>>>>>>> using either > > > > > > >>>>>>>>>>>>>>>>>>>>>> mris_anatomical_stats (on > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each >>>>>>>>>>>>>>>>> label) > > > > > > > > > > or > > > > > > >>>>>>>>>>>> > > > > > > > > > > usinga > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>> script by >>>>>>>>>>>>>>>>>>>>>>>>> Jamaan to get the table >>>>>>>>>> (since I > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already >>>>>>>>>>>>>>>>> have the > > > > > > > > > > > > > > > > > >>>>>>>>>>> > > > > > > > > > > > > > > > > > > ?.BA.stats > >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>> files), >>>>>>>>>>>>>>>>>>>>>>>>> right? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> My question is, >>>>>>>>>> which is > > > > > > > > > > > > > > > > > > > > > > the >>>>>>>>>>>>>>>>> better/correct > > > > > > > > > > > > > > >>>>>>>>>> way > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>> to > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > > > > > > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>>>>>>>> get the > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>> thickness >>>>>>>>>>>>>>>>>>>>>>>>> and surface area values >>>>>>>>>> of the BA > > > > > > > > > > > > > > > > > > to > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export >>>>>>>>>>>>>>>>> for > > > > > > > > > > > > > > > > > > >>>>>>>>>> > > > > > > > > > > for > > > > > > > > > > > > >>>>>>>>>> statistical > > > > > > > > > > > > > > > > > for > > > > > > >>>>>>>>>>>>>>>>> for > > > > > > > > > > > > > > > > > > > > >>>>>>>>>> for > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> analysis >>>>>>>>>>>>>>>>>>>>>>>>> since there are the >>>>>>>>>> thresolds > > > > > > > > > > > > > > > > > > issue. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I want to study >>>>>>>>>> mainly > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> cortical >>>>>>>>>>>>>>>>> thickness > > > > > > > > > > > > > > and >>>>>>>>>>>>>>>>>>>>>>>> thickness > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thickness > > > > > >>>>>>>>>>>>>>>>>>>>> thickness > > > > > > > > > > > >>>>>>>>>> thickness > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> thickness > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> surface > > > > > > > > > > > > > > >>>>>>>>>>>> > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> area but > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>> also >>>>>>>>>>>>>>>>>>>>>>>>> look also at the volume (which is >>>>>>>>>>>>>>>>> surface-based, > > > > > > > > > > thus >>>>>>>>>>>>>>>>>>>>>>>>> thickness*surface are >>>>>>>>>> will not be > > > > > > > > > > > > > > > > > > = > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> volume >>>>>>>>>>>>>>>>> since > > > > > > > > > > they > > > > > >>>>>>>>>>>>> > > > > > > > > > > since > > > > > > > > > > are > >>>>>>>>>>>>>>>>> since > > > > > > > > > > > since > > > > > > > >>>>>>>>>>>>>>>>>>>>>> an > > >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>> > average >>>>>>>>>>>>>>>>>>>>>>>>> from each label, right?). >>>>>>>>>>>>>>>>>>>>>>>>>>>>> I' not sure of >>>>>>>>>> which > > > > > > > > > > > > > > > > > > > > > > approach > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>> follow > > > > > > > > > > > > > > now... >>>>>>>>>>>>>>>>>>>>>>>> follow > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follow > > > > > > >>>>>>>>>>>>>>>>>> follow > > > > > > > > > > > > > > > > >>>>>>>>>> follow > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>> follow > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>> Does > > > > > > > > > > > > > > > >>>>>>>>>>> > > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> it depend on > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>> > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>> measure I'll be using? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you! >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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 > > > > >>>>>>>>>>>>> > > > > > > > > > > the > > > > > > > > > sent > > >>>>>>>>>>>>>>>> the > > > > > > > > > > > > > > the > > > > > > > >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> to > > > > > > > > > > > > you in error >>>>>>>>>>>>>>>>>>>>>>>> but does not contain >>>>>>>>>> patient > > > > > > > > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>> information, >>>>>>>>>>>>>>>>> please > > > > > > > > > contact > > > > >>>>>>>>>>>>> > > > > > > > > > > please > > > > > > > > > the > >>>>>>>>>>>>>>>>> please > > > > > > > > > > > please > > > > > > >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> sender > > > > > > > > > > > > and properly >>>>>>>>>>>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> ----- > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Fim > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> de > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> mensagem > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> reenviada > > > > > > > > > > > > > > > > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ----- >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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 >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
