Thanks Bruce! Those are the main questions now (not only to V1, but also to the rest of the Brodmann areas). I really want to be sure where the measures come from. I want that the different measures (i.e. cortical thickness and area are really from the same region in the cortex), to know what should be exported to run the statistical analysis.
At some point the list email was not in Cc anymore... Here it goes to the list too. Thank you so much for your help! Andreia Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > where do the V1 stats in the stats dir come from? What binary and > what surface? > > On Wed, 16 May 2012, Douglas N Greve wrote: > >> sorry, what is the question? >> >> On 05/16/2012 11:23 AM, Bruce Fischl wrote: >>> I'm not sure where the stats dir output comes from, Doug would >>> know. The others seem reasonable, and certainly the pial should be >>> bigger than the white. We also generate a couple of V1 labels, one >>> from the Hinds atlas and one from the Zilles labels I think, >>> although maybe the Hinds one isn't generated by default anymore. >>> Nick can answer that question. >>> >>> Also, please cc the list on these emails! You will get a faster >>> response time and the right people will be able to help you >>> >>> cheers >>> Bruce >>> >>> >>> On Wed, 16 May 2012, _andre...@sapo.pt wrote: >>> >>>> Hi Bruce! >>>> >>>> Ok! >>>> >>>> In fact I've already tried to use 0 as threshold, here's what happens: >>>> >>>> surface area from >>>> - stats directory output: 2081 >>>> - label_area -t 0 -s white rh S11 rh.V1: 2840.946 >>>> - label_area -t 0 -s pial rh S11 rh.V1: 3509.024 >>>> >>>> That's way too different. Using label_area is given higher >>>> values. Why? Could this have something to do with the >>>> substitution of the label_area file? This would mean that at some >>>> poit recon-all used the previous one to generate the output of >>>> the stats directory? >>>> >>>> Since pial and white surfaces usually do not follow exactly the >>>> same shape and, thus the same area (since there are different >>>> thickness in between) , I'm antecipating reviwers questions of >>>> things like "from what surface are you reporting the values?" >>>> >>>> >>>> >>>> Cheers, >>>> Andreia >>>> >>>> >>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>> >>>>> Hi Andreia >>>>> >>>>> did I say use 1.1? If I did, I'm sorry and take it back. 0 would >>>>> give you all the vertices in the label (this is the default). >>>>> 1.1 would give you an empty label since nothing would pass that >>>>> threshold. >>>>> >>>>> I wouldn't worry about thresholding the aparc boundaries, as >>>>> there we want a complete parcellation of the cortex, so if you >>>>> took it out of one parcel you would have to give it to another >>>>> (less likely) one. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote: >>>>> >>>>>> Sorry now I'm confused. I understood you said that I should try >>>>>> 1.1 as threshold. Anyway, this means that the values in the >>>>>> outputs from the stats directory do not take into account any >>>>>> threshold. Thus, the surface area given is from the bigger >>>>>> probable area no matter how unlikely all the points belong to >>>>>> it, correct? Could this be a problem when interpreting results >>>>>> using cortical thickness, surface area and/or volume of the >>>>>> studied regions? >>>>>> >>>>>> And concerning the aparc areas, is the ideia the same? >>>>>> >>>>>> I'm sorry to be insisting on this but I need to know what is >>>>>> the meaning of the values I'm using, principally because when >>>>>> discussing measures like these one must be carefull, as you >>>>>> know :) >>>>>> >>>>>> Thanks!! >>>>>> Andreia >>>>>> >>>>>> >>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>> >>>>>>> Hi Andreia >>>>>>> >>>>>>> the threshold should be in [0 1], as the label->stat is a >>>>>>> fraction not a pct. You should be able to run it for multiple >>>>>>> subjects. Nick or Doug might have some suggestions about how >>>>>>> to create a table of values. You can probably get something >>>>>>> similar out of other binaries. >>>>>>> >>>>>>> cheers >>>>>>> Bruce >>>>>>> >>>>>>> >>>>>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote: >>>>>>> >>>>>>>> Hi Bruce, >>>>>>>> >>>>>>>> So if label_area is not used by recon-all when I run it I'll >>>>>>>> just use it to obtain the area from the surface I specify, >>>>>>>> that's ok. Is it possible to use it to get these measures >>>>>>>> from multiple subjects and areas (areas from the aparc file >>>>>>>> also) at once (and maybe to create an output where they all >>>>>>>> come together?). However it would be good if one could be >>>>>>>> sure of the surface that is being used to stats output in >>>>>>>> fact. In fact, I was trying to know that by using the >>>>>>>> label_area, but I cannot find a coincident value because I >>>>>>>> can't use a threshold higher than 1. >>>>>>>> >>>>>>>> The rh.V1.label file exists. >>>>>>>> >>>>>>>> Thanks for you guidance! >>>>>>>> Andreia >>>>>>>> >>>>>>>> >>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>> >>>>>>>>> Hi Andreia, >>>>>>>>> >>>>>>>>> recon-all doesn't use label_area I don't think, so that >>>>>>>>> should be fine. Does the file rh.V1.label exist? >>>>>>>>> On Tue, 15 May 2012, _andre...@sapo.pt wrote: >>>>>>>>> >>>>>>>>>> Hello again! >>>>>>>>>> >>>>>>>>>> I've been out for while and now I'm back to this subject. >>>>>>>>>> >>>>>>>>>> When I try a threshold of 1.1 it gives me the following error: >>>>>>>>>> >>>>>>>>>> label_area -t 1.1 -s white rh S11 rh.V1 >>>>>>>>>> thresholding label stat field at 1.100000 >>>>>>>>>> using metric properties from surface white >>>>>>>>>> reading /home/user/visao/Freesurfer//S11/surf/rh.white... >>>>>>>>>> label_area: no data in label file >>>>>>>>>> /home/user/visao/Freesurfer//S11/label/rh.V1.label >>>>>>>>>> No such file or directory >>>>>>>>>> >>>>>>>>>> I think it might be because of the dot. However, if I use a >>>>>>>>>> coma instead the value is the same as using only threshold=1. >>>>>>>>>> >>>>>>>>>> How can I use higher threshold to check the values and >>>>>>>>>> figure out what surface was used to generate BA.stats? >>>>>>>>>> >>>>>>>>>> I have another question: I'll be processing new subjects, >>>>>>>>>> will the stats be given using this new label_area file? if >>>>>>>>>> so, do I need to re-run all the previous subjects to have >>>>>>>>>> the stats given in the same way? >>>>>>>>>> >>>>>>>>>> Thanks for your help! >>>>>>>>>> >>>>>>>>>> Andreia >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>> >>>>>>>>>>> try a thresh of 1.1 (it's stat < thresh, not stat <= thresh) >>>>>>>>>>> On Wed, 2 May 2012, _andre...@sapo.pt wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Nick, >>>>>>>>>>>> >>>>>>>>>>>> Thanks, that solved the problem =) >>>>>>>>>>>> >>>>>>>>>>>> However I get different values from the ones in the rh.BA >>>>>>>>>>>> stats for surface area. Even if i put pial or white in >>>>>>>>>>>> the command line both value do not coincide with the >>>>>>>>>>>> output from BA areas (and with a threshold of 1): >>>>>>>>>>>> >>>>>>>>>>>> Using pial in the command line: rh.V1=1538.720 >>>>>>>>>>>> Using white in the command line= rh.V1=1491.789 >>>>>>>>>>>> In the output = V1= 2214 >>>>>>>>>>>> >>>>>>>>>>>> Which will be the more accurate value to use for statistics? >>>>>>>>>>>> >>>>>>>>>>>> Thank you for the help! >>>>>>>>>>>> >>>>>>>>>>>> Andreia >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Citando Nick Schmansky <ni...@nmr.mgh.harvard.edu>: >>>>>>>>>>>> >>>>>>>>>>>>> Hi, you will need to change the order of the parameters, >>>>>>>>>>>>> like this: >>>>>>>>>>>>> >>>>>>>>>>>>> label_area -t 0.9 -s pial rh S11 rh.V1 >>>>>>>>>>>>> >>>>>>>>>>>>> Nick >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, 2012-05-02 at 14:11 +0100, _andre...@sapo.pt wrote: >>>>>>>>>>>>>> Hi! >>>>>>>>>>>>>> >>>>>>>>>>>>>> I've replaced the previous file for this new one and >>>>>>>>>>>>>> now I get this message: >>>>>>>>>>>>>> >>>>>>>>>>>>>> "[user@host118 Freesurfer]$ label_area rh S11 rh.V1 -t >>>>>>>>>>>>>> 0.9 -s pial >>>>>>>>>>>>>> reading /home/user/visao/Freesurfer//S11/surf/rh.white... >>>>>>>>>>>>>> S11: rh.V1 - 2840.946 square mm >>>>>>>>>>>>>> label_area: could not open label file >>>>>>>>>>>>>> /home/user/visao/Freesurfer//S11/label/-t.label >>>>>>>>>>>>>> No such file or directory" >>>>>>>>>>>>>> >>>>>>>>>>>>>> I don't understand what is happening since it gives me >>>>>>>>>>>>>> a value. Also, >>>>>>>>>>>>>> if I replace "pial" by "wm" it gives me same value and >>>>>>>>>>>>>> the same error: >>>>>>>>>>>>>> >>>>>>>>>>>>>> "[user@host118 Freesurfer]$ label_area rh S11 rh.V1 -t 0.9 -s wm >>>>>>>>>>>>>> reading /home/user/visao/Freesurfer//S11/surf/rh.white... >>>>>>>>>>>>>> S11: rh.V1 - 2840.946 square mm >>>>>>>>>>>>>> label_area: could not open label file >>>>>>>>>>>>>> /home/user/visao/Freesurfer//S11/label/-t.label >>>>>>>>>>>>>> No such file or directory" >>>>>>>>>>>>>> >>>>>>>>>>>>>> These two values are different from the value in the BA >>>>>>>>>>>>>> output in the >>>>>>>>>>>>>> stats directory: 2081 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Cheers, >>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Citando Nick Schmansky <ni...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> you can download it from here: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> n. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, 2012-04-26 at 13:40 +0100, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>> Hi Bruce and Nick, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I'm using an Intel Zeon CPU W3520 @ 2.67GHz (4 >>>>>>>>>>>>>>>> cores), RAM 4GB, NVIDIA >>>>>>>>>>>>>>>> Quadro FX 580 (2295MB graphical memory). Total free >>>>>>>>>>>>>>>> disk space 164GB >>>>>>>>>>>>>>>> (of 293GB). This info was taken while in Wndows and >>>>>>>>>>>>>>>> not in Linux, >>>>>>>>>>>>>>>> maybe the RAM could be different, I don't know... >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Is this the info you need? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Andreia >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> can you tell us what kind of hardware you are >>>>>>>>>>>>>>>>> running on? Nick: can >>>>>>>>>>>>>>>>> you get Andreia a new version of label_area for her machine? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, 26 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I don't know much about linux and I don't know what >>>>>>>>>>>>>>>>>> am I doing >>>>>>>>>>>>>>>>>> wrong... I've replaced the label_area in the bin >>>>>>>>>>>>>>>>>> folder by the >>>>>>>>>>>>>>>>>> unzipped one (and this icon appears different from >>>>>>>>>>>>>>>>>> the others, see >>>>>>>>>>>>>>>>>> attached file "label_area"). I gave all permissions >>>>>>>>>>>>>>>>>> by using the >>>>>>>>>>>>>>>>>> command chmod -R u+w label_area in the root accout. >>>>>>>>>>>>>>>>>> I also used the >>>>>>>>>>>>>>>>>> graphical interface to give all permissions (see >>>>>>>>>>>>>>>>>> attached file >>>>>>>>>>>>>>>>>> "permissions"). If I don't select "allow executing >>>>>>>>>>>>>>>>>> file as program" >>>>>>>>>>>>>>>>>> an error appears of "permission denied". If I >>>>>>>>>>>>>>>>>> select that option >>>>>>>>>>>>>>>>>> then another error shows up (see attached file "error". >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> What should I do? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> in $FREESURFER_HOME/bin (and unzip and chmod it) >>>>>>>>>>>>>>>>>>> On Wed, 25 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Where should I put it? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> try this one >>>>>>>>>>>>>>>>>>>>> On Wed, 25 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> I'm using >>>>>>>>>>>>>>>>>>>>>> freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0. >>>>>>>>>>>>>>>>>>>>>> I will also be using FS 5.1 paralelly. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Thank you very much!! >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Andreia >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I just modified label_area to allow the >>>>>>>>>>>>>>>>>>>>>>> specification of a >>>>>>>>>>>>>>>>>>>>>>> threshold (with -t <thresh>) and a surface >>>>>>>>>>>>>>>>>>>>>>> (with -s <surface >>>>>>>>>>>>>>>>>>>>>>> name>), and to use white by default. If you >>>>>>>>>>>>>>>>>>>>>>> let us know what >>>>>>>>>>>>>>>>>>>>>>> hardware/software platform you are running on >>>>>>>>>>>>>>>>>>>>>>> we can send you >>>>>>>>>>>>>>>>>>>>>>> an updated binary >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>>>>>>>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> (sorry, here it is for the list again) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ----- Mensagem encaminhada de Bruce Fischl >>>>>>>>>>>>>>>>>>>>>>>> <fis...@nmr.mgh.harvard.edu> ----- >>>>>>>>>>>>>>>>>>>>>>>> Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) >>>>>>>>>>>>>>>>>>>>>>>> De: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>>>>>>>>>> Assunto: Re: [Freesurfer] Load Brodmann >>>>>>>>>>>>>>>>>>>>>>>> surface area into >>>>>>>>>>>>>>>>>>>>>>>> inflated surface >>>>>>>>>>>>>>>>>>>>>>>> Para: _andre...@sapo.pt >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Andreia, >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> can you cc the list so others can answer? I >>>>>>>>>>>>>>>>>>>>>>>> just took a look and >>>>>>>>>>>>>>>>>>>>>>>> label_area is so old that is uses ?h.smoothwm >>>>>>>>>>>>>>>>>>>>>>>> without any >>>>>>>>>>>>>>>> ability to >>>>>>>>>>>>>>>>>>>>>>>> change it. I think there are probably other >>>>>>>>>>>>>>>>>>>>>>>> tools around >>>>>>>>>>>>>>>> that will do >>>>>>>>>>>>>>>>>>>>>>>> it, but someone else will know. If not I'll >>>>>>>>>>>>>>>>>>>>>>>> fix label_area >>>>>>>>>>>>>>>> to be less >>>>>>>>>>>>>>>>>>>>>>>> obstinate. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks for the help! How do I know from >>>>>>>>>>>>>>>>>>>>>>>>> which surface, >>>>>>>>>>>>>>>> i.e. pial or >>>>>>>>>>>>>>>>>>>>>>>>> wm is the command label_area getting the >>>>>>>>>>>>>>>>>>>>>>>>> value? I compared V1 >>>>>>>>>>>>>>>>>>>>>>>>> surface area given in the BA.stats and the >>>>>>>>>>>>>>>>>>>>>>>>> one I get with the >>>>>>>>>>>>>>>>>>>>>>>>> command, and the late is higher (V1 from >>>>>>>>>>>>>>>>>>>>>>>>> BA.stats= 2081 and from >>>>>>>>>>>>>>>>>>>>>>>>> label_area = 2592.272). >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Now, imagine the follwing: I have no >>>>>>>>>>>>>>>>>>>>>>>>> differences in cortical >>>>>>>>>>>>>>>>>>>>>>>>> thickness (CT) and surface area of this BA >>>>>>>>>>>>>>>>>>>>>>>>> but the volume is >>>>>>>>>>>>>>>>>>>>>>>>> different (with p values near 0.04...). >>>>>>>>>>>>>>>>>>>>>>>>> Also, other BA shows no >>>>>>>>>>>>>>>>>>>>>>>>> differences in CT neither in volume, but >>>>>>>>>>>>>>>>>>>>>>>>> with differences >>>>>>>>>>>>>>>> showing up >>>>>>>>>>>>>>>>>>>>>>>>> in the surface area (with lower p value >>>>>>>>>>>>>>>>>>>>>>>>> here). Since the >>>>>>>>>>>>>>>> values for >>>>>>>>>>>>>>>>>>>>>>>>> volume and surface are computed in different >>>>>>>>>>>>>>>>>>>>>>>>> ways, can >>>>>>>>>>>>>>>> this account >>>>>>>>>>>>>>>>>>>>>>>>> for these odd results? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thanks! >>>>>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Andreia, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> yes, they will always shrink since the >>>>>>>>>>>>>>>>>>>>>>>>>> label contains every >>>>>>>>>>>>>>>>>>>>>>>>>> point that >>>>>>>>>>>>>>>>>>>>>>>>>> could possibly be in the BA, no matter how >>>>>>>>>>>>>>>>>>>>>>>>>> unlikely. I'll >>>>>>>>>>>>>>>>>>>>>>>>>> try to find time >>>>>>>>>>>>>>>>>>>>>>>>>> to automatically threshold the BAs so that >>>>>>>>>>>>>>>>>>>>>>>>>> they have the >>>>>>>>>>>>>>>>>>>>>>>>>> average area of >>>>>>>>>>>>>>>>>>>>>>>>>> the individual examples, but for now V2 is >>>>>>>>>>>>>>>>>>>>>>>>>> probably around >>>>>>>>>>>>>>>>>>>>>>>>>> .7 and MT around >>>>>>>>>>>>>>>>>>>>>>>>>> .4 I think. And yes, I would use ?h.sulc as >>>>>>>>>>>>>>>>>>>>>>>>>> the background >>>>>>>>>>>>>>>>>>>>>>>>>> gray scale. The >>>>>>>>>>>>>>>>>>>>>>>>>> volume of the BAs would be computed using >>>>>>>>>>>>>>>>>>>>>>>>>> both surfaces, >>>>>>>>>>>>>>>>>>>>>>>>>> but the surface >>>>>>>>>>>>>>>>>>>>>>>>>> area can be from either one. I think we use >>>>>>>>>>>>>>>>>>>>>>>>>> the white by >>>>>>>>>>>>>>>>>>>>>>>>>> default, but you >>>>>>>>>>>>>>>>>>>>>>>>>> can use label_area to measure on whatever >>>>>>>>>>>>>>>>>>>>>>>>>> surface you want. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, 23 Apr 2012, >>>>>>>>>>>>>>>>>>>>>>>>>> _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> (forgot to do answer all, here it goes for >>>>>>>>>>>>>>>>>>>>>>>>>>> the list too) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Citando _andre...@sapo.pt: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Bruce, >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The ideia is to show one control subject >>>>>>>>>>>>>>>>>>>>>>>>>>>> vs. one patient >>>>>>>>>>>>>>>>>>>>>>>>>>>> inflated surface >>>>>>>>>>>>>>>>>>>>>>>>>>>> with BA surface (not volume, sorry) to >>>>>>>>>>>>>>>>>>>>>>>>>>>> show the difference >>>>>>>>>>>>>>>>>>>>>>>>>>>> (reduced surface >>>>>>>>>>>>>>>>>>>>>>>>>>>> area in one patient). Loading the >>>>>>>>>>>>>>>>>>>>>>>>>>>> relevant labels worked >>>>>>>>>>>>>>>>>>>>>>>>>>>> (I have the >>>>>>>>>>>>>>>>>>>>>>>>>>>> statistics shown in bar graphs, the >>>>>>>>>>>>>>>>>>>>>>>>>>>> images are only for >>>>>>>>>>>>>>>>>>>>>>>>>>>> visualizing the >>>>>>>>>>>>>>>>>>>>>>>>>>>> difference between controls and patients). When I >>>>>>>>>>>>>>>>>>>>>>>>>>>> threshold the labels in >>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject's inflated surface they >>>>>>>>>>>>>>>>>>>>>>>>>>>> shrink a lot, is this >>>>>>>>>>>>>>>>>>>>>>>>>>>> supposed to >>>>>>>>>>>>>>>>>>>>>>>>>>>> happen? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> The BA are V1, V2 and MT. What is the >>>>>>>>>>>>>>>>>>>>>>>>>>>> thresghold for V2? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> And is it correct to load ?h.sulc in a >>>>>>>>>>>>>>>>>>>>>>>>>>>> gray scale to have >>>>>>>>>>>>>>>>>>>>>>>>>>>> the usual cortex >>>>>>>>>>>>>>>>>>>>>>>>>>>> representation, or I should do it other way? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> And getting back to my previous email: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Another question is, how is the volume of the BA >>>>>>>>>>>>>>>> calculated? Is it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the surface-based stream? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And, which surface area is the on in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the output of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> BA stats? Is it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the pial or wm? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>>>>>>>>>>>>>> Andreia >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Andreia >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> sorry, I don't understand. What do you >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mean when you say >>>>>>>>>>>>>>>>>>>>>>>>>>>>> you want to " >>>>>>>>>>>>>>>>>>>>>>>>>>>>> show the resulting Brodmann area (only 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> BA) volume in >>>>>>>>>>>>>>>>>>>>>>>>>>>>> the inflated >>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface of my subjects". Do you mean >>>>>>>>>>>>>>>>>>>>>>>>>>>>> just to show what >>>>>>>>>>>>>>>>>>>>>>>>>>>>> portion of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface is in each of 3 Brodmann areas? >>>>>>>>>>>>>>>>>>>>>>>>>>>>> That you would >>>>>>>>>>>>>>>>>>>>>>>>>>>>> do by loading the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> relevant labels, although you will >>>>>>>>>>>>>>>>>>>>>>>>>>>>> probably want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>> threshold them >>>>>>>>>>>>>>>>>>>>>>>>>>>>> differently (e.g. V1 you could threshold >>>>>>>>>>>>>>>>>>>>>>>>>>>>> at .9 which is >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 90% and it would >>>>>>>>>>>>>>>>>>>>>>>>>>>>> have about the surface area of an >>>>>>>>>>>>>>>>>>>>>>>>>>>>> individual, while MT >>>>>>>>>>>>>>>>>>>>>>>>>>>>> would need to be >>>>>>>>>>>>>>>>>>>>>>>>>>>>> closer to .4 or .5). Or do you actually >>>>>>>>>>>>>>>>>>>>>>>>>>>>> mean the volume >>>>>>>>>>>>>>>>>>>>>>>>>>>>> of gray matter >>>>>>>>>>>>>>>>>>>>>>>>>>>>> within each BA? If the latter, it's just 3 >>>>>>>>>>>>>>>>>>>>>>>>>>>>> numbers/subject, so I would >>>>>>>>>>>>>>>>>>>>>>>>>>>>> think you would want a scatter plot or >>>>>>>>>>>>>>>>>>>>>>>>>>>>> something, not a >>>>>>>>>>>>>>>>>>>>>>>>>>>>> map on the >>>>>>>>>>>>>>>>>>>>>>>>>>>>> surface. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi all, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm sorry if these questions have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been covered >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> here, but I've >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> looked into the archives and still >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can't do what I need >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (and since I'm >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running out of time for this task I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> decided to post here): >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm using version 5.0.0. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I want to show the resulting Brodmann >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> area (only 3 BA) >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> volume in the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inflated surface of my subjects to show the >>>>>>>>>>>>>>>> differences between >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and controls (for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visualization purpose only). >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I've managed >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to overlay the volume in the curvature >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> menu but this is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for the entire >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cortex and I can't show the values bar. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> How can I show >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the volume of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only 3 BAs and have the scale bar? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Another question is, how is the volume of the BA >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calculated? Is it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the surface-based stream? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> And, which surface area is the on in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the output of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> BA stats? Is it >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the pial or wm? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks in advance, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ----- 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
