Freesurfer

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30132 discussions

aseg.stats not matching up
by Joshua Lee 16 May '12

16 May '12

Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill tool to relabel the *entire* left hippocampus segmentation to 'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left hippocampus volume from the original aseg.stats be identical to the volume of MyImaginaryLabel in the newly generated aseg.stats? Every voxel from the prior label is now assigned to the new label; yet, I am getting different results (by about 100 voxels in the ones I've tried). The command Im using to recalculate: mri_segstats --seg /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz --sum /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats --pv /usr/local/freesurfer/subjects/s02/mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/s02/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab /usr/local/freesurfer/8regions.txt --subject s02; Now if I were to relabel 'MyNewImaginaryLabel' to 'AthirdLabel', and again changing every voxel in 'MyNewImaginaryLabel' to the new label, the computed volumes do not change. This led me to suspect that aseg.mgz contains probability estimates at each voxel that are then subsequently overwritten by my tkmedits. However, per a previous conversation from a year ago or so with Bruce and also the relevant Freesurfer documentation this does not seem to be the case. Partial volume information is not contained within the aseg.mgz (right!?), but is computed by mri_segstats by comparing border voxels with intensities in the norm.mgz. So I am at a loss on why these should be different. This has been replicated in version 4.5 and 5.1 - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

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FsFastIndividual Retinotopy - Polar Only
by Daniel Cole 16 May '12

16 May '12

Hello, I have some questions regarding the FsFastIndividual pipeline. I hope you can take a look at the commands I have run and give me some insight into what the problem might potentially be. I have 5 rotating wedge stimuli runs 1. I set up my subject's directories according to the freesurfer tutorial powerpoint and declare my environmental variables using- <*export FREESURFER_HOME=/Volumes/RCBI/freesurfer* *export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy* *source $FREESURFER_HOME/SetUpFreeSurfer.sh*> Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc) rtopy.par=" stimtype polar direction neg" 2. I then reconstruct the strucutural data using- <*recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01*> 3. I create the subjectname file, run preprocessing, and make the analysis files. <*preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold* *mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5* *mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5*> 4. Then I run the analysis using- <*selxavg3-sess -analysis rtopy.self.lh -sf sessid* *selxavg3-sess -analysis rtopy.self.lh -sf sessid*> ~This step was giving me an error until I added "faux" eccentricity run folders with runs 1-5 functional data copied and rtopy.par files with stimtype eccen. Rerunning these 2 steps with the faux eccentricity data fixed the error message. 5. Create occipital patch with (http://www.alivelearn.net/?p=65) as guideline. Flatten patch using- <*mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat* *mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat*> And create fieldsign map using- <*fieldsign-sess -a rtopy.self.lh -occip -sf sessid* *fieldsign-sess -a rtopy.self.rh -occip -sf sessid*> ~Error that analysis isn't retinotopy (because I used -abblocked), retrying step 3 with -retinotopy allowed me to create the fieldsign map. --- For the -abblocked and -retinotopy analysis I am able to look at the results using <*tksurfer-sess -a rtopy.self.lh -sf sessid*>*.* My questions are: - Should I be using -abblocked or -retinotopy for a polar only design? - Is it ok to create "faux" eccentricity folders and then only look at the polar data? - Why is it for either of these analyses I can't view the angle map using <*tksurfer-sess -a rtopy.self.?h -s sessid -map angle*>? In fact the angle file is not created. Thanks so much for your time and help. Daniel * * -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcole10(a)u.rochester.edu

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Flip brain
by Tadeu Kubo 16 May '12

16 May '12

Dear FS experts, How can I flip hemispheres? I read the mail list and Doug said that (2010): The problem with this is that you will get different results when you use the left hemi and the right-flipped-to-left hemi as compared to the right hemi and the left-flipped-to-right hemi. You'll actually get different areas that appear to be significant. This is because the right-flipped-to-left is registered to the left template target and it does not register as well as the left registered to the left template target (and the same in the other direction). I'm sure it means something, but I don't know how to interpret it. doug I'm specially interesting because we're studying MTS. The status of this procedure remains the same or it is possible to do it ? Thank you, Tadeu

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Dependent measures qdec
by Mahinda Yogarajah 16 May '12

16 May '12

Dear All, Could someone explain (or point me in the right direction) as to the meaning of the dependent measures (which can be used in qdec) - intensity_deep/intensity_superficial - intensity_deep.mgz/intensity_superficial.mgz - white K/H What do they represent ? Thanks. Mahinda

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Re: [Freesurfer] Asegstat2 table error
by Douglas N Greve 16 May '12

16 May '12

It just loads in a single file and creates a "table" with one row. On 05/16/2012 02:02 PM, Rashmi Singh wrote: > Can you also let me know what does the following command do. > Thanks, > Rashmi. > > On 5/16/12 12:58 PM, "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> wrote: > >> I was able to load both of those. Try this: >> >> cd /opt/freesurfer/subjects/AA262.G1/stats >> asegstats2table -i aseg.stats -t test.dat >> >> doug >> >> >> >> >> On 05/16/2012 01:25 PM, Rashmi Singh wrote: >>> Doug, >>> Attached are the aseg.stat files of the two different runs (AA262.G1 and >>> AB054.G1) where I got the error message. >>> Thanks >>> Rashmi. >>> >>> >>> On 5/16/12 11:41 AM, "Douglas N Greve"<greve(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats? >>>> Also, please remember to copy the list so that others can see the >>>> answer >>>> and so that others can help with the answer. >>>> thanks! >>>> doug >>>> >>>> On 05/16/2012 11:56 AM, Rashmi Singh wrote: >>>>> Dough, >>>>> >>>>> Yes, the stat files exist with all its content. I can individually >>>>> import the text aseg files into xcell sheet, but I have 44 data >>>>> files, so I was trying asegstat2table option. >>>>> What do you think may be going wrong. The output file says that recon >>>>> all completed without error for all my subject files. >>>>> >>>>> Thanks, >>>>> Rashmi. >>>>> >>>>> >>>>> >>>>> >>>>> Do those files exist? Do they have content in them? >>>>> doug >>>>> >>>>> On 05/15/2012 05:51 PM, Rashmi Singh wrote: >>>>> >>>>> Hello, >>>>> I am trying to get the asegmentation information after the >>>>> recon-all >>>>> run in the table form, but I am continuously getting the >>>>> following >>>>> error >>>>> >>>>> asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas >>>>> volume >>>>> --tablefile asegstats.txt >>>>> SUBJECTS_DIR : /opt/freesurfer/subjects >>>>> Parsing the .stats files >>>>> ERROR: The stats file >>>>> /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found >>>>> or >>>>> is >>>>> too small to be a valid statsfile >>>>> Use --skip flag to automatically skip bad stats files >>>>> >>>>> I did try to use the skip option , but then , it skips all the >>>>> files >>>>> giving the same error. >>>>> When I individually open the aseg files from the stats folder, >>>>> those >>>>> look fine to me. >>>>> >>>>> Please advise. >>>>> >>>>> Rashmi. >>>>> >>>>> >>>>> >>>>> ----------------------------------------------------------------------- >>>>> - >>>>> >>>>> This document may contain information covered under the Privacy Act, 5 >>>>> USC 552(a), and/or the Health Insurance Portability and Accountability >>>>> Act (PL 104-191) and its various implementing regulations and must be >>>>> protected in accordance with those provisions. Healthcare information >>>>> is personal and sensitive and must be treated accordingly. If this >>>>> correspondence contains healthcare information it is being provided to >>>>> you after appropriate authorization from the patient or under >>>>> circumstances that don't require patient authorization. You, the >>>>> recipient, are obligated to maintain it in a safe, secure and >>>>> confidential manner. Redisclosure without additional patient consent >>>>> or as permitted by law is prohibited. Unauthorized redisclosure or >>>>> failure to maintain confidentiality subjects you to application of >>>>> appropriate sanction. If you have received this correspondence in >>>>> error, please notify the sender at once and destroy any copies you >>>>> have made. >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> 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. >>>> >>> ________________________________ >>> >>> This document may contain information covered under the Privacy Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and Accountability >>> Act (PL 104-191) and its various implementing regulations and must be >>> protected in accordance with those provisions. Healthcare information is >>> personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being provided to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient consent or >>> as permitted by law is prohibited. Unauthorized redisclosure or failure >>> to maintain confidentiality subjects you to application of appropriate >>> sanction. If you have received this correspondence in error, please >>> notify the sender at once and destroy any copies you have made. >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> > > ________________________________ > > This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Asegstat2 table error
by Douglas N Greve 16 May '12

16 May '12

Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats? Also, please remember to copy the list so that others can see the answer and so that others can help with the answer. thanks! doug On 05/16/2012 11:56 AM, Rashmi Singh wrote: > > Dough, > > Yes, the stat files exist with all its content. I can individually > import the text aseg files into xcell sheet, but I have 44 data > files, so I was trying asegstat2table option. > What do you think may be going wrong. The output file says that recon > all completed without error for all my subject files. > > Thanks, > Rashmi. > > > > > Do those files exist? Do they have content in them? > doug > > On 05/15/2012 05:51 PM, Rashmi Singh wrote: > > Hello, > I am trying to get the asegmentation information after the recon-all > run in the table form, but I am continuously getting the following > error > > asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume > --tablefile asegstats.txt > SUBJECTS_DIR : /opt/freesurfer/subjects > Parsing the .stats files > ERROR: The stats file > /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is > too small to be a valid statsfile > Use --skip flag to automatically skip bad stats files > > I did try to use the skip option , but then , it skips all the files > giving the same error. > When I individually open the aseg files from the stats folder, those > look fine to me. > > Please advise. > > Rashmi. > > > ------------------------------------------------------------------------ > > This document may contain information covered under the Privacy Act, 5 > USC 552(a), and/or the Health Insurance Portability and Accountability > Act (PL 104-191) and its various implementing regulations and must be > protected in accordance with those provisions. Healthcare information > is personal and sensitive and must be treated accordingly. If this > correspondence contains healthcare information it is being provided to > you after appropriate authorization from the patient or under > circumstances that don't require patient authorization. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Redisclosure without additional patient consent > or as permitted by law is prohibited. Unauthorized redisclosure or > failure to maintain confidentiality subjects you to application of > appropriate sanction. If you have received this correspondence in > error, please notify the sender at once and destroy any copies you > have made. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Different values for cortical thickness
by Nooshin Zadeh 16 May '12

16 May '12

Dear Freesurfer Friends I have a question about cortical thickness. I do not understand why these commands give us DIFFERENT values for "average cortical thickness". Can you please let me know if you have any idea. Thanks a lot mris_anatomical_stats N2207 lh number of vertices = 157417 total surface area = 102378 mm^2 total gray matter volume = 234251 mm^3 average cortical thickness = 2.080 mm +- 0.889 mm average integrated rectified mean curvature = 0.198 average integrated rectified Gaussian curvature = 0.223 folding index = 13893 intrinsic curvature index = 1137.3 mris_anatomical_stats -t N2207/label/lh.cortex.label -b N2207 lh same as mris_anatomical_stats -t -b N2207 lh number of vertices = 157417 total surface area = 102378 mm^2 total gray matter volume = 0 mm^3 average cortical thickness = 0.000 mm +- 0.000 mm average integrated rectified mean curvature = 0.198 average integrated rectified Gaussian curvature = 0.223 folding index = 13893 intrinsic curvature index = 1137.3

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Re: [Freesurfer] gzipRe: Fwd: Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 16 May '12

16 May '12

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 <fischl(a)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, _andreia_(a)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 <fischl(a)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, _andreia_(a)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 <fischl(a)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, _andreia_(a)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 <fischl(a)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, _andreia_(a)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 <fischl(a)nmr.mgh.harvard.edu>: >>>>>>>>>> >>>>>>>>>>> try a thresh of 1.1 (it's stat < thresh, not stat <= thresh) >>>>>>>>>>> On Wed, 2 May 2012, _andreia_(a)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 <nicks(a)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, _andreia_(a)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 <nicks(a)nmr.mgh.harvard.edu>: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> you can download it from here: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… >>>>>>>>>>>>>>> n. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, 2012-04-26 at 13:40 +0100, _andreia_(a)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 <fischl(a)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, _andreia_(a)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 <fischl(a)nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> in $FREESURFER_HOME/bin (and unzip and chmod it) >>>>>>>>>>>>>>>>>>> On Wed, 25 Apr 2012, _andreia_(a)sapo.pt wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Where should I put it? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> try this one >>>>>>>>>>>>>>>>>>>>> On Wed, 25 Apr 2012, _andreia_(a)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 <fischl(a)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, _andreia_(a)sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> (sorry, here it is for the list again) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ----- Mensagem encaminhada de Bruce Fischl >>>>>>>>>>>>>>>>>>>>>>>> <fischl(a)nmr.mgh.harvard.edu> ----- >>>>>>>>>>>>>>>>>>>>>>>> Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) >>>>>>>>>>>>>>>>>>>>>>>> De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>>>>>>>>>>>>>>>>>>>>> Assunto: Re: [Freesurfer] Load Brodmann >>>>>>>>>>>>>>>>>>>>>>>> surface area into >>>>>>>>>>>>>>>>>>>>>>>> inflated surface >>>>>>>>>>>>>>>>>>>>>>>> Para: _andreia_(a)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, _andreia_(a)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 <fischl(a)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, >>>>>>>>>>>>>>>>>>>>>>>>>> _andreia_(a)sapo.pt wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> (forgot to do answer all, here it goes for >>>>>>>>>>>>>>>>>>>>>>>>>>> the list too) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Citando _andreia_(a)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 <fischl(a)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, _andreia_(a)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(a)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(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> ----- Fim de mensagem reenviada ----- >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>> >>> >> >>

1 0

vertex-wise correlation
by Kemmotsu, Nobuko 15 May '12

15 May '12

Dear Freesurfer experts, I have fMRI data that are processed in AFNI that I would like to examine the relationship with cortical thickness measures. In particular, I am interested in vertex-wise correlation of thickness and BOLD % signal change. The problem is I am new to Freesurfer. So far I have found that the program "mri_glmfit" appears to be able to handle vertex-wise regressor, with the -pvr option. First, does this enable me to do vertex-wise bivariate correlation? Second, if so, it appears that the input files need to be concatenated (or stacked??), and for FreeSurfer measures, "mris_preproc" seems to take care of it. But, how can I stack/concatenate the afni-generated files (which are registered to and mapped on to each individual's surface that are in .mgh format)?? I appreciate any input you may have- -- Nobuko Kemmotsu, Ph.D. University of California, San Diego

1 0

asegstats2table error
by Rashmi Singh 15 May '12

15 May '12

Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I did try to use the skip option , but then , it skips all the files giving the same error. When I individually open the aseg files from the stats folder, those look fine to me. Please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

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