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Fsgd file format
by Clint Johns 31 Mar '14

31 Mar '14

I have a clarifying question about fsgd file format. We have 40 participants, and a large battery of individual difference measures (egg., vocabulary, phonological skill, etc.) We applied a PCA to the battery and found 4 components, corresponding to WMC, processing speed, comprehension ability, and phonological ability. We tested for main effects of each of these on thickness, area, and volume via QDEC. However, we also want to check for interactions - and since this is essentially 4 continuous factors, this is not QDEC-able (at least, it does not appear to be). A nuisance variable (e.g., mean thickness) is also present. Nregressors = Nclasses*(Nvariables+1) = 1*((4 components + 1 nuisance) +1) = 1*(5+1) = 6 Null contrast is 1 0 0 0 0 0 Main effect, e.g., of the working memory component (#1) is 0 1 0 0 0 0 Main effect, e.g., of the WM component modulated by the nuisance variable is 0 1 0 0 0 1 So the format to examine possible interactions, e.g., component 1 and component 2 interact to affect thickness, is 0 1 1 0 0 0 And with the nuisance variable 0 1 1 0 0 1 Do we have this right? THANKS!! Clint -- I remain... Clinton L. Johns, Ph.D. Research Scientist, Haskins Laboratories 300 George Street New Haven CT 06511 speech: 203-865-6163 x240 fax: 203-865-8963 net: johns(a)haskins.yale.edu

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The FreeSurfer lab is seeking Research Technicians
by Allison Stevens 31 Mar '14

31 Mar '14

Please see the job descriptions at the following links: https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchTechnologist Allison

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Fwd: Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 31 Mar '14

31 Mar '14

Hi list, ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- Data: Mon, 31 Mar 2014 13:22:14 +0100 De: _andreia_(a)sapo.pt Assunto: Re: [Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer(a)nmr.mgh.harvard.edu Hi Bruce, The surfaces look pretty good along the 3 labels. Although it is hard to get the whole picture from one slice I've attached some images of 2 labels (since my previous email was rejected due to excessive size). The surfaces look as accurate in the rest of the slices. Should I do any different procedure? Could this be due to the intersection of the labels along the grey matter that are not picking up exactly the same area in the white and pial surfaces?? Moreover, I've obtained the stats using aparcstats2table before running qcache with the new mris_preproc (I'm using 5.0), but as far as I'm aware the measures obtained from aparcstats2table are not affected by the mri_preproc bug, right? Thanks, Andreia Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > the easiest way is to just use the aparc+aseg.mgz > > cheers > Bruce > On Sun, 30 Mar 2014, > _andreia_(a)sapo.pt wrote: > >> How do I overlay aparc labels in tkmedit? I can load Brodmann area >> labels, but not aparc. >> >> Thanks! >> Andreia >> >> >> Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> >>> and what do the surfaces look like in those regions? For the wm surface >>> are to be larger it probably needs to be a lot less smooth >>> >>> On Sun, 30 Mar 2014, _andreia_(a)sapo.pt wrote: >>> >>>> Hi, >>>> >>>> Sorry, I mixed it up in text of the first email. The WM is bigger. The >>>> values of the example are correct. >>>> >>>> Thanks! >>>> >>>> >>>> Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> >>>>> Hi Andreia, >>>>> >>>>> which one is bigger? In your first email you said pial (which should be) >>>>> and in your second you said white matter >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Sun, 30 Mar 2014, >>>>> _andreia_(a)sapo.pt wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> What could be the reason to get bigger surface area from WM surface >>>>>> than from the pial surface in the 3 labels? >>>>>> >>>>>> Thank you! >>>>>> Andreia >>>>>> >>>>>> >>>>>> >>>>>> ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- >>>>>> Data: Fri, 28 Mar 2014 17:43:43 +0000 >>>>>> De: _andreia_(a)sapo.pt >>>>>> Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and >>>>>> aparcstats2table >>>>>> Para: freesurfer(a)nmr.mgh.harvard.edu >>>>>> >>>>>> Hi Doug, >>>>>> >>>>>> Thank you very much! It did the trick! >>>>>> >>>>>> However, I've noticed that the surface area obtained from the pial >>>>>> surface is bigger than the one obtained from white surface in 3 labels: >>>>>> >>>>>> Example of a control subject:Bankssts(WM=1161; pial=1026), >>>>>> pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756). >>>>>> >>>>>> Example of a patient:Bankssts(WM=1096; pial=1076), >>>>>> pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121). >>>>>> >>>>>> This only happens in these 3 labels and in both hemispheres. Is >>>>>> this expected? >>>>>> >>>>>> >>>>>> Andreia >>>>>> >>>>>> >>>>>> Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>>>>> >>>>>>> try this >>>>>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f >>>>>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c >>>>>>> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial >>>>>>> >>>>>>> >>>>>>> On 03/28/2014 06:31 AM, _andreia_(a)sapo.pt wrote: >>>>>>>> Hello all, >>>>>>>> >>>>>>>> How do I get aparc stats (area) using the pial surface, please? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Andreia >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- >>>>>>>> Data: Thu, 27 Mar 2014 11:31:13 +0000 >>>>>>>> De: _andreia_(a)sapo.pt >>>>>>>> Responder Para: Freesurfer support list >>>>>>>> <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and >>>>>>>> aparcstats2table >>>>>>>> Para: freesurfer(a)nmr.mgh.harvard.edu, >>>>>>>> vinke(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>> Hi Louis, >>>>>>>> >>>>>>>> It didn't work either. This is what shows up in the terminal after >>>>>>>> running mris_anatomical_stats: >>>>>>>> >>>>>>>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a >>>>>>>> ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial >>>>>>>> INFO: assuming MGZ format for volumes. >>>>>>>> computing statistics for each annotation in ./rh.aparc.annot. >>>>>>>> reading volume >>>>>>>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz... >>>>>>>> reading input surface >>>>>>>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... >>>>>>>> reading input pial surface >>>>>>>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... >>>>>>>> reading input white surface >>>>>>>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white... >>>>>>>> reading colortable from annotation file... >>>>>>>> colortable with 36 entries read (originally >>>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>>> Saving annotation colortable ./aparc.ctab >>>>>>>> >>>>>>>> table columns are: >>>>>>>> number of vertices >>>>>>>> total surface area (mm^2) >>>>>>>> total gray matter volume (mm^3) >>>>>>>> average cortical thickness +- standard deviation (mm) >>>>>>>> integrated rectified mean curvature >>>>>>>> integrated rectified Gaussian curvature >>>>>>>> folding index >>>>>>>> intrinsic curvature index >>>>>>>> structure name >>>>>>>> >>>>>>>> 1272 793 2092 2.485 0.342 0.141 0.042 24 2.4 >>>>>>>> bankssts >>>>>>>> 1184 957 2200 2.419 0.757 0.226 0.187 248 11.5 >>>>>>>> caudalanteriorcingulate >>>>>>>> 3222 2408 5307 2.324 0.512 0.136 0.040 58 4.8 >>>>>>>> caudalmiddlefrontal >>>>>>>> 2468 1735 2917 1.798 0.388 0.150 0.064 54 >>>>>>>> 5.2 cuneus >>>>>>>> 504 582 1801 3.807 0.663 0.256 0.084 24 2.0 >>>>>>>> entorhinal >>>>>>>> 4892 3757 9658 2.696 0.715 0.183 0.073 167 15.0 >>>>>>>> fusiform >>>>>>>> 8153 6383 13887 2.315 0.543 0.160 0.049 179 16.6 >>>>>>>> inferiorparietal >>>>>>>> 4885 3695 10298 2.929 0.668 0.171 0.069 187 14.8 >>>>>>>> inferiortemporal >>>>>>>> 1470 1045 2169 2.137 0.673 0.200 0.129 154 8.8 >>>>>>>> isthmuscingulate >>>>>>>> 6612 4848 10068 2.208 0.530 0.161 0.058 217 15.6 >>>>>>>> lateraloccipital >>>>>>>> 3665 2871 6467 2.380 0.684 0.186 0.067 123 11.1 >>>>>>>> lateralorbitofrontal >>>>>>>> 4593 3224 5598 1.811 0.528 0.170 0.072 165 >>>>>>>> 13.4 lingual >>>>>>>> 2623 2020 4262 2.290 0.776 0.191 0.072 179 8.1 >>>>>>>> medialorbitofrontal >>>>>>>> 4570 3991 10068 2.785 0.605 0.169 0.052 154 10.0 >>>>>>>> middletemporal >>>>>>>> 1041 802 1923 2.621 0.705 0.161 0.058 20 2.4 >>>>>>>> parahippocampal >>>>>>>> 2067 1415 2808 2.156 0.580 0.115 0.024 20 2.1 >>>>>>>> paracentral >>>>>>>> 1534 1130 2779 2.551 0.445 0.149 0.042 29 2.5 >>>>>>>> parsopercularis >>>>>>>> 1366 1265 2718 2.458 0.607 0.184 0.049 23 2.9 >>>>>>>> parsorbitalis >>>>>>>> 2166 1826 3699 2.258 0.484 0.166 0.048 34 4.8 >>>>>>>> parstriangularis >>>>>>>> 2637 1647 2528 1.563 0.436 0.137 0.043 47 4.7 >>>>>>>> pericalcarine >>>>>>>> 6180 4524 7746 1.879 0.596 0.122 0.030 62 7.3 >>>>>>>> postcentral >>>>>>>> 1694 1270 2783 2.265 0.721 0.188 0.088 64 7.6 >>>>>>>> posteriorcingulate >>>>>>>> 7118 5162 11283 2.336 0.590 0.115 0.027 67 8.4 >>>>>>>> precentral >>>>>>>> 5554 4071 8657 2.206 0.527 0.149 0.051 108 12.8 >>>>>>>> precuneus >>>>>>>> 975 856 2003 2.660 0.591 0.167 0.063 27 2.8 >>>>>>>> rostralanteriorcingulate >>>>>>>> 8524 6942 13736 2.121 0.581 0.163 0.047 168 16.2 >>>>>>>> rostralmiddlefrontal >>>>>>>> 9820 7927 17866 2.426 0.605 0.150 0.043 144 16.4 >>>>>>>> superiorfrontal >>>>>>>> 8910 6920 12666 1.952 0.561 0.134 0.033 102 11.5 >>>>>>>> superiorparietal >>>>>>>> 5164 4064 9880 2.602 0.579 0.141 0.041 129 8.5 >>>>>>>> superiortemporal >>>>>>>> 4538 3307 6832 2.129 0.591 0.140 0.035 63 6.4 >>>>>>>> supramarginal >>>>>>>> 395 426 864 2.488 0.541 0.199 0.057 6 0.9 >>>>>>>> frontalpole >>>>>>>> 612 699 2018 3.610 0.559 0.213 0.073 17 2.2 >>>>>>>> temporalpole >>>>>>>> 479 330 680 2.330 0.353 0.110 0.024 3 0.5 >>>>>>>> transversetemporal >>>>>>>> 3442 1950 6183 2.886 0.890 0.376 1.131 154 >>>>>>>> 291.0 insula >>>>>>>> [user@localhost label]$ aparcstats2table --hemi rh --subjects >>>>>>>> FERNANDORODRIGUES --parc aparcpial --meas area -t >>>>>>>> rh_FERNANDORODRIGUES.aparc.surface.pial.txt >>>>>>>> Number of subjects : 1 >>>>>>>> Building the table.. >>>>>>>> ERROR: cannot find >>>>>>>> /home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/rh.aparcpial.stats >>>>>>>> Use --skip flag if you want to continue in such cases >>>>>>>> >>>>>>>> >>>>>>>> Maybe is the mris_anatomical_stats that has something wrong? I've been >>>>>>>> using the command for Brodmann Areas and just tried to adapt it to >>>>>>>> aparc. For BA I've also had to run label2label and had to create a new >>>>>>>> BA.annot but that was because I had to get the thresholded BA values, >>>>>>>> I think this doesn't apply to aparc. From aparc I only want to get >>>>>>>> surface area based on the pial surface. >>>>>>>> >>>>>>>> Thank you, >>>>>>>> Andreia >>>>>>>> >>>>>>>> >>>>>>>> Quoting Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu>: >>>>>>>> >>>>>>>>> Hi Andreia, >>>>>>>>> If you remove the underscore from aparc_pial for the --parc >>>>>>>>> flag in the >>>>>>>>> aparcstats2table command, that should do the trick. >>>>>>>>> -Louis >>>>>>>>> >>>>>>>>> On Wed, 26 Mar 2014, _andreia_(a)sapo.pt wrote: >>>>>>>>> >>>>>>>>>> Hello list, >>>>>>>>>> >>>>>>>>>> I'm trying to get aparc surface area from the pial surface >>>>>>>>>> in a table >>>>>>>>>> using aparcstats2table but I'm not being able to... >>>>>>>>>> >>>>>>>>>> I've already created the file aparc_pial.stats inside the stats dir >>>>>>>>>> running the following command line from the subjects's label dir: >>>>>>>>>> >>>>>>>>>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a >>>>>>>>>> ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial >>>>>>>>>> >>>>>>>>>> And if I open the aparc_pial.stats file the surfaces are bigger then >>>>>>>>>> in aparc (white matter). >>>>>>>>>> >>>>>>>>>> But when I try to get the table using: >>>>>>>>>> >>>>>>>>>> aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial >>>>>>>>>> --meas area -t rh_aparc_surface_pial.txt >>>>>>>>>> >>>>>>>>>> I get the message: >>>>>>>>>> >>>>>>>>>> Number of subjects : 1 >>>>>>>>>> Building the table.. >>>>>>>>>> ERROR: cannot find >>>>>>>>>> /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats >>>>>>>>>> Use --skip flag if you want to continue in such cases >>>>>>>>>> >>>>>>>>>> What's wrong? >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> Andreia >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(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 >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ----- Fim de mensagem reenviada -----

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Export label to T1.nii
by gong jinnan 31 Mar '14

31 Mar '14

Hi FreeSurfer team, After recon -all, I got some labels. I would like to export FS labels as seed region for tractography in FSL. My ROI is precentral which is 24th region in DKTatlas40. But I have 2 small questions about dong that: 1. Is there any way to extra this region from labels like a2009s or DKTatlas40? 2. I tried using "mri_label2vol —label label/rh.BA1.label —temp /sub_1_t1.nii —identity —o BA1_in_vol.nii” to study the mri_label2vol script, but my result is very inaccuracy. My T1 image is in 1*1*1 mm³ and FOV is 256*256*158 mm. My results is in attachment，and I really don’t know what’s wrong with it. And could you tell me how to do that in a right way. I would appreciate if you could help me! Sincerely， Jinnan Best wishes for you!

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MeanThickness
by Yang, Daniel 30 Mar '14

30 Mar '14

Dear FreeSurfer Experts, I would like to extract the mean thickness for each subject, and I can see that in the lh.aparc.stats, there are three lines. For example: # Measure Cortex, NumVert, Number of Vertices, 107414, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2 # Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm I am wondering what command I can run with aparcstats2table or mris_calc to retrieve these three pieces of information for each subject? And is the MeanThickness across the whole brain supposed to be (lh + rh)/2? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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problem about 'mri_glmfit-sim
by yd li 30 Mar '14

30 Mar '14

Hello experts, I'm working with FS 5.3.0. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a mri_glmfit.log in folder /.../g2.lh, and copied this file to folder /.../g2.lh/C1/.But i still got an error 'fwhm: Undefined variable.' Can anybody help me settle this problem? Thank you!

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transform common space into original space
by charujing123 30 Mar '14

30 Mar '14

Hi FS experts I have done the group thickness analysis(two group t-test), and get the result(i.e. sig.mgh). I got one cluster in the sig.mgh file. I want to convert this cluster into each subject specific original space(i.e brainmask.mgz). Thanks. All the best. Rujing Zha 2014-03-30 charujing123

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see result by tksurfer
by charujing123 30 Mar '14

30 Mar '14

Hi FS experts I completed group analysis by this method:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Cl… . Now I want to represent the result just the way as non-surface(please see attachment). I want to know how to load sig.mgh by tksurfer? Thanks. All the best Rujing Zha 2014-03-30 charujing123

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Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 30 Mar '14

30 Mar '14

Hello, What could be the reason to get bigger surface area from WM surface than from the pial surface in the 3 labels? Thank you! Andreia ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- Data: Fri, 28 Mar 2014 17:43:43 +0000 De: _andreia_(a)sapo.pt Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table Para: freesurfer(a)nmr.mgh.harvard.edu Hi Doug, Thank you very much! It did the trick! However, I've noticed that the surface area obtained from the pial surface is bigger than the one obtained from white surface in 3 labels: Example of a control subject:Bankssts(WM=1161; pial=1026), pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756). Example of a patient:Bankssts(WM=1096; pial=1076), pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121). This only happens in these 3 labels and in both hemispheres. Is this expected? Andreia Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > try this > mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f > ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c > ../label/aparc.annot.ctab vrfp-oct11-anat lh pial > > > On 03/28/2014 06:31 AM, _andreia_(a)sapo.pt wrote: >> Hello all, >> >> How do I get aparc stats (area) using the pial surface, please? >> >> Thanks, >> Andreia >> >> >> >> ----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- >> Data: Thu, 27 Mar 2014 11:31:13 +0000 >> De: _andreia_(a)sapo.pt >> Responder Para: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and >> aparcstats2table >> Para: freesurfer(a)nmr.mgh.harvard.edu, vinke(a)nmr.mgh.harvard.edu >> >> Hi Louis, >> >> It didn't work either. This is what shows up in the terminal after >> running mris_anatomical_stats: >> >> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a >> ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial >> INFO: assuming MGZ format for volumes. >> computing statistics for each annotation in ./rh.aparc.annot. >> reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz... >> reading input surface >> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... >> reading input pial surface >> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial... >> reading input white surface >> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white... >> reading colortable from annotation file... >> colortable with 36 entries read (originally >> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >> Saving annotation colortable ./aparc.ctab >> >> table columns are: >> number of vertices >> total surface area (mm^2) >> total gray matter volume (mm^3) >> average cortical thickness +- standard deviation (mm) >> integrated rectified mean curvature >> integrated rectified Gaussian curvature >> folding index >> intrinsic curvature index >> structure name >> >> 1272 793 2092 2.485 0.342 0.141 0.042 24 2.4 >> bankssts >> 1184 957 2200 2.419 0.757 0.226 0.187 248 11.5 >> caudalanteriorcingulate >> 3222 2408 5307 2.324 0.512 0.136 0.040 58 4.8 >> caudalmiddlefrontal >> 2468 1735 2917 1.798 0.388 0.150 0.064 54 >> 5.2 cuneus >> 504 582 1801 3.807 0.663 0.256 0.084 24 2.0 >> entorhinal >> 4892 3757 9658 2.696 0.715 0.183 0.073 167 15.0 >> fusiform >> 8153 6383 13887 2.315 0.543 0.160 0.049 179 16.6 >> inferiorparietal >> 4885 3695 10298 2.929 0.668 0.171 0.069 187 14.8 >> inferiortemporal >> 1470 1045 2169 2.137 0.673 0.200 0.129 154 8.8 >> isthmuscingulate >> 6612 4848 10068 2.208 0.530 0.161 0.058 217 15.6 >> lateraloccipital >> 3665 2871 6467 2.380 0.684 0.186 0.067 123 11.1 >> lateralorbitofrontal >> 4593 3224 5598 1.811 0.528 0.170 0.072 165 >> 13.4 lingual >> 2623 2020 4262 2.290 0.776 0.191 0.072 179 8.1 >> medialorbitofrontal >> 4570 3991 10068 2.785 0.605 0.169 0.052 154 10.0 >> middletemporal >> 1041 802 1923 2.621 0.705 0.161 0.058 20 2.4 >> parahippocampal >> 2067 1415 2808 2.156 0.580 0.115 0.024 20 2.1 >> paracentral >> 1534 1130 2779 2.551 0.445 0.149 0.042 29 2.5 >> parsopercularis >> 1366 1265 2718 2.458 0.607 0.184 0.049 23 2.9 >> parsorbitalis >> 2166 1826 3699 2.258 0.484 0.166 0.048 34 4.8 >> parstriangularis >> 2637 1647 2528 1.563 0.436 0.137 0.043 47 4.7 >> pericalcarine >> 6180 4524 7746 1.879 0.596 0.122 0.030 62 7.3 >> postcentral >> 1694 1270 2783 2.265 0.721 0.188 0.088 64 7.6 >> posteriorcingulate >> 7118 5162 11283 2.336 0.590 0.115 0.027 67 8.4 >> precentral >> 5554 4071 8657 2.206 0.527 0.149 0.051 108 12.8 >> precuneus >> 975 856 2003 2.660 0.591 0.167 0.063 27 2.8 >> rostralanteriorcingulate >> 8524 6942 13736 2.121 0.581 0.163 0.047 168 16.2 >> rostralmiddlefrontal >> 9820 7927 17866 2.426 0.605 0.150 0.043 144 16.4 >> superiorfrontal >> 8910 6920 12666 1.952 0.561 0.134 0.033 102 11.5 >> superiorparietal >> 5164 4064 9880 2.602 0.579 0.141 0.041 129 8.5 >> superiortemporal >> 4538 3307 6832 2.129 0.591 0.140 0.035 63 6.4 >> supramarginal >> 395 426 864 2.488 0.541 0.199 0.057 6 0.9 >> frontalpole >> 612 699 2018 3.610 0.559 0.213 0.073 17 2.2 >> temporalpole >> 479 330 680 2.330 0.353 0.110 0.024 3 0.5 >> transversetemporal >> 3442 1950 6183 2.886 0.890 0.376 1.131 154 >> 291.0 insula >> [user@localhost label]$ aparcstats2table --hemi rh --subjects >> FERNANDORODRIGUES --parc aparcpial --meas area -t >> rh_FERNANDORODRIGUES.aparc.surface.pial.txt >> Number of subjects : 1 >> Building the table.. >> ERROR: cannot find >> /home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/rh.aparcpial.stats >> Use --skip flag if you want to continue in such cases >> >> >> Maybe is the mris_anatomical_stats that has something wrong? I've been >> using the command for Brodmann Areas and just tried to adapt it to >> aparc. For BA I've also had to run label2label and had to create a new >> BA.annot but that was because I had to get the thresholded BA values, >> I think this doesn't apply to aparc. From aparc I only want to get >> surface area based on the pial surface. >> >> Thank you, >> Andreia >> >> >> Quoting Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu>: >> >>> Hi Andreia, >>> If you remove the underscore from aparc_pial for the --parc flag in the >>> aparcstats2table command, that should do the trick. >>> -Louis >>> >>> On Wed, 26 Mar 2014, _andreia_(a)sapo.pt wrote: >>> >>>> Hello list, >>>> >>>> I'm trying to get aparc surface area from the pial surface in a table >>>> using aparcstats2table but I'm not being able to... >>>> >>>> I've already created the file aparc_pial.stats inside the stats dir >>>> running the following command line from the subjects's label dir: >>>> >>>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a >>>> ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial >>>> >>>> And if I open the aparc_pial.stats file the surfaces are bigger then >>>> in aparc (white matter). >>>> >>>> But when I try to get the table using: >>>> >>>> aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial >>>> --meas area -t rh_aparc_surface_pial.txt >>>> >>>> I get the message: >>>> >>>> Number of subjects : 1 >>>> Building the table.. >>>> ERROR: cannot find >>>> /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats >>>> Use --skip flag if you want to continue in such cases >>>> >>>> What's wrong? >>>> >>>> Thank you, >>>> Andreia >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >> >> > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ----- Fim de mensagem reenviada -----

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Problem with license for running mris_make_face_parcellation
by Mahshid Najafi 28 Mar '14

28 Mar '14

Hi, I have an openSUSE 12.2 (x86_64) and my freesurfer version is freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/Mahshid/fsl When I run freeview, it works correctly, but when I try to run tkmedit and mris_make_face_parcellation it gives following error: -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I updated the .license recently and tried some suggestion previously uploaded on mailing list, but none worked. Would you please let me know how to solve it? my .license is: mhshid(a)gmail.com 17259 *CJUIGOoAoZws Thanks, Mahshid

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