Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

SEEDING in Tracula
by Durai Arasan 01 Apr '14

01 Apr '14

Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts. However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc? I guess I am asking if it can do LOCAL tractography of any kind? Thank you!

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native or fsaverage spherical space for distance measures?
by Milde, Christopher 01 Apr '14

01 Apr '14

Dear Freesurfers, according to my research and 'playing-around' with Freesurfer tools on measuring distances between vertices or peak voxels, I'm still unsure about the most adequate way of comparing distances between peak voxels corrected for folding patterns. To my current knowledge, I figured out the following procedures: Goal: comparing cortical distances between peak voxels between subjects of different clinical populations 1.) Manual procedure using Freeview spline tool: using orig.mgz + white and pial surfaces + thresh_zstat images (FSL) è Using Measure tool (spline) to create a smoothed line within the cortical ribbon è Output: absolute cortical distances in [mm] è Problem: topologically remote but geometrically close by peak voxels (maybe avoidable by using the RAS to vertex transformation information of the inflated brain) 2.) Automated procedure: using mris_pmake with start vertex stop vertex coordinates derived from the population averaged sphere coordinate systems (fsaverage sphere) (functional data mapped into common sphere by either feat2surf or mris_preproc) è Output: only relative distance measures, but the comparability between peak voxel distances of different subjects is ensured (due to distance measures within a common spherical coordinate system)*. è Problem: no absolute measure of distances anymore (but this is actually no problem because I'm interested in relative differences in cortical reorganization) - Do you have any suggestions which procedure is preferable?? - *Am I right about the comparability of distance measurements between subjects, when using mris_pmake within a common spherical coordinate space?? I appreciate any helpful comment Sincerely yours, Christopher Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.milde(a)zi-mannheim.de Homepage: http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230

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Apply talairach.xfm to orig.mgz
by Francesco Baldacchini 01 Apr '14

01 Apr '14

Hi everybody, I'm in the process of studying all the Recon-all steps to find the step that is giving me problems in my study. Now I've just run the -talairach input and I would like to see if the talairach.xfm came out correctly by applying it to my ORIG.mgz, how can it do it? Which command do I have to use? I tried MRI_XFORM_TO_HEADER but it didn't work. Thanks everybody in advance and sorry if my question is too silly, but I'm a beginner. Francesco Baldacchini

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Invalid license when run recon-all
by gong jinnan 01 Apr '14

01 Apr '14

Dear FS experts, I want to report an error: I have installed FreeSurfer in my another computer using my license file which works in my old computer. But when I run “recon-all” its shown -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /media/datas/study_tools/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. ————————————————————————————————————— Then,I obtained another license. This error still exists. My environment is : -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/datas/study_tools/freesurfer FSFAST_HOME /media/datas/study_tools/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/datas/study_tools/freesurfer/subjects INFO: /home/zhangxx/matlab/startup.m does not exist ... creating MNI_DIR /media/datas/study_tools/freesurfer/mni FSL_DIR /usr/local/fsl My CPU is:Intel Core i5-3470 CPU @ 3.20GHZ My OS is:CentOS 6.5 x64. And log is in the attachment. Please let me know if you have any suggestions! Sincerely， Jinnan

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quality T1 scans for new study
by Kok, JG (neuro) 01 Apr '14

01 Apr '14

Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough? By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes. It you need any more information, please let me know. Many thanks in advance for your advice. Jelmer Kok ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Fwd: Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 01 Apr '14

01 Apr '14

----- Mensagem encaminhada de _andreia_(a)sapo.pt ----- Data: Mon, 31 Mar 2014 14:45:00 +0100 Hello! I'm reposting my email without attachments this time since it is not getting to the list if I have attachments. Could you advice please? Thank, Andreia ----- 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 ----- ----- Fim de mensagem reenviada -----

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What coordinate space is freesurfer output in?
by Salil Soman 31 Mar '14

31 Mar '14

Hi, I was wondering what the default freesurfer coordinate space is called? (MNI, something else)? Thanks, Sal

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extracting mean thickness values across subjects from qdec clusters
by Tudor Popescu 31 Mar '14

31 Mar '14

Dear Freesurfer experts, After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can then plot externally against the score values. I tried applying answers to previous similar questions with no success; some of them suggested using mri_segstats, however I'm not very clear on how annotation files are to be used (I've only used the QDEC GUI), and I wasn't able to work out the syntax that would give me what I wanted (assuming mri_segstats is in fact the command to be used) Thanks for any help! Best wishes, Tudor

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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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