Freesurfer

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30135 discussions

Difference in ROI analysis results?
by Clint Johns 28 Mar '14

28 Mar '14

Hi there, After conducting a DODS analysis (One group, four factors, one covariate), we were able to identify a region (LH pars opercularis) whose mean thickness differed when two of the four factors interacted. In order to further investigate the interaction, we obtained each participant's mean thickness by drawing an ROI (using QDEC, which also applied the mri_label2label function to map the new ROI to all the participants). However, when we extract the thickness data in this way, and then run a glm on the ROI data (with the same four factors), the interaction is no longer significant, and instead we observe a main effects of only one of the factors. Does anyone have an idea why there is such a disconnect between the freesurfer output and the subsequent analysis (using glm in R)? 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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Fwd: mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 28 Mar '14

28 Mar '14

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 -----

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Problem about the fMRI Analysis of correlation？
by Linda Xu 28 Mar '14

28 Mar '14

Dear Sir, My experiment design is let the two group of subjects watch a movie and calculate the correlation between two condition. Now I get the correlation result from AFNI. I want to calculate the correlation different between the two group by using freesurfer. However the group analysis in freesurfer need the paradigm file to get the constrast file for matlab. But I do not know how can a stimulate as movie can be serve as? I do not know how to write the paradigm at this time. My question is: My stimulate is a 10 minute movie. How can I get the correlation different of two group by using freesurfer? Could you give me some advice?

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Re: [Freesurfer] Problem about the fMRI Analysis?
by Linda Xu 28 Mar '14

28 Mar '14

Dear Douglas, What should I do next? I do not know how to use the freesurfer to calculate the correlation different of two group. So could you give me some advice? Yours Linda 2014-03-27 19:18 GMT-04:00 Linda Xu <lynda.bme(a)gmail.com>: > Dear Douglas, > OK, I will figure it out. And my next question is that, What should I do > next? I do not know how to use the freesurfer to calculate the correlation > different of two group. So could you give me some advice? > > > 2014-03-27 19:06 GMT-04:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > > >> Surface-based analysis is an alternative to talairach-based analysis. It >> does not make sense to do both. Is the AFNI talairach space affine (ie, 12 >> dof)? If so, then it is possible to undo the resampling to talairach space. >> You will need to know which space the afni results are in (ie, MNI152 or >> MNI305 or something else? 1mm or 2mm?) >> doug >> >> >> >> >> >> On 3/27/14 5:06 PM, Linda Xu wrote: >> >> Dear Douglas, >> I do not understand what's your meaning? Yes I think the afni results has >> already alined to T1.mgz, so it is already in talairach space. I do not >> know what to do next? As I have two groups subjects. I do not know what to >> analysis the correlation different between two groups by using >> surface-based analysis of freesurfer. >> Linda >> Message: 5 >> Date: Wed, 26 Mar 2014 14:05:46 -0400 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problem about the fMRI Analysis? >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <533316FA.50903(a)nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Are the AFNI results already in talairach space? If so, then there is no >> point in going to surface space. >> doug >> >> >> On 03/26/2014 01:22 PM, Linda Xu wrote: >> > I get the correlation result between two condition of the functional >> > data by using AFNI( I do not know how to do correlation by using >> > freesurfer) >> > And then I use the bbregister to aline the correlation result (produce >> > by Afni) to the anatomical result produced by using freesurfer. >> > Next I using mri_vol2surf to aline the each one's functional result to >> > the fsaverage offer by freesurfer. >> > My question is :1 Should I need to do mri_vol2vol next for each subject? >> > 2 I have two group of subjects. I want to know >> > if there is some correlation different between them? What should I do >> > next? >> > Thanks very much! >> > Linda >> > >> >> >> 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. >> > >

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how to capture blurred GM/WM junction?
by Markus Gschwind 28 Mar '14

28 Mar '14

Dear all, I would like to capture regions where the gray matter/ white matter junction is blurred in order to detect possible focal cortical dysplasias. As I understood the WM/GM segmentation is done by the script mri_segment. Would it be possible detect those regions where the gradient between GM and WM regions is low? I imagined that running mri_segment several times, with each time a different lower GM threshold and higher WM threshold, and then calculating the diference between the results, might give such information. I am very much interested in what you think about this approach and how to do it practically. For info here are the optional flags of mri_segment: -slope <s> set the curvature slope (both n and p) -pslope <p> set the curvature pslope (default=1.0) -nslope <n> set the curvature nslope (default=1.0) -debug_voxel <x y z> set voxel for debugging -auto automatically detect class statistics (default) -noauto don't automatically detect class statistics -log log to ./segment.dat -keep keep wm edits. maintains all values of 0 and 255 -ghi, -gray_hi <h> set the gray matter high limit (default=100.000) -wlo, -wm_low <l> set the white matter low limit (default=90.000) -whi, -wm_hi <h> set the white matter high limit (default=125.000) -nseg <n> thicken the n largest thin strands (default=20) -thicken toggle thickening step (default=ON) -fillbg toggle filling of the basal ganglia (default=OFF) -fillv toggle filling of the ventricles (default=OFF) -b <s> set blur sigma (default=0.25) -n <i> set # iterations of border classification (default=1) -t <t> set limit to thin strands in mm (default=4) -v verbose -p <p> set % threshold (default=0.80) -x <filename> extract options from filename -w <w> set wsize (default=11) -u usage Thank you very much for all comments! Markus

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freesurfer install
by limengsecret 28 Mar '14

28 Mar '14

Hi freesurfer， I ?installed the package of freesurfer according to the intruction of freesurfer website. But when I checked whether it was installed successfully, I inputed?the commands following: 1)?tksurfer bert rh pial? Couldn't create output file .xdebug_tksurfersubject is bert hemi is rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/bin surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz 2) tkmedit bert orig.mgz?Couldn't create output file .xdebug_tkmedit =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : 3) ?qdec?qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory yxk-ThinkStation-D30:/usr/local/freesurfer/bin> ? Thus, I want to know the reason why these problems occurred, and the solution to these problems. Thank you very much Meng

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Extracting ROI information using created label
by Clint Johns 28 Mar '14

28 Mar '14

Hi, We are having some trouble extracting ROI (thickness) information using a label we created. After conducting a group analysis, we drew an ROI label based on the results. We used tksurfer to draw the label (we couldn't do this in freeview, which would freeze for some reason). However, at this point we're kind of stuck. The tutorial slides give the way to extract ROI information using existing labels, and then how to create a label, but not how to use the custom label to extract the relevant information. Any advice would be appreciated! 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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error
by xiangbo_2010 28 Mar '14

28 Mar '14

Dear experts, when I run the "qdec", and the wrong information appear in following: qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory I hope some experts to help me ,thank you very much! -- Bo Xiang State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China The Mental Health Center and the Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China Phone: +8615281056345 QQ: 529111494 Skype: xiang.bo3 向波四川大学华西医院生物治疗国家重点实验室，华西医院精神医学研究室成都市武侯区人民南路三段中四川大学华西校区，610041 E-mail: xiangbo_2010(a)126.com / xiangboyulan2012(a)gmail.com 电话：15281056345 QQ：529111494 Skype：xiang.bo3

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mc-bbr
by SHAHIN NASR 27 Mar '14

27 Mar '14

Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.…) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Problem about the fMRI Analysis?
by Linda Xu 27 Mar '14

27 Mar '14

Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using surface-based analysis of freesurfer. Linda Message: 5 Date: Wed, 26 Mar 2014 14:05:46 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Problem about the fMRI Analysis? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <533316FA.50903(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Are the AFNI results already in talairach space? If so, then there is no point in going to surface space. doug On 03/26/2014 01:22 PM, Linda Xu wrote: > I get the correlation result between two condition of the functional > data by using AFNI( I do not know how to do correlation by using > freesurfer) > And then I use the bbregister to aline the correlation result (produce > by Afni) to the anatomical result produced by using freesurfer. > Next I using mri_vol2surf to aline the each one's functional result to > the fsaverage offer by freesurfer. > My question is :1 Should I need to do mri_vol2vol next for each subject? > 2 I have two group of subjects. I want to know > if there is some correlation different between them? What should I do > next? > Thanks very much! > Linda >

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