Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

generating automatic functional label
by Yagmur Ozdemir 19 02 Oct '17

02 Oct '17

Hello FreeSurfer developers, This is a piece of code I came across for producing a functional label with using time course estimates from MEG/EEG data, for freesurfer use. I am wondering if something similar is available to estimate a functional label/region from fMRI data with similar tresholding. https://martinos.org/mne/stable/auto_examples/inverse/plot_label_from_stc.h… Best, Idil

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Fwd: Call for OHBM 2018 Award Nominations
by Douglas N Greve 02 Oct '17

02 Oct '17

FYI -------- Forwarded Message -------- Subject: Call for OHBM 2018 Award Nominations Date: Mon, 02 Oct 2017 09:56:32 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu *Call for OHBM 2018 Award Nominations* Dear Douglas, The Organization for Human Brain Mapping is pleased to announce the Call for Nominations is now open for all 2018 OHBM Awards. A short description is listed below along with a link to the criteria and processes for each award. Please note that following the process and meeting the criteria is essential for an eligible submission, and not following instructions may result in disqualification. Recipients will receive their awards at the 2018 Annual Meeting in Singapore during the Opening Ceremonies. Awardees will be given the opportunity to give a brief remark during the Annual Meeting. *Please note: Current OHBM elected leadership are ineligible to receive OHBM Awards. * ------------------------------------------------------------------------ *Glass Brain Award* The Organization for Human Brain Mapping Council has established an award to recognize lifetime achievement by leading researchers using or facilitating neuroimaging to discover original and influential findings regarding the organization and function of the human brain today. *DEADLINE: November **10**, 201**7* Click here for additional information and nomination process <https://www.humanbrainmapping.org/files/2018/Glass%20Brain%20Award%20wordin…> ------------------------------------------------------------------------ *Education In Neuroimaging Award* The Education in Neuroimaging Award will be given to an OHBM member who has made a significant contribution to education and training in the field of neuroimaging. *DEADLINE: November **10**, 201**7* Click here for additional information and nomination process <https://www.humanbrainmapping.org/files/2018/Education%20Award%20wording.pdf> ------------------------------------------------------------------------ *Young Investigator Award* The Young Investigator Award will be given to recognizing a young investigator who is a member of OHBM and has made significant contributions to the field of human brain mapping. *DEADLINE: November **10**, 201**7* Click here for additional information and nomination process <https://www.humanbrainmapping.org/files/2018/Young%20Investigator%20Award%2…> ------------------------------------------------------------------------ *Replication Award* The Replication Award recognizes the best published replication study. This award highlights OHBM’s commitment to reproducibility in neuroimaging research and helps begin to reshape the incentives towards replication. *DEADLINE: January 12, 2018* Click here for additional information and nomination process <https://www.humanbrainmapping.org/files/2018/Replication%20Award%20wording.…> ------------------------------------------------------------------------ We look forward to your involvement in the nomination process. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=34…>.

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fwhm in area analysis
by Daniel Yang 02 Oct '17

02 Oct '17

Hi FreeSurfer experts, When I specify fwhm=15 to analyze area, mri_surfcluster said that it cannot find fwhm31 in fsaverage/${hemi}/cortex/fwhm31/... This did not happen when I used FreeSurfer 5.3.0 I am wondering if FreeSurfer 6.0.0 pre-smooths the surface area? Thanks, Daniel

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qdec error
by Seung-Gul Kang (강승걸) 02 Oct '17

02 Oct '17

Dear Freesurfer, I have a question during qdec. I tried to compare the surface area between two groups using qdec program. Strange to say, if I control some combination of confounding factors, then the error develops and qdec is closed. When I control age, sex, HAMD (hamilton depression) score, and mean surface area, there was no error. When I control age and sex, there was no error. When I control only surface area, there was no error. However, when I control age, sex, and mean surface area, then error happens. Could you let me how to manage this problem? I am looking forward to receive your answer. Thank you. Best, Seung-Gul ---------------------------------------------------------------------------------below is the messages containing error SUBJECTS_DIR is '/mnt/hgfs/share/suicide' lh-Avg-Intercept-area ----------------------- Does the average area differ from zero? Nuisance factors: age area 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; lh-Diff-NS-S-Intercept-area ----------------------- Does the average area, accounting for sex, differ between NS and S? Nuisance factors: age area 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; lh-Diff-M-F-Intercept-area ----------------------- Does the average area, accounting for diagnosis, differ between M and F? Nuisance factors: age area 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; lh-X-diagnosis-sex-Intercept-area ----------------------- Is there a diagnosis--sex interaction in the mean area? Nuisance factors: age area 1.000 -1.000 -1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; ninputs = 38 Checking inputs nframestot = 38 Allocing output Done allocing nframes = 38 Writing to /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh gdfReadHeader: reading /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 41.5263 12.8201 1 area 163656 15524.4 Class Means of each Continuous Variable 1 diagnosisNS-sexM 36.2000 176040.8391 2 diagnosisS-sexM 40.6250 170897.0234 3 diagnosisNS-sexF 46.5556 151977.3351 4 diagnosisS-sexF 42.9091 156686.6932 INFO: gd2mtx_method is dods Reading source surface /mnt/hgfs/share/suicide/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/sgk cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/area_LH_AA --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Avg-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-NS-S-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-M-F-Intercept-area.mat --C /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-X-diagnosis-sex-Intercept-area.mat sysname Linux hostname localhost.localdomain machine x86_64 user sgk FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh logyflag 0 usedti 0 FSGD /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd labelmask /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label maskinv 0 glmdir /mnt/hgfs/share/suicide/qdec/area_LH_AA IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /mnt/hgfs/share/suicide/qdec/area_LH_AA Loading y from /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /mnt/hgfs/share/suicide/qdec/area_LH_AA/Xg.dat Normalized matrix condition is 2083.95 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /mnt/hgfs/share/suicide/qdec/area_LH_AA/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 26 Starting fit and test Fit completed in 0.0923167 minutes Computing spatial AR1 on surface Residual: ar1mn=0.997068, ar1std=0.001719, gstd=7.468720, fwhm=17.587492 Writing results lh-Avg-Intercept-area maxvox sig=3.56625 F=17.7049 at index 25775 0 0 seed=1506511386 lh-Diff-NS-S-Intercept-area maxvox sig=3.42944 F=16.7076 at index 10791 0 0 seed=1506511386 lh-Diff-M-F-Intercept-area maxvox sig=-3.12066 F=14.5487 at index 103184 0 0 seed=1506511386 lh-X-diagnosis-sex-Intercept-area maxvox sig=3.53629 F=17.4843 at index 158713 0 0 seed=1506511386 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 age 41.5263 12.8201 1 area 163656 15524.3 Class Means of each Continuous Variable 1 diagnosisNS-sexM 36.2000 176040.6000 2 diagnosisS-sexM 40.6250 170897.1250 3 diagnosisNS-sexF 46.5556 151977.4444 4 diagnosisS-sexF 42.9091 156686.6364 MatrixMultiply: m1 is null! No such file or directory [sgk@localhost ~]$

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R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 02 Oct '17

02 Oct '17

Hi, on 4 groups, 1 covariate (4GV1) I run mri_glmfit using the following .mtx C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 Please: 1) Could you check whether the all .mtx are complete and corrected, in particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs-gr3+gr4.slope? 2) Could you explain the meaning of: gr1+gr2-vs-gr3+gr4.slope gr1+gr2-vs-gr3+gr4.intercept group.effect.slope group.effect.intercept 3) Which is the contrast identifying the effect of covariate on group differences? Thanks Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 5-set-2017 22.59 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: Map of covariance > >you would need to create a contrast to look for the interaction. If you >have four gruops and 1 covariate, then it would be > >0 0 0 0 1 -1 0 0 > >0 0 0 0 1 0 -1 0 > >0 0 0 0 1 0 0 -1 > > > >On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >> Hi, >> e.g., by considering two or more groups, I would like to map the clusters >> reporting the covariance between the functional connectivity or cortical >> thickness (dependent variable) and age, tacking in account the group >> differences. >> Instead, I'm not interested to map the group differences, taking in account >> the nuisance factors. >> Thanks, >> Stefano >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 5-set-2017 18.12 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] Map of covariance >>> >>> I don't understand what you are asking. can you elaborate? >>> >>> >>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>> Hi list, >>>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence >>>> of group differences taking in account the effect of covariate. >>>> Anyway, where I should look if I want assess the the map showing the >>>> clusters in which the dependent variable is associated to covariate, >>>> tacking in account the group difference? Please could you suggest my >>>> the path? >>>> Thanks >>>> >>>> Stefano >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> 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 >> >> > >-- >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 >

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Can someone tell me why my subcorticals look like this?
by Jeff Crawford 02 Oct '17

02 Oct '17

Hi list! I was wondering what could cause this type of subcortical effect during FS preprocessing? I am referring to the white blank space where half the thalamus, part of the putamen, and all of the globus pallidus are not visable and Freesurfer just sort of "assumes" that they exist with its segmentation. My theory is that the dimensions of the Nii file I am using are being stretched and it is causing this "assumption" of white space. My dimensions on this Nii files are X = 160 , Y = 240, and Z = 256. This would lead me to believe that the FSaverage brain that my nii is being warped to match has a greater x axis than my nii. Is this correct? If so, is there any fsaverage options that has smaller dimensions? I assume this is an issue for analysis of subcortical measures, but should this effect cortical regions at all? Hope you all are well and my message finds someone promptly, Jeffrey Crawford

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bad midline cut
by Gabor Perlaki 01 Oct '17

01 Oct '17

Dear all, Here is my question again. Somehow, it didn't appear on the Freesurfer forum. I'm resending it without the attachments. > I've a subject, where the midline cut is bad (see the attached pictures), > therefore the segmented left lateral ventricle also includes considerable > number of voxels from the right one. > Is it possible to correct it somehow? >

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Peripheral CSF
by angel angel 01 Oct '17

01 Oct '17

Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you!

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cortical marker
by N Saf 30 Sep '17

30 Sep '17

Dear FreeSurfer experts, I have 2 questions: 1- I try to measure average convexity for temporal lobe by FreeSurfer, I can see the values for each vertex when I overlay the e.g. lh.sulc in lh.inflated, but I wonder if I can find these values somewhere else like in stats files? 2- Is FreeSurfer compute metric distortion for a specific ROI (e.g. ROIs segmented in parcellation ) according following equation? and if that's the case where can I find these values of metric distortion? Metric distortion = k ∗ area of a triangle on registered sphere/ area of triangle on original gray/white interface surface Where k = total surface area of original gray/white interface surface/ total surface area of individual sphere could you help me to solve the problem, I am looking forward to receive your answer. Thank you for your help. Best Regards, Nazanin

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Freesurfer October 2017