Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

mri_vol2surf failed, segmentation error
by Qingyang Li 04 Feb '14

04 Feb '14

Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang ------ Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Mailing list subscription confirmation notice for mailing list > Freesurfer > > We have received a request from 67.244.70.75 for subscription of your > email address, "congel(a)gmail.com", to the > freesurfer(a)nmr.mgh.harvard.edu mailing list. To confirm that you want > to be added to this mailing list, simply reply to this message, > keeping the Subject: header intact. Or visit this web page: > > > https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbce… > > > Or include the following line -- and only the following line -- in a > message to freesurfer-request(a)nmr.mgh.harvard.edu: > > confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > freesurfer-owner(a)nmr.mgh.harvard.edu. > > > 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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Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
by Darren Gitelman 06 Dec '13

06 Dec '13

Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Check the aseg and see if it was labeled ventricle (and make sure it > really isn't). You may need to edit the aseg > > > > On Sep 16, 2012, at 5:19 PM, Darren Gitelman <d-gitelman(a)northwestern.edu> > wrote: > > Hi > > I have run into an issue that I'm not sure how to correct. What happens > is that in some subjects the surfaces don't seem to properly track sulci > coming off the medial part of temporo-occipital cortex. Please see green > arrows on the attached image. > > In fact the tutorial on topological defects shows an image with a > similar issue, but fixing it is not discussed. > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?actio… > > I have checked and these are sulci and not the occipital extent of the > lateral ventricle. > > Perhaps it is not a problem, or if it is then how to approach fixing it? > > Thank you, > Darren > -- > Darren Gitelman, MD > Northwestern University > 710 N. Lake Shore Dr. > Abbott 11th Floor > Chicago, IL 60611 > Ph: (312) 908-8614 > Fax: (312) 908-5073 > > <3809-error.png> > > _______________________________________________ > 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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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vertices don't match
by Darren Gitelman 11 Jun '13

11 Jun '13

Dear List I am adding to the post on this error from yesterday regarding problems with running qcache. I know this has been posted to the list before, but the suggested fixes and checks don't fix the problem. See the error below (ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file) 1) Running recon-all -s <subjid> -vno-check does not find any problems. It says everything is verified and checks out ok. 2) Running recon-all -s <subjid> -make all returns the message: make: Nothing to be done for `all'. But when I try recon-all -s <subjid> -qcache I get the error on this and several other subjects, but not all subjects. Checking the modification times on some files it looks like the thickness file came after the curv file. [drg@quser03 surf]$ ll *.thickness -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:54 lh.thickness -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:10 rh.thickness [drg@quser03 surf]$ ll *.curv -rwxrwxrwx 1 dek322 d20277 588607 Sep 11 21:45 lh.curv -rwxrwxrwx 1 dek322 d20277 593959 Sep 11 22:01 rh.curv Any suggestions for fixing the qcache error would be appreciated. Darren -- --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6938/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012 -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0
by Andrew Bock 08 Mar '13

08 Mar '13

Hello, I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock(a)u.washington.edu

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entorhinal cortex volume question
by Cat Chong 29 Jan '13

29 Jan '13

Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine

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selxavg3 error : NaN in Xtmp.mat file
by Sid Kundu 07 Dec '12

07 Dec '12

Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 248) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject. _________________________________ Sid Kundu Biomedical Engineering Boston University

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flipping surface data
by kelsi 04 Dec '12

04 Dec '12

Hi Freesurfers, Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you! Kelsi

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Fw:contrast matrix
by Meng Li 13 Nov '12

13 Nov '12

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Any help will be very appreciated. Best wishes, Meng Li

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AAL labels
by MCLAREN, Donald 23 Oct '12

23 Oct '12

Has anyone created an AAL label file for Freesurfer? I've done some ROI analysis using AAL regions and want to display regional values on the freesurfer surface. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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coordinate transform
by octavian lie 22 Oct '12

22 Oct '12

Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file (see attached) in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie.

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Freesurfer September 2012