Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 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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hippocampal segmentation converting mgz to nii
by lorenzo pasquini 13 Aug '13

13 Aug '13

Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz I have calculated the number of voxels in the converted .nii files using SPM and realized that they do not fit the estimated volumes through freesurfer Example for CA2-2 estimated voxel number though freesurfer: 6851 voxels found in .nii file: 15812 Did somebody had similar problems? Do you have any suggestion? Are there any incompatibilities between SPM and freesurfer? I did not find any apparent error in my counting script. Thank you very much and regards, Lorenzo Pasquini Can. Ph. D., Medical Life Science and Technology (Technische Universität Muenchen) Neuroimaging Lab, Neuroradiology Klinikum r. d. Isar (Technische Universität) 81675 München Tel.: 0049 (0) 89 4140-7666

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LME - lme_mass_FDR2 correction doesn't work
by Alex Hanganu 07 Aug '13

07 Aug '13

Hi Jorge, I got an error in the correction, and I can't find a way out. this is the cmd I use: ------------- /[Y,mri] = fs_read_Y('.../thickness-sm10.mgh'); Qdec = fReadQdec('.../LME.dat'); Qdec = rmQdecCol(Qdec,1); sID = Qdec(2:end,1); Qdec = rmQdecCol(Qdec,1); M = Qdec2num(Qdec); ni = [2 2... 2]; X = [ones(length(M),1) M M(:,1).*M(:,2)]; [stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex); CM.C = [0 0 0 1]; fstats = lme_mass_F1(stats,CM); fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig'); nv = length(stats); Beta2 = zeros(1,nv); //Beta//4////= zeros(1,nv);// //for ....// //. .// //end; //Beta2_Beta//4//_sum = Beta2//+Beta4;// //mri1 = mri;// //mri1.vols//z(//4) = 1;// //fs//_write_Y(Beta2,mri1,'..../Beta2.mgh'//);// //[detvtx,sided_pval,pth//] = lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);// //fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');// // //??? Error using //===> reshape// //To RESHAPE the number of elements must not change.// // //Error in ==//> fs_write_Y at 21// //save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/ ------------- the cmd: /[detvtx ....//]/ didn't work, but there was no error message. I remember in the past this cmd took around 1 day to analyzebut now it didn't work at all. /fs_write_Y/ worked fine for Beta, alsothis time I used the /mri//1 //= mri/ cmd- so the /reshape /error shouldn't be associated with this. Please help ! best regards, Alex.

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Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 14 Jul '13

14 Jul '13

Doug, Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need. Thanks, -Jeff Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <50E7214B.6010407(a)nmr.mgh.harvard.edu<mailto:50E7214B.6010407@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer. doug On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu%3E>> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu> <mailto:eriksenj@ohsu.edu><mailto:eriksenj@ohsu.edu%3E>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate....

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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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Probably activation due to vessels
by Jörg Pfannmöller 07 May '13

07 May '13

Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe

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Re: [Freesurfer] Longitudinal analysis of one timepoint
by Sarah Whittle 03 May '13

03 May '13

Hi, RE the below post, we have longitudinal data from three time points, but a number of participants have scans for only one or two time points. We've done all of the cross-sectional analysis (including a lot of manual editing) and are ready to run everything through the longitudinal stream. Our plan was to run sets of analyses for all of the possible combinations of longitudinal scans. e.g., Time 1, Time 2, Time 3; Time 1, Time 2; Time 1, Time 3; Time 2, Time 3 Obviously the new feature in version 5.2 (i.e., being able to run all images together, regardless of whether some time points are missing for some people) would be MUCH better. Is this possible to do using our 5.1 cross-sectionally processed images? Given the time we've put into manual editing, we really wouldn't want to have to run everything again through 5.2. Thanks, Sarah .... Hi Henk-Jan, to avoid bias between subjects with single time points and others, we run them through the same steps. This way it is possible to include them into the statistical analysis. (For this an artificial base is created with the head in an upright and straight position). This feature will be available in 5.2. Nothing with respect to processing commands changes, you will simply pass only a single time point to the -base and then run it with -long. Nice and transparent :-). Anyway, you probably should wait till 5.2. There is several programs that changed for this to work. Also the current recon-all contains many changes not related to this. If you absolutely cannot wait, let me know and I'll take a look at how difficult it is to go back and adjust 5.1. Best, Martin On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote: > Hi Freesurfer experts, > > > > This week a read the article of Bernal-Rusiel et al. titled > “Statistical analysis of longitudinal neuroimage data with Linear > Mixed Effects models”. In this article you described the submission of > single time-point scans to the longitudinal pipeline of Freesurfer. > I’m very interested in how to do this. Your help will be appreciated. > > > > Thanks in advance, > > > > Henk-Jan > > > > ______________________________________________________________________ > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht > onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de > afzender direct te informeren door het bericht te retourneren. Het > Universitair Medisch Centrum Utrecht is een publiekrechtelijke > rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en > Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van > Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > > ______________________________________________________________________ > > This message may contain confidential information and is intended > exclusively for the addressee. If you receive this message > unintentionally, please do not use the contents but notify the sender > immediately by return e-mail. University Medical Center Utrecht is a > legal person by public law and is registered at the Chamber of > Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21
by Rotem Saar 30 Apr '13

30 Apr '13

Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high). I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual "The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA". All my values are above 0.4.... Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz why do I get 182 regions ? in my wmparc.stats I have only 70... I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help. Attached is the table again, Thanks Rotem > The values look about right in the table. Your pipeline looks ok, > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output > of mri_vol2vol (fa_FOLDER-NAME.nii). > doug > > > > On 03/17/2013 02:16 AM, Rotem Saar wrote: > > > > Hi all, > > I run into somthing that seems odd to me and wanted to consult - > > I run the following script for getting the FA values from my DTI > > scans: > > > > 1) dt_recon --i > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > > FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > > 2) tkregister2 --s fsaverage --surf white --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > > --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > > -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > > -fthresh 0.2 -fmax 1 > > 4) mri_vol2vol --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > > FOLDER-NAME --interp nearest --o > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > > 5) tkregister2 --mov > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > > --reg > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > > 6) mri_segstats --seg > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > > --sum > > > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > > > > I got a table with all the FA values (see attached), for each > > segment, but I suspect a problem: I think that the values are too > > high (I set the threshold to 0.2-1), am I right ? > > Can u guide me regarding what I can do to solve the problem ? in > > addition I attached a figure of the corpus-callosum, in which I'm > > interested - i't seems that the green area in not big enough, is > > this fixable ? > > > > Thanks ! > > > > Rotem >

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Very different results between 5.1.0 and 5.2.0
by Yang, Daniel 15 Apr '13

15 Apr '13

Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Freesurfer March 2013