Freesurfer

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30132 discussions

mri_ca_train UCHAR/FLOAT
by Mark Plantz 07 Aug '13

07 Aug '13

Hello freesurfers, I am currently attempting to run mri_ca_train to create a .GCA atlas based of off a series of subjects. I am receiving the following error: *************************************************************************** processing subject CMH-3074, 1 of 10... mri_ca_train: segmentation file /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-3074/mri/seg_edited.mgz is not type UCHAR or FLOAT Is there an easy way to convert the file to UCHAR or FLOAT in FreeSurfer? Will this change the data/labels? Thank you! -MP

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Tracula question
by Alan Francis 07 Aug '13

07 Aug '13

Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my dmrirc for this brain? thanks, Alan

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 07 Aug '13

07 Aug '13

I see, you're using the old version of tracula (from freesurfer 5.1). In that version, you had to define the number of low-b images in the configuration file. I strongly recommend updating to freesurfer 5.3. A lot of things have improved in tracula since then. Also, in the future please attach any log files as separate attachments instead of pasting them into the body of your email - this causes the body of the email to exceed the limit allowable on the list. Thanks, a.y

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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 Annotation2label
by Linn Mittlestein 07 Aug '13

07 Aug '13

Hi all, I bit confused about how to create labels from annotation2label command to create DLPFC. I want make DLPFC label by merging G_frontal_middle.label, S_frontal_inferior.label and S_frontal_middle.label (available in the 2009 atlas). But I only can get annotation2label to work with the other atlas; eg using this command: mri_annotation2label --subject $subject --hemi rh --outdir ./$subject/label But I would like 2009 atlas so for example mri_annotation2label --a2009s --subject $subject --hemi rh --outdir ./subject/label But this flag doesnt seem to work. Any other suggestions to get the label files (so i can then do mri_mergelabels and Mris_anatomical stats would be very appreciated, I dont think I need use tksurfer, I think mri_annotation2label should work somehow? Kind Wishes, Linn * *

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Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 07 Aug '13

07 Aug '13

Hi Bruce, Thanks very much for the explanation. According to your suggestion, I think maybe I should try to figure it out with a 2D fast marching process. I could extract it to a 2 dimension matrix by matlab with FreeSurfer package, right? Best, Yunxin 2013/8/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Yunxin > > could you cc the list so that others can answer? I don't think you will be > able to get a reasonable surface out of a discretized 256*3 volume for the > pial surface. There are many, many places where the pial surface comes > within a fraction of a mm of itself that you will not be able to represent. > > cheers > Bruce > > > On Tue, 6 Aug 2013, Yunxin Wang wrote: > > Hi Bruce, >> Thanks for your response. Actually I want to use the fast marching toolbox >> to further analyze the pial surface that FreeSurfer has reconstructed >> automatically, but according to the procedure only the pial surface will >> be >> used for fast marching process and I found out the input file of fast >> marching is a 256*256*256 matlab file which I could just load in matlab >> but >> couldn't see any detail. Do you think I can use the freesurfer_read_surf >> function in matlab to transfer the surface? >> >> Best, >> Yunxin >> >> >> 2013/8/5 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Yunxin >> >> the surface lives in a continuum and is 2D. Do you mean filling >> the space between the ?h.white and ?h.pial surfaces? We do that >> as part of recon-all and create ribbon volumes in the mri dir >> cheers >> Bruce >> >> >> On Mon, 5 Aug 2013, Yunxin Wang wrote: >> >> Hi dear all, >> I'm new here and I've a simple question that how >> could I transfer the reconstructed pial surface >> file(like lh.pial) into a >> 256*256*256 matlab matrix used in later fast >> marching process? >> >> Any suggestion will be appreciated! >> Thank guys. >> >> Best, >> Yunxin Wang >> >> >> >> >> >> >> 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<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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Postdoctoral position: the brain connectome in twins populations
by Katell Mevel 07 Aug '13

07 Aug '13

Dear brain imaging fellows, One post-doc position is available in our group, the deadline is 30-08-2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND) (www.ki.se/kind) KIND is a competence center for research, development and education within the area of developmental psychopathology. The center is established in collaboration between Karolinska Institutet and Stockholm County Council, and aims at improving clinical practice, generating basic research, and spreading new knowledge to stakeholders. The Roots of Autism Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins being discordant for autism spectrum disorder and other neurodevelopmental disorders, e.g. ADHD. For the first time ever, twins are examined on multiple levels, among them functional and structural neuroimaging using MRI. Scanning is performed in the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750), and more than 45 pairs have now been examined. *** Duties As a post-doc, you will be mainly responsible for the acquisition and analyses of the multimodal neuroimaging data. This includes DTI, resting-state fMRI and structural T1, to be combined according to a brain connectome approach. This work will be done in close collaboration with the department of Clinical Neuroscience. The position also includes several other responsibilities, e.g. coordination of the neuroimaging works at KIND, involvement in international collaborations, administrative tasks, grant application and article writing. All the details about this position can be found here:https://ki.mynetworkglobal.com/en/what:job/jobID:24397/where:4/ Applications should be submitted here:https://ki.mynetworkglobal.com/what:login/jobID:24397/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best Regards, Katell MEVEL for KIND ________________________________ Katell Mevel | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B | 113 30 Stockholm +46 (0)8 514 52706 | +46 (0)721 980 350 katell.mevel(a)ki.se | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130><http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ______________________________________ Karolinska Institutet – a medical university

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job offer
by Anton Eberharter 07 Aug '13

07 Aug '13

Please post the following job offer, see attachment. Thanks in advance, Anton Eberharter ===================================== PD Dr. Anton Eberharter Lab Manager & Dozent Physiologische Chemie / Medizinische Fakultät Ludwig Maximilians Universität München Butenandtstr. 5B 81377 München Tel.: 089 2180 77096 anton.eberharter(a)med.lmu.de<mailto:anton.eberharter@med.lmu.de> www.ladurnerlab.de<http://www.ladurnerlab.de/> =====================================

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Fwd: How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 06 Aug '13

06 Aug '13

---------- Forwarded message ---------- From: Yunxin Wang <yunxinwang(a)gmail.com> Date: 2013/8/6 Subject: Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thanks for your response. Actually I want to use the fast marching toolbox to further analyze the pial surface that FreeSurfer has reconstructed automatically, but according to the procedure only the pial surface will be used for fast marching process and I found out the input file of fast marching is a 256*256*256 matlab file which I could just load in matlab but couldn't see any detail. Do you think I can use the *freesurfer_read_surf*function in matlab to transfer the surface? Best, Yunxin 2013/8/5 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Yunxin > > the surface lives in a continuum and is 2D. Do you mean filling the space > between the ?h.white and ?h.pial surfaces? We do that as part of recon-all > and create ribbon volumes in the mri dir > cheers > Bruce > > > > On Mon, 5 Aug 2013, Yunxin Wang wrote: > > Hi dear all, >> I'm new here and I've a simple question that how could I transfer the >> reconstructed pial surface file(like lh.pial) into a >> 256*256*256 matlab matrix used in later fast marching process? >> >> Any suggestion will be appreciated! >> Thank guys. >> >> Best, >> Yunxin Wang >> >> >> >> >> > > 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<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. >

1 0

How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?
by Yunxin Wang 06 Aug '13

06 Aug '13

Hi dear all, I'm new here and I've a simple question that how could I transfer the reconstructed pial surface file(like lh.pial) into a 256*256*256 matlab matrix used in later fast marching process? Any suggestion will be appreciated! Thank guys. Best, Yunxin Wang

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