Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

DEPRECATED warning in Freesurfers
by Peter Wendorff 13 Oct '15

13 Oct '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I'm working with freesurfer as a software developer in a cloud project. My task is to enable control of freesurfer via network (e.g. REST interfaces). That works fine so far, but I stumbled over the following pearl deprecated warning: "Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer//mni/bin/sharpen_volume line 153." Which has been printed to the log files repeatingly. I'm not a pearl expert, but I think, it's due to a more up to date pearl version used here, that deprecated the usage of ? delimiters for patterns without explicit operator. Using / as a delimiter works fine. I changed that locally to (new line 153): ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; (the original code here was): ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; I'm not sure this is the best solution. It's even not strictly necessary to change this - it's only a warning that's thrown; but I think, it's useful. How can I submit this as a patch? Is it enough to report here? What to do? regards Peter Wendorff P.S.: For referene the header parameters of my sharpen_volume for revision comparison: #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author: bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header - ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGTa5kACgkQi8ffXNvWmYSCUQCghMg1EffqfeJK4PSfo20uF8/J H0MAnjJc0WbHPf5gLDUw70K8fnQPjS+L =g+6e -----END PGP SIGNATURE-----

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Douglas Greve 25 Sep '14

25 Sep '14

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: > Dear Dr. Greve, > > Is it possible to register a nonstructural MR sequences (e.g. an ADC > map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, > using the segmentation from the aseg (or aparc+aseg) file to output a > mean ADC value for each anatomic area segmented? > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS

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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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Converting fsaveraged EPI to volume
by Marcel Falkiewicz 03 Sep '13

03 Sep '13

Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds? Thanks in advance, Marcel

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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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Re: [Freesurfer] How to extract subjects' volume based on mask from spm?
by Douglas N Greve 09 Aug '13

09 Aug '13

Hi Mingxia, if you have a binarized map, then just use --id 1 with mri_cor2label (not need to for mri_binarize if it is already binary) doug On 05/21/2013 03:55 AM, zhang mingxia wrote: > Hi Doug, > > Thanks very much. A few more question after I read the description of > mri_cor2label. > > 1. there is a compulsory of mri_cor2label: --id (0-255). How can I > find the 'labelid'? > > 2. If I understand correctly, the final label will be made within > one particular 'labelid'. How if this mask is in more than one labels > (Sorry I haven't used Freesurfer for a long time, my understanding is > the labelids represent different regions. It may be wrong) ? > > 3. I have had the binarized mask created from spm, do I also need to > use mri_binarize? > > Mingxia > > > On Mon, May 20, 2013 at 6:51 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Try mri_binarize followed by mri_cor2label > doug > > > > > > On 05/20/2013 03:57 AM, zhang mingxia wrote: > > Dear Freesurfer experts, > > > > I analyzed functional data by spm and made a mask (analyze > format). I > > have also run recon-all of structural data. > > > > My question is: how to extract mean volume (from structural data) of > > the mask(from spm)? > > > > I only extracted volume(or thickness) of ROI of a label edited by > > myself and annotation file. If I can convert analyze format to a > label > > or annotation file, I can use that method. But how to convert > analyze > > format to a label or annotation? > > > > Or is there any easy way? > > > > Thanks in advance! > > > > Mingxia Zhang > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@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. > > -- 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/

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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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retinotopy betas
by dgw 26 Jul '13

26 Jul '13

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see that it has a size of: 1 #of vertices 1 39 Can you explain to me, how I figure out where each of the 39 come from (and possibly point me to which of these might be appropriate to use?)? Thank You, Dan

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HypoIntense Lesions
by Fotiadis, Panagiotis 26 Jul '13

26 Jul '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

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Freesurfer June 2013