Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

remove skull from gtmseg.mgz
by miracle ozzoude 07 Jul '17

07 Jul '17

Hello Freesurfer, After running the first step of PETsurfer ( https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer) I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks. Please, see attached image Best, Paul

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glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters
by Damien MARIE 07 Jul '17

07 Jul '17

Hi, I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 mm, population 1, population 2 , and age as nuisance factor. After POS MC simulation CW correction, I had two significant clusters resulting from this in the planum temporale and Heschl’s sulcus. The contrast being population 1 - population 2, my interpretation was higher R1 values in these two clusters in Pop 1 as compared to Pop 2. After that I wanted to run some post-hoc tests let say, in a statistical software similar to SPSS, JMP, on the mean R1 values from each of these clusters. The strategy I picked was to stay in the common space, fsaverage, and apply mri_segstats: #Extract mean R1 in montecarlo's significantcluster for i in `cat subjects` do mri_segstats --mul 1000 --annot fsaverage lh PT_mc-z.pos.sig.ocn --i $SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.PT.R1.${i}.stats done for i in `cat subjects` do mri_segstats --mul 1000 --annot fsaverage lh HS_mc-z.pos.sig.ocn --i $SUBJECTS_DIR/${i}/surf/lh.R1.fsaverage.fwhm8.mgh --sum lh.HS.R1.${i}.stats done Everything when fine but as compared to my glm analysis when looking at mean group differences in my stat software I have the opposite : larger R1 values in Pop 2 as compared to Pop 1 (after removing the effect of age or not, and removing one outlier or not). I went back to my glm and checked everything, fsgd file, matrix and so on, everything seems ok I am not mistaken on the direction of my glm contrast (pop 1 - pop 2) so I do not get it at all. Any advices? For now I am thinking about going back in the individual space, registering my clusters in the individual surfaces (label2surf something like that) and then extract my mean R1 values, or extract values in non-smoothed maps, but I do not think it will change anything. Damien

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Re: [Freesurfer] Brainmask Shifted
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Hi Doug, Our freeview command is: freeview -v ${fs_id}/mri/T1.mgz ${fs_id}/mri/brainmask.mgz:colormap=heat:opacity=0.4 Thank you, Kaley Message: 7 Date: Wed, 14 Jun 2017 16:32:38 +0200 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Brainmask Shifted To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <02f67013-f90c-699f-0307-9f1bf9b131be(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your freeview command? On 6/14/17 3:51 PM, KALEY E ELLIS wrote: > > Dear FreeSurfer Developers, > > > We are using FreeSurfer v6.0 and our operating system is OS X El > Capitan version 10.11.6. > > > We are going through the manual editing process and are checking the > brainmask by following these instructions: > > http://freesurfer.net/fswiki/FsTutorial/SkullStripFixV6.0 > > We have two subjects who appear to have brainmasks that are shifted up > considerably (see attached image). The recon-all.log file indicates > that it finished without errors: > > > reading volume > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/mri/wm.mgz... > reading input surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > reading input pial surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.pial... > reading input white surface > /study1/nccam3/data/mri/freesurfer_v6/subjects/2083_base/surf/rh.white... > INFO: assuming MGZ format for volumes. > > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 277 173 970 3.493 0.659 0.107 0.039 3 0.4 > ./rh.entorhinal_exvivo.label > > #------------------------------------------ > > Started at Thu Jun 8 10:50:24 CDT 2017 > Ended at Fri Jun 9 00:06:58 CDT 2017 > #@#%# recon-all-run-time-hours 13.276 > recon-all -s 2083_base finished without error at Fri Jun 9 00:06:58 > CDT 2017 > > Could you please advise me on how to correct this issue? We have run > all of these subjects the same way, but only two have had this problem. > > > Thank you! > > Kaley > > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...

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glmfit_sim for CVS mapped data
by Magnús Ingvi 07 Jul '17

07 Jul '17

Hi, I've been trying to run glmfit_sim on a glm analysis with data in the AVG_35_CVS space but it doesn't seem to finish (tried almost two weeks). Does anyone have an idea what might be going on here? I used mc_full for 1000 iterations for my simlation.

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Re: [Freesurfer] WM surface ignoring wm.mgz edits
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Hi Bruce, We are using the "voxel-edit" tool and "recon editing" is selected. Thank you, Kaley ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, July 7, 2017 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 16 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---------------------------------------------------------------------- Message: 1 Date: Fri, 7 Jul 2017 10:42:23 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM surface ignoring wm.mgz edits To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1707071041590.9265(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Kaley are you using the "recon edit" tool in freeview? cheers Bruce On Fri, 7 Jul 2017, KALEY E ELLIS wrote: > > Dear?FreeSurfer?Developers, > > > We are attempting to make manual white matter edits to our subjects. The > edits are saving; however, after running with recon-all, the WM surface does > not appear to be taking into account our edits made to wm.mgz. Below is > additional information, and I have attached our recon-all.log. We are only > editing the cross because our dataset is comprised of single timepoints. > > > We are using?FreeSurfer?v5.3 and our operating system is OS X El?Capitan > version 10.11.6. > > Command to open and edit WM:? > > freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f > surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red > surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red > > > Command to submit edits: > > recon-all -autorecon2-wm -autorecon3 -subjid? > > > Recon-all log (see attached) > > > Thank you, > > Kaley?Ellis > > > > Associate Research Specialist > Center for?Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > > ------------------------------ Message: 2 Date: Fri, 7 Jul 2017 14:51:53 +0000 From: "Boyd, Emma" <EBOYD2(a)mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MWHPR04MB0558426F0D765C043BEDCABAD1AA0(a)MWHPR04MB0558.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 A FreeSurfer-compliant consistent manual segmentation of ...<https://www.ncbi.nlm.nih.gov/pubmed/25741260> www.ncbi.nlm.nih.gov 1. Front Hum Neurosci. 2015 Feb 18;9:21. doi: 10.3389/fnhum.2015.00021. eCollection 2015. A FreeSurfer-compliant consistent manual segmentation of infant ... Emma ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Das S. <Sarbani.Das(a)soton.ac.uk> Sent: Friday, July 7, 2017 4:58:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > Dear Lilla, > In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon. > If you give me little more details will be easy for me to understand the gap. > many thanks > Sarbani > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzollei(a)nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > We use a similar pipeline but with different atlases and processing > steps for the newborns. > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> >> Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate. >> >> Autorecon Processing Stages: >> Motion Correction and Conform >> NU (Non-Uniform intensity normalization) >> Talairach transform computation >> Intensity Normalization 1 >> Skull Strip >> EM Register (linear volumetric registration) >> CA Intensity Normalization >> CA Non-linear Volumetric Registration >> Remove Neck >> LTA with Skull >> CA Label (Volumetric Labeling, ie Aseg) and Statistics >> Intensity Normalization 2 (start here for control points) >> White matter segmentation >> Edit WM With ASeg >> Fill (start here for wm edits) >> Tessellation (begins per-hemisphere operations) >> Smooth1 >> Inflate1 >> QSphere >> Automatic Topology Fixer >> Final Surfs (start here for brain edits for pial surf) >> Smooth2 >> Inflate2 >> Spherical Mapping >> Spherical Registration >> Spherical Registration, Contralateral hemisphere >> Map average curvature to subject >> Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >> Cortical Parcellation Statistics >> Cortical Ribbon Mask >> Cortical Parcellation mapping to Aseg >> >> BW >> S Das >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Lilla Zollei >> [lzollei(a)nmr.mgh.harvard.edu] >> Sent: 04 July 2017 22:04 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all on newborn >> >> Hi S Das, >> >> We are trying to release the infant pipeline by the end of the summer. >> >> Lilla >> >> On Tue, 4 Jul 2017, Das S. wrote: >> >>> Dear Freesurfer expert, >>> I want to perform recon-all pipeline on neonates data.Can I do so? >>> I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all. >>> But again there is another paper where it says Freesurfer can perform segmentation of neonates image. >>> Any input will be appreciated. >>> Thanks >>> S Das >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] wm.mgz in the internal structures
by Karla Rivera Figueroa 07 Jul '17

07 Jul '17

Thank you for the clarification. Have a nice weekend, Karla On Jul 7, 2017 10:16 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Karla you shouldn't have to worry about the wm.mgz in those regions if the aseg is accurate. cheers Bruce On Fri, 7 Jul 2017, Karla Rivera Figueroa wrote: Hi all, Do you need to edit the wm mask where the internal structures shown > in the aseg are? are the structures supposed to be covered entirely with > the > wm mask? > > Karla > > _______________________________________________ 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.

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WM surface ignoring wm.mgz edits
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Dear FreeSurfer Developers, We are attempting to make manual white matter edits to our subjects. The edits are saving; however, after running with recon-all, the WM surface does not appear to be taking into account our edits made to wm.mgz. Below is additional information, and I have attached our recon-all.log. We are only editing the cross because our dataset is comprised of single timepoints. We are using FreeSurfer v5.3 and our operating system is OS X El Capitan version 10.11.6. Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Recon-all log (see attached) Thank you, Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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wm.mgz in the internal structures
by Karla Rivera Figueroa 07 Jul '17

07 Jul '17

Hi all, Do you need to edit the wm mask where the internal structures shown in the aseg are? are the structures supposed to be covered entirely with the wm mask? Karla

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Matlab Problem LME
by Clara Kühn 07 Jul '17

07 Jul '17

Dear FreeSurfer experts, I am following the LME tutorial for the spatiotemporal mass-univariate model on Matlab 8.2. When I get to the point where the covariance estimates are segmented into homogeneous regions I run into a problem. Nothing really happens in Matlab anymore. This is my command: [lhRgs,lhRgMeans] = lme_mass_RgGrow (lhsphere, lhRe, lhTh0, lhcortex, 2, 95); And this is what the Matlab output looks like: connected to 12 workers. Starting region growing algorithm Computing seeds ... I've tried this already last week and nothing happened for a few days. When I terminate the command this is the Matlab output: Operation terminated by user during kron (after line 36) In lme_mass_RgGrow>homogenity (line 299) if (sum(sum(DistRgParams <= kron(ones(1,nv),thr),1) == np) >= prc*nv/100) &&... In lme_mass_RgGrow>merge (line 320) if homogenity(Re,Params,auxRgs,Rkn,nst,prc) In lme_mass_RgGrow>split (line 269) [Rgs,mrg] = merge(Rgs,Re,Params,mrgRgs(i),mrgRgs(j),nst,prc); In lme_mass_RgGrow>seeds (line 208) [Rgs,spltf(i),nnRgs] = split(Rgs,Re,Params,coord,splRgs(i),nst,prc); In lme_mass_RgGrow>vtxwGrowing (line 77) [Rgs1,Rgseed,Rgstd]= seeds(Re(:,maskvtx),Params(:,maskvtx),coord(:,maskvtx),nst,prc); In lme_mass_RgGrow (line 62) Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc); I have then copied the function and added a few "fprintf" (see attachment) to get an idea as to where matlab has problems and the output looks like this: Starting region growing algorithm Computing seeds ... point5 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 [...] If I understand that correctly, matlab gets hung up on functions 'function tf = homogenity(Re,Params,Rgs,Rn,nst,prc)' and 'function [Rgs,tf] = merge(Rgs,Re,Params,Rn1,Rn2,nst,prc)'. Does anybody have an idea what that means and how it can be fixed? How long is this step supposed to take? I have 81 subjects with 1 - 3 time points. Any help or suggestions would be much appreciated! Cheers Clara -- Clara Kühn, Phd Candidate Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

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Freesurfer July 2017