Freesurfer

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question on invoking partial volume calculations in freesurfer 4.3
by John Drozd 30 Nov '12

30 Nov '12

Hello, My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm x 1mm voxels, eventhough the .mgz grayscale mri image file remains as per the original voxel size and is not 1x1x1. mri_convert .nii to .mgz translates the grayscale image down the y direction in the horizontal plane transverse/axial slices. I noticed that the aseg.stats files list the number of voxels and the volume, and these numbers match because the voxel size is 1 x 1 x 1. My question is whether freesurfer 4.3 can be invoked to perform partial volume error corrections, and if so how do you invoke this feature? My interests lie in segmentations of the lateral ventricles including their posterior and inferior horns. thank you, john

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Public Supercomputing service to process FreeSurfer data
by Pedro Paulo de Magalhães Oliveira Junior 30 Nov '12

30 Nov '12

We are announcing today the release of the Public Beta of CerebralVol.com<http://cerebralvol.com/>, a public cloud based supercomputer service to process FreeSurfer data. CerebralVol.com users can process large amount of data using recon-all in a single day without the hassle of dealing with Unix commands, scripts, etc. Users can upload input data (NifTI and MGZ) through the web and download the results of the recon-all from the web interface. It's also possible to separate your cases in Groups and have Studies associated with the Groups. This week we are shipping the service with 20 CPUs and we are growing it to 1024 CPUs by the end of next week. The system will be fully operational by January with 4096 nodes available to process more than 4000 recon-all per day. Those of you who want to know more about the technical details of the project can find more information at https://www.cerebralvol.com/about.html also you can find information regarding HIPAA at https://www.cerebralvol.com/hipaa.html Signup for free at: https://www.cerebralvol.com We strongly appreciate any suggestions and feedback. Pedro Paulo Oliveira Jr. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Re: [Freesurfer] p-value too small?
by Douglas N Greve 30 Nov '12

30 Nov '12

On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > I'll do that. > Two quick follow-up questions regarding 5.1: > - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is > there another argument that would allow me to set the autocorrelation? What do you mean by "set the autocorrelation"? You can turn it off with -no-whiten. > - in a block design, would refeventduration be the block length or the > length of the individual events within a block? The block length. This will not change the p-values, only percent signal change values (often not even looked at). doug > Thanks, > Caspar > > 2012/11/26 Douglas N Greve<greve(a)nmr.mgh.harvard.edu>: >> Hi Caspar, I think I fixed this in later versions. If you upgrade, you >> can run the stats from 5.1 with recons from 4.5 (just don't mix recons >> from different versions). >> doug >> >> On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote: >>> Hi! >>> I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0. >>> Namely, the center of my cluster of significant voxels has a p-value >>> of -0.0, resulting in a funny whole where you would otherwise expect >>> to find the most significant voxel(s). >>> It seems that the p-value is too small. Is there a workaround available? >>> Thank you very much, >>> Caspar >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: 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 >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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tkmedit background color
by Righart, Ruthger Dr. 30 Nov '12

30 Nov '12

Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display purposes? (to avoid laborious photoshop work). Best Regards, Ruthger Righart

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mergecontrasts-sess group map
by Alexandra Tanner 30 Nov '12

30 Nov '12

Hi Doug and Freesurfers, I recently used mergecontrasts-sess to merge two contrasts of an analysis in 50 different subjects. The command ran on each subject individually and created a sig.nii and sig.ovpl file within a merged contrast folder for each subject. I'd now like to look at an average map of the merged contrasts across all 50 subjects. Does anyone know how to go about getting this average map for my group of 50 subjects? Command I ran to get the sig.nii/sig.ovpl file for each subject: mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix 3 pos 0 -map sig -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects -df /cluster/roffman/users/Stable5_PerRun Any help would be greatly appreciated! Thanks, Alex

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Re: [Freesurfer] TRACULA tract path failure
by Arman Eshaghi 30 Nov '12

30 Nov '12

Dear Anastasia, Thanks for your response. I have sent a subject that the problem in forceps minor persists. What I have done so far was to re-run the pipeline with "reinit=1", check the eigenvectors, increase control points, switch off brain anatomical mask in dmric. It made the tracts look better for many subjects but this one still has problems in forceps minor. Thanks, Arman On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi <arman.eshaghi(a)gmail.com>wrote: > Dear Anastasia, > > Thanks for your response. I have sent a subject that the problem in > forceps minor persists. > What I have done so far was to re-run the pipeline with "reinit=1", check > the eigenvectors, increase control points, switch off brain anatomical mask > in dmric. It made the tracts look better for many subjects but this one > still has problems in forceps minor. > > Thanks, > Arman > > > On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki < > ayendiki(a)nmr.mgh.harvard.edu> wrote: > >> >> Hi Arman - Have you ruled out any issues with the gradient directions? In >> situations where the problem is wide-spread, this seems to be the usual >> suspect. If you've checked the eigenvectors and they're ok, can you send an >> example case where the problem persists? You can use this page to upload a >> tar ball of all the tracula-related directories of the subject: >> https://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> Thanks! >> a.y >> >> >> On Mon, 26 Nov 2012, Arman Eshaghi wrote: >> >> Dear all, >>> I have difficulty sorting out the problem with some tracts in several >>> subjects, tracts are incomplete or >>> missing. As it has come up quite a few times on the list, for this sort >>> of problem I have first set >>> "reinit=1" and then increased control points to 7, and re-ran trac-all >>> with "-prior" flag. This has worked >>> for some tracts in several subjects, however there are a few subjects >>> that still have this problem. >>> >>> It would be great if someone could let me know what else I might be able >>> to do in order to correct >>> missing/faulty tracts in my subjects. (The problem is not limited to a >>> specific tract, it varies in >>> different subjects) >>> >>> All the best, >>> -Arman >>> >>> >>> >> >> 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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Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
by Anastasia Yendiki 30 Nov '12

30 Nov '12

Fantastic, thanks! On Fri, 30 Nov 2012, Fernando Ventrice wrote: > Dear Anastasia, now it worked perfectly well changing the Z gradient with *(-1)! Here I send you a screenshot. > Best, > Fernando > > -----Mensaje original----- > De: Fernando Ventrice > Enviado el: 29 November 2012 11:39 > Para: Anastasia Yendiki > Asunto: RE: [Freesurfer] FW: TRACULA some fiber volumes being too small > > Hi Anastasia, > I'll rerun all steps changing the Z gradient with *(-1). Thanks and I'll write with the results. Best, > Fernando > > -----Mensaje original----- > De: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] En nombre de Anastasia Yendiki > Enviado el: 28 November 2012 15:30 > Para: Fernando Ventrice > CC: freesurfer(a)nmr.mgh.harvard.edu > Asunto: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small > > > Hi Fernando - I looked at your data and changing the sign of the z > coordinate in your gradient table gave me eigenvectors that looked fine in > both fslview and freeview. Why you would get eigenvectors that look > different in freeview and fslview before flipping z but not after is still > a mystery to me, but at this point I'd just try starting clean, changing > the sign in the 3rd column of your gradient table, and testing the whole > pipeline on a test subject to see if that fixes things. Let me know how it > goes! > > a.y > >> Dear Anastasia, >> When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions actually are OK, but when I open them with FSLview they are similar to your screen-shot. Here I also send a screen-shot with the comparison between the two softwares in each monitor. >> Best, >> Fernando >> >> El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. >> http://www.fleni.org.ar >> > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar >

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Re: [Freesurfer] Fwd: (no subject)
by Bruce Fischl 29 Nov '12

29 Nov '12

Hi Hugh how far is the closest visible white matter? Do you have any other image types (e.g. a FLAIR)? Bruce On Wed, 28 Nov 2012, Hugh Pemberton wrote: > Hi freesurfers, > Just want to ask how I might go about including parts of the temporal lobes > that have been left out of the the surfaces due to severe atrophy but where > there's no white matter so control points are of no use? I have attached a > jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 21 November 2012 11:29, Hugh Pemberton <hughpemberton1(a)gmail.com> wrote: > Hi Bruce, > Just to let you know the new mris_topo_fixer worked and there was no > error with the recon. > > I also meant to ask how I might go about including parts of the > temporal lobes that have been left out of the the surfaces due to > severe atrophy but where there's no white matter so control points are > of no use? I have attached a jpg few screen shots as examples.. > > Cheers, > Hugh > > > On 16 November 2012 14:44, Hugh Pemberton <hughpemberton1(a)gmail.com> > wrote: > Hi Bruce, > I also meant to ask how I might go about including parts of the > temporal lobes that have been left out of the the surfaces due > to severe atrophy but where there's no white matter so control > points are of no use? I have attached a few screen shots as > examples.. > > Cheers, > Hugh > > > On 16 November 2012 11:14, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > this is a bug in the topology fixer. Maybe Zeke or > Nick can post a new version of it? Was it > mris_topo_fixer that was runing or > mris_fix_topology? > On Fri, 16 Nov 2012, Hugh Pemberton wrote: > > Hi Bruce, > Thanks for getting back to me. In > terminal window it says > "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0" > but recon-all -version > give me "$Id: recon-all,v 1.379.2.17 > 2011/05/20 22:48:18 nicks Exp $" > > Hugh > > > On 16 November 2012 11:05, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Hugh > This is fixed in the newest version. > What version are you running? > Bruce > > > > On Nov 15, 2012, at 6:48 PM, Hugh > Pemberton <hughpemberton1(a)gmail.com> > wrote: > > Hi, > I have just received this error after a > recon-all subjid- ___ > all : > > ERROR: _FindFacePath: could not find > path! > /home/hughp/freesurfer/subjects/B______________/scripts > > mris_remove_intersection > ../surf/lh.orig ../surf/lh.orig > > intersection removal took 0.00 hours > removing intersecting faces > writing corrected surface to > ../surf/lh.orig > > rm ../surf/lh.inflated > > > cp ../surf/lh.orig_corrected > ../surf/lh.orig > > Linux naoshi-WS 3.2.0-32-generic > #51-Ubuntu SMP Wed Sep 26 > 21:33:09 UTC 2012 x86_64 x86_64 x86_64 > GNU/Linux > > recon-all -s B______________ exited with > ERRORS at Thu Nov 15 > 11:40:44 EST 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Many thanks in advance, > Best, > Hugh > > > _______________________________________________ > 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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Re: [Freesurfer] Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

I see. Yes. Thanks a lot. Best Wei Those values are radians. Does that help? doug On 11/29/2012 06:09 PM, Zhou, Wei wrote: > Hi Doug, > > Thank you for your patient. I wanted to see how the polar angle > correlates with the map and I expect a wheel bar which distinguish > different polar angles. > I typed: > > rtview --s SUBJ1 --lh --polar --real > SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag > SUBJ01/bold/rtopy.self.lh/polar/imag.nii.gz --fsig > SUBJ01/bold/rtopy.self.lh/polar/fsig.nii.gz > > I could see some blue, red and green region in the cortex. Then i > click "show the color scale bar" and I get a all-blue and vertical bar > ranging from -1.18 to -0.4 and 0.4 to 1.18. I do not know how to > interpret the image with this bar. > > I am asking if wheel bar is still supported in freesurfer5. If so, how > can I get it to interpret the maps? > > Thank you. > >

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Re: [Freesurfer] Retinotopy Maps
by Zhou, Wei 29 Nov '12

29 Nov '12

Hi Doug, Thank you for your patient. I wanted to see how the polar angle correlates with the map and I expect a wheel bar which distinguish different polar angles. I typed: rtview --s SUBJ1 --lh --polar --real SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag SUBJ01/bold/rtopy.self.lh/polar/imag.nii.gz --fsig SUBJ01/bold/rtopy.self.lh/polar/fsig.nii.gz I could see some blue, red and green region in the cortex. Then i click "show the color scale bar" and I get a all-blue and vertical bar ranging from -1.18 to -0.4 and 0.4 to 1.18. I do not know how to interpret the image with this bar. I am asking if wheel bar is still supported in freesurfer5. If so, how can I get it to interpret the maps? Thank you. _________________ Hi Wei, I don't think I understand your question. Can you elaborate? doug On 11/29/2012 04:06 PM, Zhou, Wei wrote: > Hi Doug, > > Thank you very much. I have thrown all the fixation sessions and run > the analysis again. So in rtview how can i get the color scale bar > which indicates the corresponding time points of polar or eccen? Is it > still supported in free surfer 5? > > Best > Wei > --------------------------- > Hi Wei, the argument to -retinotopy should be the period of stimuluation > (ie, how long it takes the wedge to go around 360 degrees), not the > duration of your run. Also, it is not set up to handle fixation at the > beginning or the end, so you might want to cut those frames out. > doug > On 11/29/2012 12:30 PM, Zhou, Wei wrote: > > Dear freesurfers, > > > > I am doing retinotopy analysis using freesurfer 5 with > >http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > >. > > I have four runs, two eccen and two polar. For each run I have 15 > > seconds fixation, 300 seconds stimuli and 15s fixation at the end > > (total 330s and 300s for stimuli). > > > > 1) For -retinotopy option in mkanalysis-sess I typed "300". Do you > > think this setting is fine? > > > > 2) After finishing running, I use tksurfer-sess to display the result. > > When I typed "tksurfer-sess -s SUBJ01 -analysis rtopy.self.lh -map > > angle" with "-c polar" or "-c eccen'" I got two maps with -4.0 to 4.0 > > color range. I learn from mail list, the two maps do not represent > > time course of retinotopy, right? So what are these two maps tell us? > > > > 3) I tried rtview cmd and the maps look strange. Color scale is from > > -1.185 to -0.4 and 0.4 to 1.185 and it does not include all the colors > > in display. > > > > 4) I tried to use -run-wise in selxavg3-sess, it fails with: > > "/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat > > Error using svd > > Input to SVD must not contain NaN or Inf." > > > > Could you please give me some idea? Thank you very much in advance.

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