Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

freeview
by Yaniv Kaufman 03 Dec '12

03 Dec '12

Dear Freesurfer experts, I am trying to display DTI using freeview, however, every time I attempt to run freeview from the command line (I am using Ubuntu 12.4), I receive the following error: "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory" libjpeg.sp.62 is present in /home/freesurfer, when I attempt to open it directly, it gives the following error: "The link cannot be used, because its target 'libjepg.so.8' doesn't exist" libjepg.so.8 does in fact exist but in /usr/lib. I am not quite sure how to direct libjpeg.so.62 to libjepg.so.8 or whether that would solve the problem at all. I am able to use tkmedit, tksurfer and do all the pre processing for MRI and DTI. Thank you in advance. Yaniv Kaufman

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Coregister a combination of T1, and Flair images ?
by Assaf B. Spanier 02 Dec '12

02 Dec '12

Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. *= A =* In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the " recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? *= B =* As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -iimage1 - i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier

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recon-all error
by aini ismafairus 01 Dec '12

01 Dec '12

Hello, I still new in using freesurfer. the freesurfer was successfully installed. but when i tried to run recon-all it give an error. [Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer [Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Applications/freesurfer FSFAST_HOME Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Applications/freesurfer/subjects MNI_DIR Applications/freesurfer/mni FSL_DIR FSL/fsl Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz -o us03 -all ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Sat Dec 1 11:42:54 CET 2012 Advice on how to troubleshoot this would be appreciate. Thank you. Regards, Isma

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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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Freesurfer