Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Correction for multiple comparisons error
by Fotiadis, Panagiotis 31 May '13

31 May '13

Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x0000000006e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x0000000006e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos

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TRACULA outputs out of expected range
by Ali Ezzati 31 May '13

31 May '13

Hello Experts, I would be grateful if you could help me with this problem: I was able to run all steps of TRACULA on several subjects without any error message, but all the final outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA values for all tracts are >1). I tried to identify the source of this problem... clearly FA values in "dmri/dtifit_FA", which is an output of "prep" step are all out of range. The only source of error that I can think of is .bvecs file. My input .bvecs files are in 3 columns, exactly as described in the manual. There are two .bvecs file in the "dmri" folder. one is "dwi_orig.mghdti.bvecs" which is exactly the same as my input .bvecs file and the other one's name is just "bvecs", which has completely different values. Could this be the source of my problem? or something else is causing this. Thank you, Ali

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CUDA install; libcudart; 64-bit detection
by Graham Wideman 30 May '13

30 May '13

Hi all, probably mostly Bruce and co., I've just got a new linux box set up and am able to run all graphical tools and recon-all OK. Linux Mint 15 x64 RC (based on Ubuntu 13) Intel i5 Ivy Bridge nVidia GTX 650 Ti nVidia drivers: Selected from System > Device Drivers; nvidia-313-updates; automatically installed. Freesurfer 5.3 Centos 6 version Now I'm hoping to get CUDA working. The proximate problem is that when I run Freesurfer's cudadetect I get: "error while loading shared libraries: libcudart.so.5: cannot open shared object file: No such file or directory" Indeed, searching the file system, there appears to be no libcudart.* anywhere. But there do appear to be CUDA components installed with the installation of the nvidia video driver: /usr/lib/nvidia-313-updates/libcuda.so 10.4 MB (plus some version-named links to same) So, my current model is that nvidia has installed what it considers to be the necessary components for an application to use to operate the CUDA hardware. Googling around, there seem to be some mentions that libcudart.so.* is something that would be supplied with a particular application (in this case Freesurfer). I'm not sure I believe that, but... The only other alternative I see is to download the nvidia CUDA developer kit and install that. However I'm very loath to do that because it replaces the video driver along with installing a lot of other unneeded apparatus. I have no idea the extent to which that installation works with or against the Ubuntu/Mint installation scheme, and what would happen on next video driver update. Not to mention that the latest Ubuntu-compatible package nvidia has is for 11.10, while my Mint is based on Ubuntu 13. Any idea how to proceed? Any chance of getting libcudart.so.5 a la carte? SIDE NOTE ON 64-bit detection in cuda_setup ============================================ I see that in script cuda_setup there's a section which detects 64-bit by looking for directory: /usr/lib64 However, on Mint (so I assume Ubuntu and Debian) 64-bit, there is no such directory. Instead, there are: /usr/lib /usr/lib32 Suggestions for other ways to detect 64-bit: http://stackoverflow.com/questions/246007/how-to-determine-whether-a-given-… I'm pretty sure this is not pertinent to the hunt for missing libcudart.so, but seems like that needs to be fixed too for Ubuntu/Mint. ---------------- Thanks, -- Graham

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recon-all error
by Borzello, Mia 30 May '13

30 May '13

Hi freesurfers, I encountered an error using recon-all for a scan series of 177 slices. I'm not sure exactly why it errorred, but I included the error log. Thanks so much, Mia

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combining masks in freesurfer ??
by Subhabrata Chaudhury 30 May '13

30 May '13

Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha

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Download difficulty
by Michael Paldino 30 May '13

30 May '13

Hello all, I seem to be having some difficulty downloading the freesurfer software to my MAC computers. I have tried my laptop (MacBook pro, I don't remember the version but it is approx. 10.3) as well as a desktop (imac, mac osx version 10.8.3) and also tried two different networks. I have tried just clicking on the link (on your download page) as well as the curl -O command line. I get an NSURL error everytime, prior to any significant downloading. I have not have this difficulty with other freeware downloading to the same computers or on these networks. Any thoughts? Thanks Mike

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Re: [Freesurfer] combining masks in freesurfer ??
by Subhabrata Chaudhury 30 May '13

30 May '13

Hello Doug, Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface data, right ? Best wishes Subha ----- Original Message ----- From: Douglas N Greve Sent: 05/30/13 05:40 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] combining masks in freesurfer ?? you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: > Hi All, > Is there a way to combine multiple binary volumetric masks into a > single binary volumetric mask in freesurfer ? > Please let me know. > Thankyou > Subha > > > _______________________________________________ > 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: 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/ _______________________________________________ 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.

2 1

tkmedit on ssh remote machine error
by Jon Wieser 30 May '13

30 May '13

hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) i have set X11forwarding to yes in the /etc/sshd_config file so xeyes works ok remotely Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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How to determine a smoothing kernel size for surface that is approx. equal to 4mm in volumetric data?
by Glen Lee 30 May '13

30 May '13

Hello Freesurfer users I'm trying to replicate my earlier findings in 3D space by warping the data into surface using freesurfer. Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm wondering what size of smoothing kernel for 2D would be equivalent to 4mm for volumes. Any help would be greatly appreciated. Glen

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Re: [Freesurfer] mris_divide_parcellation color table error (fwd)
by Bruce Fischl 30 May '13

30 May '13

Hi Tina is this (attached) more what you wanted? If so, then I think you want to use mris_make_face_parcellation instead of mris_divide_parcellation. I can't remember what they used in that paper, but in mris_divide_parcellation I try to have the different units within a parcel have similar colors (which evidentally fails when you split it so finely) Bruce On Thu, 30 May 2013, Tina Jeon wrote: > I am running version 5.3- the latest version. I also tried running the codes > on v5.0 and got the same result. Is there any way I can change the color > table so that the colors of the parcellation are unique? > > Thanks, > Tina > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wednesday, May 29, 2013 8:41 PM > To: Tina Jeon > Subject: Re: [Freesurfer] mris_divide_parcellation color table error > > Sure > > > > On May 29, 2013, at 9:36 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> wrote: > >> The colors are visually different by a shade then loop every 4 or so colors. >> I think the color table may be running on a loop? I can send the annot and >> surface file if you need that as well. >> >> Best, >> Tina >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, May 29, 2013 8:02 PM >> To: Tina Jeon >> Subject: Re: [Freesurfer] mris_divide_parcellation color table error >> >> p.s. can you send me the splittable text file ? I seem to have deleted >> it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon >> wrote: >> >>> Yes same result as with freeview. >>> >>> Sent from my iPhone >>> >>> On May 29, 2013, at 7:46 PM, "Bruce Fischl" >>> <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> Hi Tina >>> Did you try visualizing it in tksurfer? >>> Bruce >>> >>> >>> >>> On May 29, 2013, at 7:22 PM, Tina Jeon <Tina.Jeon(a)utsouthwestern.edu> >>> wrote: >>> >>> Hello freesurfers, >>> >>> >>> >>> I am trying to create a figure similar to the Hagmann et >>> al 2008 paper with 998 rois overlaid onto the surface, >>> however, I am finding that there is no random, unique >>> color for each parcellation unit like described in the >>> help file for mris_divide_parcellation. >>> >>> >>> >>> I have attached a snapshot of my annotation file overlaid >>> onto the surface, as you can see, the color iterates the >>> same/similar color for a particular label. Can you tell me >>> what I am doing wrong? Is there a pre-existing atlas as >>> described in the Hagmann paper? >>> >>> >>> >>> My input: >>> >>> mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh >>> ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 >>> -03-25.gcs ./lh.aparc.998rois.annot >>> >>> >>> >>> mris_divide_parcellation subject_name lh >>> ./lh.aparc.998rois.annot ./splittable.txt >>> ./lh.annotation.998rois_26.annot >>> >>> >>> >>> >>> >>> Many thanks, >>> >>> >>> >>> Tina Jeon, MS >>> >>> UT Southwestern Medical Center ‘14 >>> >>> >>> >>> >>> _____________________________________________________________________ >>> _______ >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >>> >>> <neonate_buckner40_atlas.png> >>> >>> <splittable.txt> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >> <splittable.txt> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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