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30132 discussions

Unknown label in Parcellation
by Pedro Paulo de Magalhães Oliveira Junior 27 Apr '11

27 Apr '11

In one study we are conducting we found significant difference in cortical thickness between the two groups in some areas. One of those areas are lh_unknown. Is this an error or it's a still unlabelled area? thanks Pedro Paulo Jr

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Re: [Freesurfer] about mri_vol2surf
by greve＠nmr.mgh.harvard.edu 27 Apr '11

27 Apr '11

> > Hi Doug: > > When you talk about zero out subcortical region, when does this zero > out happen? it should happen after register vertex into functional > space, right? Then it happens before functional space interpolation > or after interpolation? It happens after interpolation. > > And one more question about the register.dat file used for this > process. whose resolution info is used in register.dat file ? the low > resolution functional image (moving image) or high resolution anatomy > image? Is the resolution of fsaverage is 2mm*2mm*0.15mm? The low resolution (though those numbers are no longer used internally -- the resolution is obtained from the mov volume). doug > > Thanks much! > > Jing > > Date: Tue, 26 Apr 2011 17:11:45 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] about mri_vol2surf > > > > > > > > > > Hi Jing, by default it does include all the non-cortical structures > in the medial wall, including any subcortical structures. If you > include --cortex in the command-line it zeros them out. The way it > works is that it goes through each vertex on the surface, gets the > RAS coordinate for that vertex, applies the registration matrix to > map it into the function space, then samples the function value > using nearest neighbor (can change to trilinear with --interp > trilin). > > > > doug > > > > On 4/26/11 1:51 PM, Jing Ming wrote: > > > Hi Surfers: > > > > I am using mri_vol2surf to project fMRI result into the > fsaverage surface. And the fMRI result may contain some > subcortical regions, so, I wonder mri_vol2surf will automatically > get rid of the subcortical region and only map cortical area into > surface right? Is there any material about the mapping algorithm > of mri_vol2surf? Thanks much! > > > > Jing > > > _______________________________________________ > 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.

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GroupAnaysis Tutorial question: GLM directory error
by Carl Anderson 27 Apr '11

27 Apr '11

Dear Freesurfer, My current subjects dir is: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial When I run the following (from the tutorial): mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite I get the following error: ERROR: cannot find /autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm I tried the following: mri_glmfit-sim --glmdir /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite With the same result. Any suggestions? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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wrong sagittal orientation
by Saad Ramadan 27 Apr '11

27 Apr '11

Hi all, Upon creating my .nii file from my Siemens MPRAGE data using mri_convert, and opening nii file in freesurfer, I notice that the sagital view has the wrong orientation. What I mean is that on teh scanner I can see nose on left side of image, but on freesurfer I see nose on right. I am using mri-convert with no options. Is thsi normal or am doing anything wrong? Thanks in advance.

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qdec analysis different scanner
by John Fredy 27 Apr '11

27 Apr '11

Hello all, In voxel based morphometry is not recommended use images from different scanners. This recommendation also apply in the qdec analysis? Thanks in advance John Ochoa Universidad de Antioquia Instituto Neurológico de Antioquia

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Re: [Freesurfer] high resolution segmentation
by Bruce Fischl 26 Apr '11

26 Apr '11

Hi Jon, I'll leave this to Krish, as he's the local expert on mris_volmask, but it definitely could. Do you want to upload an example of a subject that failed for us to try out? Bruce On Thu, 14 Apr 2011, Jonathan Winawer wrote: > Hmm. At least when I use tkmedit, the surfaces seem to be correctly > registered to both the high resolution volume (rawavg.mgz) and the 1x1x1 > volume (T1.mgz). So it does not look like a coordinate problem, at least to > my un-expert eyes. But maybe tkmedit does a different transform of the > surfaces than mris_volmask? > > In any case, the failure of mris_volmask to produce a good ribbon file > follows a very characteristic pattern that looks more like a topology > confusion to me, as you can see in the attached png. I say this because > voxels along the gray-white border are labeled white (with some gaps) and > voxels along the pial surface are labeled as gray. Also, some of the regions > which are unlabeled holes in the correct (original) ribbon become labeled > islands in the new, high-res ribbon. So it looks like the surfaces are in the > right place, but they are somehow not filled in correctly. This precise > pattern happens with every high-resolution brain I use when I try to re-run > mris_volmask. In contrast when I rerun mris_volmask on bert, it works > perfectly, though in this case the rawavg.mgz is already registered to T1.mgz > and has the same resolution. > > Could a coordinate problem cause this? > > Sorry for all the questions. I seem to be stuck though. Many thanks again > for your quick responses! > > Jon > >

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recon-all error
by Yunjo Lee 26 Apr '11

26 Apr '11

Dear FreeSurfer experts, I just installed FreeSurfer in a virtual machine (Ubuntu) and ran recon-all. I kept getting the following error message. Could you advise? Thanks in advance, Yunjo *Here's the error message:* 0597: dt=0.056000, rms=0.417 (0.032%), neg=0, invalid=766 0598: dt=0.028000, rms=0.417 (-0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22111.002 ms 0599: dt=0.000000, rms=0.417 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Tue Apr 26 16:21:09 EDT 2011 /usr/local/freesurfer/subjects/YC7178/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux VMBronzeWing 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:34:50 UTC 2010 i686 GNU/Linux recon-all -s YC7178 exited with ERRORS at Tue Apr 26 16:21:14 EDT 2011

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about mri_vol2surf
by Jing Ming 26 Apr '11

26 Apr '11

Hi Surfers: I am using mri_vol2surf to project fMRI result into the fsaverage surface. And the fMRI result may contain some subcortical regions, so, I wonder mri_vol2surf will automatically get rid of the subcortical region and only map cortical area into surface right? Is there any material about the mapping algorithm of mri_vol2surf? Thanks much! Jing

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Comparison between two hemispheres using QDEC.
by Krista Kelly 26 Apr '11

26 Apr '11

I'm using QDEC to analyze cortical thickness of a patient population compared to controls. One of the things I wanted to analyze is the difference between hemispheres within patients. It seems that I can only analyze one hemisphere at a time in QDEC; is there any way to analyze the difference BETWEEN hemispheres for one group? Thank you!

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(no subject)
by kevin bickart 26 Apr '11

26 Apr '11

Hi all, I am interested in projecting my functional connectivity z map to the cortical surface. I attempted to use mri_vol2surf but received a warning message (see command and output below) indicating that the voxel resolution in the source volume doesn't match the registration file. Perhaps as a result of this, when I attempt to load the resulting .mgh file in tksurfer, nothing appears on the cortical surface image. Any idea what went wrong? Thanks in advance, Kevin Here's the my command and output: mri_vol2surf --mov N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --hemi lh --trgsubject fsaverage --out lh.L_WholeAmy_buckner_YC.mgh --projfrac 1 --surf-fwhm 4 srcvol = N89_L_WholeAmyMask_g7_zfrm_avg.nii.gz srcreg = /usr/local/freesurfer/stable5_0_0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.white Done reading source surface Reading thickness /space/sake/3/users/inverse/subjects/fsaverage/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 23569 Surface smoothing by fwhm = 4 (n=12) Writing to lh.L_WholeAmy_buckner_YC.mgh Dim: 163842 1 1 -- Kevin Bickart MD-PhD Student Department of Anatomy and Neurobiology Boston University School of Medicine live UP to it

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