Freesurfer

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30133 discussions

glmfit - matrix is ill-conditioned or badly scaled
by Linda Zhang 30 Jan '14

30 Jan '14

Dear all, Whilst running mri_glmfit, the following error occurred: ERROR: matrix is ill-conditioned or badly scaled, condno = 12375.1 I've attached the design matrix, the fsgd file, and one of the contrast matrices as an example. The command line was: mri_glmfit --glmdir lh.all.thickness.glmdir --y lh.thickness.10.mgh --fsgd all.fsgd dods --C allavovsallcvo.mtx --C avovscvo.mtx --C mavovsavo.mtx --C mavovsmcvo.mtx --C mcvovscvo.mtx --surf fsaverage lh --cortex What should I change? Cheers, Linda

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longitudinal processing, template and flags
by Daniel Ferreira 30 Jan '14

30 Jan '14

Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira

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Re: [Freesurfer] freeview porblem under ubuntu 12.04
by Ruopeng Wang 30 Jan '14

30 Jan '14

This looks like graphics driver issue. Is your graphics card driver up-to-date? Is there any error/warning message in the console? Ruopeng On 01/30/2014 01:17 PM, Markus Gschwind wrote: > HI Ruopeng, > > Here it is. > > Is it related to the tbouble shoot I did for trackvis? > > Thanks for having a look, > Markus > > > 2014-01-30 Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu > <mailto:rpwang@nmr.mgh.harvard.edu>> > > Can you post a screenshot? > > Ruopeng > > > On 01/30/2014 12:58 PM, Markus Gschwind wrote: >> Dear Experts, >> >> I have installed Freesurfer 5.3 under ubuntu 12.04. >> >> It is running fine except for Freeview which is causing heavy >> graphic trouble (thousands of colored squares in the black fields >> where the brains should be displayed. >> >> Tksurfer is working fine. >> >> Glxgears is showing the rotating blue, red and green gears. >> >> There is no error in the terminal. >> >> What could I do to track down the problem? >> >> Thanks for help! >> Markus >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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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parcellation of grey and white matter is incorrect across large portions of the cortex
by Christine Smith 30 Jan '14

30 Jan '14

Hello, The parcellation of grey and white matter appears to be off in several T1-weighted structural scans I have been processing. The effect is observed in the temporal lobes, parietal lobes, and part of the occipital lobes. The frontal lobe does not seem to be affected as much. For example, the medial white matter is super white, while more distal white matter near the cortex is less white (grey). Grey matter itself is rather dark (black in some cases). If you monkey around with the brightness of the image you can see that, for example, the pial line has actually followed the distal white matter and not the grey matter. Moreover, the white matter line has followed the boundary between medial (super white) white matter and more distal (greyer) white matter. This effect is most pronounced in the temporal and parietal lobes nearest the brightest parts of the white matter across the entire scan. About 3-5 voxels are cut off. For the frontal lobe and caudal occipital lobe, though, it is only cutting off about 1 voxel around the edge of the brain. I have attached a picture of this problem with the pial and white matter lines on the image. Look at the cortex in the lower left hand part of the image (lateral temporal cortex). For the image called Missing_Voxels.tiff I have adjusted the standard brightness of the image in freesurfer to show how much of the brain we are missing. In the image called Missing_Voxels_Brighter.tiff I have left the brightness levels as they appear when you open freesurfer. The problem appears less severe in this latter image because the standard brightness level has made some of the grey matter appear black and it is easier to miss that it is actually present. Now look at the top of the image and see that the pial line there is pretty accurate, though it does appear to cut off maybe 1 voxel too much. Extracting the eTIV from one of these scans shows that their intracranial volume is much smaller than other participants whose data were obtained on a different scanner. Also, each lobe volume is reduced. For example, the parietal lobe is about 15 standard deviations smaller than a group of participants scanned on a different scanner. These types of reductions are observed if you include grey matter only and also if you include grey+white matter in the calculation of the lobe volumes. Thus, the problem appears to be that we are missing the most outer part of the grey matter across a large part of the brain. I should also mention that the skull itself is missing (on the T1 image) near the lateral temporal lobes so there may be some signal dropout there. Though the lateral temporal cortex itself becomes visible when the brightness of the scans is adjusted, the skull in that area never does become visible. Is there any way to fix this problem at a basic level in one of the earlier steps of freesurfer? I have tried putting in a bunch of control points in the "real" white matter and it does make the white matter extend out further. However, the pial line is still cutting off ~3-4 voxels of brain in the problematic areas. Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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freeview porblem under ubuntu 12.04
by Markus Gschwind 30 Jan '14

30 Jan '14

Dear Experts, I have installed Freesurfer 5.3 under ubuntu 12.04. It is running fine except for Freeview which is causing heavy graphic trouble (thousands of colored squares in the black fields where the brains should be displayed. Tksurfer is working fine. Glxgears is showing the rotating blue, red and green gears. There is no error in the terminal. What could I do to track down the problem? Thanks for help! Markus

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mris_spherical_average problem
by Sophie Maingault 30 Jan '14

30 Jan '14

Dear FS experts, I have some troubles when I'm trying to use the command mris_spherical_average. Once I have a X.label defined for all my subjects in their native space, I used mri_label2label to put all my label files in fsaverage (--trgsubject fsaverage) ? Then I ran : mris_spherical_average label lh.X lh sphere.reg s1sn lh.Xproba.label in order to create a probabilistic map as you did in this paper : "Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI". When I loaded the output label in fsaverage I obtained this image but I expected a label in heschl gyrus Do you have any idea to fix this ? Should I use label2label to put all files in a common space or not ? Which spherical surface should I use in the command mris_spherical_average ? Best regards. Sophie Maingault

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Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi"
by Kaiming Yin 29 Jan '14

29 Jan '14

Dear FreeSurfer guys, I am using longitudinal processing stream and with the RepeatedMeasuresAnova. I follow the instruction here from http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova my fsgd file is: GroupDescriptorFile 1 Title k_longitudinal Class k Variables TP1-vs-TP2 TP1-vs-TP3 Input k_1 k 1 1 Input k_2 k -1 0 Input k_3 k 0 -1 contrasts is: tp1-vs-tp2.mtx tp1-vs-tp3.mtx tp2-vs-tp3.mtx tp-effect.mtx mean.mtx 0 1 0 0 0 1 0 -1 1 0 1 0 1 0 0 0 0 1 I run the mris_preproc and mri_surf2surf commands as the same for left hemi thickness, but when I run the mri_glmfit command it reports "ERROR: you must use '--surface subject hemi' with surface data". if i add the flag as: mri_glmfit ...(as the same before)... --surface k lh or --surface k lh thickness or --surface k_1.long.k lh or --surface k_1.long.k lh thickness or --surface k_1 lh or --surface k_1 lh thickness it still goes wrong and even not make an output folder. Any problems there? thanks, Kaiming

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Fwd: trac-all -path error
by Jon Wieser 29 Jan '14

29 Jan '14

Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 I have attached the trac-all.log and trac-all.error files I am running tracula 5.3 -- 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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Fwd: trac-all -prep error
by Jon Wieser 29 Jan '14

29 Jan '14

Hello I'm getting the following error when running trac-all -c dmrirc -prep INFO: Distances between consecutive points in test subject's space are 7 9 7 8 WARN: Could not find satisfactory control point fit - try 809 Writing output files to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_* Writing spline volume to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_cpts_5.nii.gz Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Wed Jan 8 12:07:54 CST 2014 i'm running traclua 5.3 attached are the trac-all.log and trac-ll.error files -- 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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Can QDEC do a vertex-wise GM comparison?
by Manish Dalwani 29 Jan '14

29 Jan '14

Dear Freesurfer developers, Is QDEC GUI toolbox ready at this point to do a vertex-wise GM comparison? Regards Manish Dalwani Instructor Dept. of Psychiatry Univ. of Co Sent from my iPhon

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