Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

mri_glmfit
by Jenny Liu 16 Jul '12

16 Jul '12

Hello I typed in the command for multiple comparison: $ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos It starts to process, but there is an error (see below). How do I fix this? Thanks, Jenny mdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir SURFACE: average rh log file is rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir/cache.mri_glmfit-sim.log cd /study4/NCCAM/Data/MRI/processed/structural/freesurfer /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 --cache 2.0 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Thu Jul 12 15:24:55 CDT 2012 Linux balsa.keck.waisman.wisc.edu 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 09:58:09 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux jliu setenv SUBJECTS_DIR /study/NCCAM/Data/MRI/processed/structural/freesurfer FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest Original mri_glmfit command line: cmdline mri_glmfit --y rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.724818 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd

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qdec - ERROR: CSDread():
by Natalia h 16 Jul '12

16 Jul '12

Dear expert, I got an error while clicking the Monte Carlo simulation in qdec. I am using Mac 10.6 and qdec version 1.4, freesufer 5.1 Have no clue why it always gives this error in the terminal: mri_surfcluster --in /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd --mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh --cwsig /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh --vwsig /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh --sum /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary --ocn /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh --oannot /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot --csdpdf /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat --annot aparc --cwpvalthresh 0.05 --surf white ERROR: CSDread(): could not open /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd ERROR! Very appreciate for the help ! Thank you in advance, Natalia

3 2

Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c
by Masaya Misaki 16 Jul '12

16 Jul '12

I've posted a question about a strange behavior of mri_segstats if voxel size isn't 1 mm3 and --pv option is used. I found a reason of this problem in the source code of mri_segstats.c (release_5_1_0 branch was checked out from read-only CVS source-code repository) In mri_segstats.c the return value from MRIvoxelsInLabelWithPartialVolumeEffects is used as the number of voxels; nhits = MRIvoxelsInLabelWithPartialVolumeEffects (seg, pvvol, StatSumTable[n].id, NULL, NULL); vol = nhits*voxelvolume; However, MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c returns volume (e.g. volume += vox_vol; or volume += vox_vol * pv;), not the number of voxels. nhits value is adjusted by voxel volume in mri_segstats.c (vol = nhits*voxelvolume), so that the voxelvolume (vox_vol) is multiplied twice. The volume reported by mri_segstats, therefore, is too small if the voxel volume is less than 1 mm^3 or too large if the voxel volume is larger than 1 mm3. Note that this is not a problem when voxel volume is conformed to 1 mm3 (default option in recon-all). I think many of FreeSurfer programs do not support high-resolution (< 1mm3) image without conforming to 1 mm3 voxel, but could you fix the problem of mri_segstats? I want to use mri_segstats with partial volume correction for high-resolution MRI image. Thank you, --Masaya On 06/26/2012 08:40 AM, Masaya Misaki wrote: > Hello all, > > I found volume size reported by mri_segstats is changed very much > depending on voxel size when partial volume correction (--pv option) is > used. The difference was much larger than that can be explained by the > difference of image resolution. > (mri_segstats version is 1.75.22 2011/4/27 in FreeSurfer v5.1.0) > > When I performed segmentation for high-resolution image (voxel size = 0.5 > mm^3), I found all volumes of segmented regions in aseg.stats was too > small; about 8 times smaller than that was estimated from 1mm^3 conformed > image. > > So I tested the effect of voxel size on mri_segstats. > At first, recon-all was run with conforming 1mm^3 voxel (default option). > Then aseg.mgz and norm.mgz were conformed to small voxel size, and > mri_segstats was applied to the conformed files: > > mri_convert aseg.mgz aseg_cs05.mgz -cs 0.5 rt nearest > mri_convert norm.mgz norm_cs05.mgz -cs 0.5 > mri_segstats --seg aseg_cs05.mgz --pv norm_cs05.mgz \ > --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ > --nonempty --excludeid 0 --sum aseg_cs05.stats > > (these are just for testing the effect of voxel size, not for actual > analysis) > > All volumes reported in aseg_cs05.stats (for 0.5mm^3 voxel) was about 8 > times smaller than aseg.stats (for 1mm^3 voxel). So the reported volume > was scaled with the same ratio as the voxel size. Same effect was observed > when voxel size was conformed to larger one (e.g. 1.5mm^3); reported > volumes were about 3 times larger than those for 1mm^3-voxel. The number > of voxels in the segmented regions (Nvoxels column in aseg.stats) were > similar across different voxel sizes while voxel sizes are different. > > When --pv option was not used, the reported volumes were almost the same > across different voxel sizes. So the partial volume correction in > mri_segstats seems to depend on voxel size. > > Can I fix this with some missed options or shouldn't I use --pv option > for the image with voxel size other than 1mm^3? > > thanks, > > > -- > Masaya Misaki Ph.D. > >

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Measuring total cortical volume
by Emelie Andersson 16 Jul '12

16 Jul '12

Hello, We have a some doubts about how to measure the total cortical volume. Is it recommendable to use GM = pial surface - white matter? Hope to hear from You, Best regards Emelie

2 1

How to register FLAIR to T1?
by Ed Gronenschild 16 Jul '12

16 Jul '12

Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed

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Ribbon
by Colin Reveley 16 Jul '12

16 Jul '12

Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin

4 3

qdec
by carolina.mr 16 Jul '12

16 Jul '12

3 2

multiple correction
by Meng Li 16 Jul '12

16 Jul '12

Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng

2 1

Error compiling FS with GPU
by Akio Yamamoto 16 Jul '12

16 Jul '12

Hi FS experts, My colleague is trying to compile FreeSurfer by configuring with a "--with-cuda" flag. The build process stopped with the error message: ===== em_register_cuda.cu(347): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(350): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(353): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(357): error: calling a host function("TransformGenerator::TransformGenerator") from a __device__/__global__ function("TransformLogps") is not allowed 4 errors detected in the compilation of ... ===== FYI, the build environment is as follows: GeForce GTX 690 CUDA Toolkit 4.2 CentOS 6.2 Are there any specific requirements for building CUDA-enabled FreeSurfer? Any information/help would be appreciated. Thanks, Akio

1 0

Cutting non-cortex
by Sourena Soheilinezhad 15 Jul '12

15 Jul '12

Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets? I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools. Thanks, Sourena Soheili

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