Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

the make_average_subject without aparc.annot
by Leon 16 Jul '12

16 Jul '12

Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_… Make a backup of your current version of make_average_surface and then copy this one over it douig

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Clusterwise correction for multiple comparisons
by Ed Gronenschild 16 Jul '12

16 Jul '12

Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the csd file I can read that it still has more than 1000 steps to go. Is it possible that it takes that much time? Cheers, Ed

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annot 2 label file conversion
by Arnaud Messé 16 Jul '12

16 Jul '12

Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I only found 770 label file. For another parcellisation scheme, I found 325 entries in annot file and 496 label files... These findings are consistent across several subjects. So my question is how mri_annotation2label processes annot file? and how to find correspondence between annot and label files? Any advice would be greatly appreciate, -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

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Repost: fsgd file
by Jacobs H (NP) 16 Jul '12

16 Jul '12

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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Coordinate Transformations
by jmd33 16 Jul '12

16 Jul '12

Hi, I'm working on a project project comparing the cortical thickness in epileptic patients to the corresponding brain area of a control subject. To do this, I have been trying to transform the patient RAS coordinates to talairach coordinates and then transforming the talairach coordinates into the RAS coordinates of the control. In doing this, I have two problems. First, when I use the transformation matrix provided in the free surfer subject folder (multiply RAS coordinate by transformation matrix in /mri/transforms/talairach.xfm) the coordinates seem to map to similar although not exactly the same area. Second, what is the best way to transform a set a talairach coordinates to RAS coordinates? Thank you for your help, Jared

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ROI from left to right hemi - cortical thickness
by Irene Altarelli 16 Jul '12

16 Jul '12

Dear all, I have a ROI on the left hemisphere and I'd like to extract cortical thickness values from the homologous region in the right hemisphere. For this I applied the interhemispheric registration process and got my ROI mapped into the right hemisphere in /subject/xhemi/label. However when I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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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

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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

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Freesurfer July 2012