Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

mni152reg error
by JacobML＠nmr.mgh.harvard.edu 18 Jul '14

18 Jul '14

Hello Freesurfer Experts, I am trying to view stats generated with FsFast in fslview/MNIspace, and in doing so I have run mni152reg to generate the registration matrix. That said, mni152reg did not complete correctly and below I have pasted the terminal output: Thu Jul 17 09:58:10 EDT 2014 setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s CD_cerv_pat4_sess1_recon Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': Permission denied Log file is /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log Thu Jul 17 09:58:11 EDT 2014 --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ purkinje Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (-0, -0, -1) k_ras = (0, 1, 0) writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii I tried to run the fslregister command from within the subject's directory (in hopes to possible correct what may be a permissions issue), but this produces the same final error, "ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii." Lastly, probably to no surprise, the /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any ideas how I may be able to correct these errors? Thank you for the help! Jacob

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selxavg3-sess error in ==> fast_selxavg3 at 434
by pfannmoelj＠uni-greifswald.de 18 Jul '14

18 Jul '14

Dear Experts, during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were: mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force The output of selxavg3-sess was: >> >> >> >> >> >> >> sxa3pwd = /.../evaluation >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessdir ############################### /.../evaluation/sessdir ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /.../evaluation Extension format = nii.gz 1 stim-v-base.mat Excluding 8 points nruns = 1 autostimdur = outanadir = /.../evaluation/sessdir/bold/analysis.lh Excluding 8 points Found 145573/155188 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 108, nX = 15, DOF = 93 Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat XCond = 64.7067 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.468819 (t=0.005249) 2 -0.25 -0.252194 (t=0.007053) 3 0 -0.0449419 (t=0.008126) 4 0.25 0.149516 (t=0.00935) 5 0.5 0.319324 (t=0.010795) AR1 Correction M: 0.0749452 1.26122 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 Global Mean Global In-Mask Mean = (0.664951) ??? Error using ==> mrdivide Matrix dimensions must agree. Error in ==> fast_selxavg3 at 434 RescaleFactor = flac0.inorm/gmean; >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Do you have an idea what went wrong? Sincerely yours pfannmoe

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Re: [Freesurfer] unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim
by wang kangcheng 18 Jul '14

18 Jul '14

Thanks doug I first merge the data using command of mris_preproc and then do the GLM analysis using command of mri_glmfit. After that, using the following command to look the result: mri_surfcluster --in leg.volume.lh.10/g2v2/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd --mask leg.volume.lh.10/mask.mgh --cwsig leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.mgh --vwsig leg.volume.lh.10/g2v2/cache.th13.pos.sig.voxel.mgh --sum leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.summary --ocn leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.mgh --oannot leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf leg.volume.lh.10/g2v2/cache.th13.pos.pdf.dat --cwpvalthresh 1 --o leg.volume.lh.10/g2v2/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Did you mean that I multiple the value by the number of vertices (NVtxs, which in the file of cache.th13.pos.sig.cluster.summary ) to get the total volume for the cluster? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 4.623 7401 1647.03 -8.8 -49.3 5.4 0.00719 0.00559 0.00878 4199 isthmuscingulate 2 3.984 46872 1185.43 -7.7 -71.9 50.4 0.06375 0.05929 0.06820 2487 precuneus 3 3.960 57039 3597.23 -10.6 64.4 -5.0 0.00020 0.00000 0.00040 5545 frontalpole Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China

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Re: [Freesurfer] unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim
by wang kangcheng 18 Jul '14

18 Jul '14

Thank you doug Data of thickness: 1.83629 3.01648 2.16078 corresponds to lateraloccipital, frontalpole and superiorparietal. Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so small ? was the unit cm^3? Wang Kangcheng

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unit of each index (thickness, volume, sulc, curv) after mri_glmfit-sim
by wang kangcheng 17 Jul '14

17 Jul '14

Dear freesurfer experts After using the command of mri_glmfit-sim (mri_glmfit-sim --glmdir aaa.thickness(or thickness, volume, sulc, curv ).lh.10 --cache 1.3 pos --cwp 1 --2spaces). I check the data in the fie of cache.th13.pos.y.ocn.dat and found that the data of volume was so small ( e.g 1.39463 1.50616 2.53250).Data of thickness was same as volume (e.g 1.83629 3.01648 2.16078). Could you tell the unit of each index? And could the data be used as further analysis, e.g correlation with IQ or other behaviors? Thank you Wang kangcheng

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template replacement
by Ilwoo Lyu 17 Jul '14

17 Jul '14

Dear FS experts, I am trying to adapt a macaque template (dim: 250 by 300 by 300, voxel size: 0.8202 mm). I changed voxel spacing and dimensions to be the same as the MNI305 template in freesurfer, but it seems not to work correctly for the affine transformation in the Talairach space. Here are my questions: 1) Should I change the voxel size and dimensions of the macaque template? 2) Should I change the original coordinate system of the macaque template into the Talairach space? If so, how can I do that (eg, roughly aligned to (or registration) the MNI template)? Thank you! Ilwoo

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Re: [Freesurfer] Temporal lobe reconstruction problem
by james pardon 17 Jul '14

17 Jul '14

Hi Louis, I would appreciate if I could get your feedback on this specific subject we are experiencing problems with. Thanks James On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi James > > I did, and one of our RAs here is going to be looking into it. Louis (ccd) > can give you more information > > cheers > Bruce > > On Tue, 15 Jul 2014, james pardon wrote: > > Hi Bruce, >> I was wondering whether you have seen my email below? >> >> Thanks so much >> >> Cheers, >> James >> >> >> On Sat, Jul 12, 2014 at 9:18 AM, james pardon <james.pardon15(a)gmail.com> >> wrote: >> Hi Bruce, >> I have sent the link for a problem subject via a private >> message. Please note since MS causes hypointense lesions in white >> matter I have used an algorithm that fills hypointense lesions in WM >> with median intensity of normal appearing WM. >> >> Thanks >> James >> >> >> On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi James >> >> if you upload a problem subject we will take a look (the >> whole subject dir please) >> cheers >> Bruce >> On Fri, 11 Jul 2014, james pardon wrote: >> >> Hi all, >> On a few subjects with a specific pathology >> (MS) I cannot easily reconstruct temporal >> lobes. >> I think this issue comes up quite regularly on >> the mailing list, and I have tried to trouble >> shoot using control points, WM edits, even >> getting back to orig/001.mgz to correct areas >> that >> may seem the culprit for breaking surface >> reconstruction. Some subjects have gone >> through 7-8 >> runs of recon-all with different edits but >> still the problem persists in a few subjects >> in my >> study. >> >> I have also tried to use -mprage and -3T flags >> along the way to allow more liberal control >> point growing, despite an improvement in my >> results some of subjects still have very bad >> surface constructions. I have attached two >> snapshots to this email and I am happy to >> upload >> the complete subject folder if you need to >> take a look at them. >> >> As far as the SNR is concerned, I have >> designed my study based on recommended >> Freesurfer >> parameters a couple of years ago on 3T Siemens >> Trio with 32-channel receiver coil. >> >> A huge thank you for your previous helps, and >> thanks in advance for helping me with this new >> issue. >> >> James >> >> >> _______________________________________________ >> 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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why the size become larger after fdr correction
by wang kangcheng 17 Jul '14

17 Jul '14

Dear experts I use the following command and the Size(mm^2) was28.65. mri_surfcluster --in leg.volume.lh.20/g2v2/sig.mgh --thmin 3.7190 --no-adjust --sign abs --subject fsaverage --hemi lh --annot aparc.a2009s --mask leg.volume.lh.20/mask.mgh --sum leg.volume.lh.20/g2v2/sig.z3.7190.txt # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 4.068 160031 28.65 -7.5 -42.6 9.2 87 G_cingul-Post-ventral However, When I used the FDR correction and found that size become larger (76467.08). mri_surfcluster --in leg.volume.lh.20/g2v2/sig.mgh --fdr 2.3 --no-adjust --sign abs --subject fsaverage --hemi lh --annot aparc.a2009s --mask leg.volume.lh.20/mask.mgh --cwsig 5 --sum fdr.2.3.txt # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 4.068 160031 76467.08 -7.5 -42.6 9.2 149953 G_cingul-Post-ventral Why the size become larger ? Or is there some problem? Thank you

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Polar angle wedge default position
by Jackie Lam 17 Jul '14

17 Jul '14

Thanks Doug. I assume that Freesurfer begins with 0 and proceeds to positive values if one specifies “counterclockwise” in the rtopy.par file, and if one chooses “clockwise” I assume Freesurfer starts with 0 and proceeds to negative values. Is that right? >On 07/16/2014 04:29 PM, Jackie Lam wrote: >> Hello all, >> >> In Freesurfer’s analysis of retinotopy data, what is the phase assigned by freesurfer to the very beginning of the > stimulation paradigm? >> I would assume that it should be 0, but it would be good to verify. > Yes, 0. > Then, how do the phases proceed after the beginning? To negative values or positive values? > positive >> >> In general, which phase values are assigned to a full cycle of the stimulation paradigm (start, 1/4cycle, 1/2 cycle and 3/4 cycle)? > I don't understand what you mean > doug >> >> Thanks >> > _______________________________________________ >> > Freesurfer mailing list >> Freesurfer at nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > > greve at nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > Fax: 617-726-7422

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Can't Remove WM
by Weber, Wade (weberw) 17 Jul '14

17 Jul '14

Hi Surfers, I am running recon-all on some subjects and have run into a strange problem. When we go back to look at the WM voxels for editing, the wm.mgz layer has a light blue tint over the whole layer. When we try to edit the WM voxels, we can add , but we cannot delete any WM voxels. Also, all the WM voxels show up as yellow instead of red as we have set them to show up as red. We tried deleting all the FS files and re-doing the recon-all, but it still shows up like this. This has only happened on 3 or 4 subjects out of about 50. I've attached a picture of our problem Thanks in advance! Wade Weber, MS Clinical Research Manager Division of Bipolar Disorder Research Department of Psychiatry and Behavioral Neuroscience University of Cincinnati

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Freesurfer July 2014