Freesurfer

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30132 discussions

first level glm analysis on surface space
by Subhabrata Chaudhury 05 Jun '13

05 Jun '13

Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take each functional volume corresponding to each TR and move each volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). Then I want to run first level glm on the data like its done for volume data in spm, fsl, afni etc. My question is are there tools in freesurfer to do this on surfaces ? If not, can the mgh file be converted to a gifti file and maybe it can be used to make first level glms in afni, spm or fsl ? I will really appreciate your opinion about this. Thank you very much, Subha

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Processing High Res. Data (0.375mm)
by Daniel LaFreniere 05 Jun '13

05 Jun '13

Dear Freesurfer Experts, I'm currently in the middle of processing high resolution MRI through the standard FS pipeline. I've recently read a very interesting article and wanted to attempt a high resolution protocol for a bit of a side project - we initially obtained an iso resolution of 0.375mm so I might as well try and make use of it and learn something along the way! However, I'm starting to run into issues straight from the get-go during -autorecon1. The flag I use is as follows: recon-all -autorecon1 -mprage -hires -nuiterations 10 -subjid fom04_hires2 Often I use -washu_mprage (dark GM) and -nuiterations closer to 50 since it doesn't seem to hurt anything (the hires protocol takes much longer so I've reduced to 10-20). After -nuiterations finishes running, I suddenly get the following error: Writing to ./tmp.mri_nu_correct.mni.902/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.902/nu20.mnc ./tmp.mri_nu_correct.mni.902/nu20.mnc mul 1.33669825436408977556 mris_calc(5163) malloc: *** mmap(size=864002048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug mris_calc: virtual memory exhausted. Cannot allocate memory Darwin dhcp-10-23-184-237.capitalhealth.ca 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s fom04_hires2 exited with ERRORS at Wed Jun 5 10:42:36 MDT 2013 For reference, I've added the more detailed recon-all log as well. I'm running a Macbook Pro, OS X 10.8 with 8GB of RAM/2.9 GHz with FS version 5.1.0. I've also been keeping my eye on the Activity Monitor and continuously purge inactive memory as freesurfer runs. I've even had the program crash when I'm sitting at 5 GB of unused memory with a VM size readout of about 420 GB. I can't seem to figure out what's happening but have a feeling that I just need a much more powerful computer to process the 0.375mm voxels. Any help, suggestions, or insight would be greatly appreciated. Thank you very much for your time, Dan

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mri_glmfit-sim error
by Glen Lee 05 Jun '13

05 Jun '13

Hello Freesurfer experts-- I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it. Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation). mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right? FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table. Any of your help would be greatly appreciated. -Glen # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot

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The v5.3 release is here
by Nick Schmansky 05 Jun '13

05 Jun '13

Freesurfers, The new version of Freesurfer, v5.3, is available for download! Recall from our prior posting that this is intended to replace v5.2, which had a problem with pial and white surface generation affecting thickness and area measures. Users should not use v5.2 for any surface-based studies. For a list of what v5.3 contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes If you have already run data through v5.2, and do not want to re-run everything again but only what is necessary, then run the following on your subjects using v5.3: recon-all -s <subjid> \ -white \ -smooth2 \ -inflate2 \ -autorecon3 This will create new surfaces and surface data. Note that if you choose to re-run the entire stream (-all), the aseg stats will differ from v5.2, but our tests show this difference to be insignificant. To download v5.3, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Download And remember our home page is here: http://surfer.nmr.mgh.harvard.edu And list info is here: http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thank you to everyone who downloaded and tested the beta release of v5.3. We apologize for the hassle and expense of releasing a problematic v5.2. We have improved our testing in the process. The Freesurfites

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Still confused by group analysis..
by Tudor Popescu 05 Jun '13

05 Jun '13

Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg thickness, accounting for gender, differ between group1 and group2?" and not also "..acounting for gender and age,.."? 2) In QDEC, if I am left with a cluster after setting the FDR rate to 0.1, does that qualify as a "trend towads significance" in the same way as when obtaining a p value <.1 for a behavioural effect? 3) From the group tutorial, I see that mris_preproc has to be called with flag "--cache-in ess.fwhm10thickn.fsaverage". However, after running recon-all (including with the –qcache option) on all my subjects, none of their folders contains a file named ?h.thickness.fwhm10.fsaverage.mgh 4) When comparing two healthy groups, is there anything to gain from using a fsaverage built from the sample (with make_average_subject) as opposed to using the default fsaverage? 5) What is the difference between running make_average_subject and running mris_preproc with --target fsaverage? 6) For my ROI mri_glmfit analysis, I wanted to use the FSGD and contrast files that were automatically created when I did my QDEC whole-brain analysis, since the design will be the same. However, although I identified the FSGD file (qdec.fsgd), I cannot see any plaintext file in the QDEC folder that looks like it contains contrast definitions! Thanks! Tudor

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Re: [Freesurfer] recon-all error
by Bruce Fischl 05 Jun '13

05 Jun '13

Hi Rafa this doesn't look like the whole subject dir, just some files from it (e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our ftp site cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote: > Hi Bruce,Thanks for your reply. I have attached the zipped subject dir (please, note that I had to compress it twice for sending > problems). > Rafa. > > > 2013/6/4 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Rafa > > that sounds like a bug. Can you gzip and upload the whole subject dir? > > cheers > Bruce > On Tue, 4 Jun 2013, Rafa X wrote: > > Dear freesurfer experts, > > I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on > this > subject. Im using FS v5.1 > > > > #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 > /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 > --excl-ctxgmwm > --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv > --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject > qsm1_17_stats2_g > > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 > --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units > MR > --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt > --subject > qsm1_17_stats2_g > sysname Linux > hostname localhost.localdomain > machine x86_64 > user root > atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) > Loading mri/aseg.mgz > Getting Cerebral WM volumes from surface > lh white matter volume 206011 > rh white matter volume 198149 > Getting Cerebral GM and WM volumes from surfaces > lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 > rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 > MRIalloc: could not allocate 540094766 frames > > Computing SupraTentVolCor > Cannot allocate memory > Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 > GNU/Linux > > recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013 > > For more details, see the log file > /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > Any help will be appreaciated, > > Many thanks in advance > Rafa > > > > > 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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R: Re: Monte Carlo simulation
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

I'd like to know the effective p correlated with colour bar in a significant cluster. Thank you very much, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 5-giu-2013 16.31 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Monte Carlo simulation what do you mean by the real value of p? On 6/5/13 10:17 AM, stdp82(a)virgilio.it wrote: Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p<0.05. Is possible to obstain form each significant cluster the real value of p? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Monte Carlo simulation
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p<0.05. Is possible to obstain form each significant cluster the real value of p? Thanks, Stefano

3 2

hippocampal subfield segmentation
by Claudia Dacquino 05 Jun '13

05 Jun '13

Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio

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Tracula
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem "set: Variable name must begin with a letter.ERROR: must specify as many DWI dicoms as subjects". I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis. I have attached the configuration file. Note that I'm using nii.gz. Thanks and best regards. Stefano

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