Freesurfer

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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

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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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processing flow
by Claudia Dacquino 05 Jun '13

05 Jun '13

Hi everyone, I'm sorry, this is a probably very basic question, but I'm a little bit confused about the recon-all correct flowchart. I mean, the first step is recon-all -s <subjid> -all (comprising autorecon1, autorecon2 and autorecon3), correct? After this step if I want to add control points then I have to re-run: recon-all -s <subject> -autorecon2-cp -autorecon3 The same if I want to edit pial surface: recon -all -s <subject> -autorecon2-pial -autorecon3 Or to edit white matter: recon-all -s <subject> -autorecon2-wm -autorecon3. Is that correct? Is there a system to reduce processing time once I've run eh first step (recon-all -s -all)? I mean if I want to add control points, then to edit pial surface and white matter, have I to do the three processes separately, or there is a way to do the three things at once and then running just one autorecon? If that is permissible, which is the correct command line at the end of the porcess? I'm sorry for the confusion. Thanks in advance to everyone. Claudia

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mri_mc vs. recon-all surfaces
by Oscar Esteban 05 Jun '13

05 Jun '13

Dear all, I need to extract three surfaces from MRI data: - GM-WM interface -> thus, lh.white and rh.white would be the answer. - Pial interface -> thus, lh.pial + rh.pial - CSF surface For CSF, as far as I know, the best option would be to generate a binary volume merging the appropriate labels from aseg.mgz. Then use mri_mc to obtain the surface, right? For white and pial I guess the best option would be to use the recon-all outcome, but I have two questions: * Is there any mean to merge both hemispheres? I've tried several methods but I get trouble with the consistency of the cells... the points are aggregated, but no work is done to merge cells and remove points. * What are the differences between the recon-all outcome (lh.pial,rh.pial,lh.white,rh.white) with respect obtaining masks from aseg.mgz and then mri_mc? Thank you so much Best regards, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

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