Hi Martin, I reran everything from scratch and this time the recons ended without error. Few more questions:
1) Is the brainmask.mgz vs wm.mgz problem that I described in my previous email (surfaces only starting to show rather late at the posterior end of some subjects) something that I need to correct (e.g., by editing wm.mgz), or is it fine as it is? 2) Given that I visually inspected all bases, Is it necessary to inspect *all *slices for the longitudinal overlaps (vols+surfs) of all subjects, or is it enough to just check the central coronal slice for each subject? I ask because it's not just *opening *freeview with all those layers that is very slow, but also navigating between slices 3) The tutorial <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial>covers the creation of long.qdec.table.dat for a single-group scenario; I have 3 groups, with scans on the first and final (fifth) day of training, and was wondering whether the following table looks correct *fsid* *fsid-base* *group* *day* *ageDemeaned * *gender* *score* subj1_day1 subj1 treatmentA 1 1.34 f 109 subj1_day5 subj1 treatmentA 5 1.34 f 109 subj2_day1 subj2 treatmentB 1 -5.85 m 102 subj2_day5 subj2 treatmentB 5 -5.85 m 102 subj3_day1 subj2 control 1 3.06 f 98 subj3_day5 subj2 control 5 3.06 f 98 4) Is this mixed design (3 groups and 2 time points, with both effect of group and of time being relevant) suitably analysed with only a simple 2 stage model, or is a linear mixed effects model necessary? Also, how are the stats different given there are 3 groups and not the usual 2 than most FS tutorials are based on? 5) Is the default long_mris_slopes command (which I understand does preliminary analyses, before going to QDEC) mentioned in the tutorial, i.e. long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR suitable for my particular case? I will also look at surface area and lGI, so I suspect it's at least "--meas area" and "--meas lGI" that I need to add to the above command? Thanks so much! Tudor On 3 June 2014 02:02, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > HI Tudor, > > you can run the -long processes in parallel. Something else is wrong. > Check if you have enough disk space. Re-run the long from scratch (to make > sure everything is generated new). > > Best, Martin > > On Jun 2, 2014, at 5:34 PM, Tudor Popescu <tud...@gmail.com> wrote: > > Hi Bruce > > I suspected this might be the case, since assessing 3D surfaces from a > succession of 2D slices can be tricky, which is why I was wondering whether > there's a better way to do these visual inspections. I checked those > apparent artefacts in the other 2 planes (axial, saggital), but did not > find it helpful in deciding whether the surfs was as they should or not. > > Something that I think is more likely to be a real problem (i.e., more > than just a viewing plane disorientation), is that for many subjects, > posterior slices only start to be followed by the surfaces quite late, e.g. > from coronal slice 80 onward. This seems to be because those slices only > appear in the brainmask.mgz, but not also in the wm.mgz (see screenshots > attached). > > Also, after having run the cross and base steps, and ended up with folders > of the type subj1_scanA, subj1_scanB etc, for the "long" step I launched > simultaneously (for all subjects&scans) commands of the type > recon-all -long subj1_scanA subj1 -all > recon-all -long subj1_scanB subj1 -all > however these resulted in two types of error messages: > * > mghRead(/vols/Scratch/tpopescu/learning/FS/subj1_scanA.long.subj1/mri/aseg.mgz, > -1): read error* > (those particular aseg.mgz files had size 0kB), and > * (standard_in) 2: Error: comparison in expression* > I initially had disk space issues, but after making space I relaunched the > same commands with the -no-isrunning flag, but with the same results. Is > it the case that the long commands for the different scans of a subject > have to be launched sequentially rather than in parallel, i.e. the command > for scanB should be run after the command for scanA has finished? > Otherwise, what could the problem be? > > Thanks again for your help. > > Tudor > > > > On 1 June 2014 15:17, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Tudor >> >> are you assessing the thickness visually? If so, you are probably being >> misled by the orientation of the surface w.r.t. the viewing plane. Same fo >> the apparent bubbles. You need to look in a different orientation >> >> cheers >> Bruce >> >> >> On Sun, 1 Jun 2014, Tudor Popescu wrote: >> >> Many thanks Martin and Nick! The rendering option was already checked, >>> but >>> the freeview inspection commands were still very very slow, so I used >>> commands of the following form, which as far as I understand should be >>> equivalent: >>> tkmedit subjID norm.mgz -surfs >>> For several subjects (maybe 20 out of the total of 72), I noticed that >>> the >>> surfaces don\t seem to quite follow the GM/WM demarcation line as >>> expected - >>> for instance, by having portions of white surface (yellow line, see >>> attached >>> screenshots) surrounded by pial surface (red line), or by having very >>> large >>> cortical thickness in some parts of the brain. Is it possible that these >>> apparent artefacts make sense "in context" (by looking at the adjacent >>> slides), or is it the case that I need to go back and do white surface >>> correction, and then redo all 3 steps of the longitudinal process? >>> >>> Thanks again for your help! >>> Tudor >>> >>> >>> On 29 May 2014 17:39, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: >>> Tudor, >>> >>> in your virtual machine, make sure the 3D rendering option, or >>> 'use >>> hardware rendering' (or something like that) is enabled. this >>> would be on >>> the Windows VM config side of things. otherwise it will do >>> software >>> rendering which is painfully slow. >>> >>> Nick >>> >>> >>> > Hi Tudor, >>> > >>> > I don't think there is a way to speed things up. >>> > Let me know if you find a case where the template is blurry or >>> has >>> > ghosts. It should not happen, but if it does it indicates a >>> bad >>> > registratration, you'd have to run the mri_robust_template >>> command with >>> > different parameters manually then. >>> > >>> > Best, Martin >>> > >>> > On 05/27/2014 06:13 PM, Tudor Popescu wrote: >>> >> >>> >> Hi Martin, >>> >> Wasn't sure whether you'd seen my reply below, look forward >>> to hear >>> >> back your thoughts, thanks! >>> >> Tudor >>> >> >>> >> On 25 May 2014 21:40, "Tudor Popescu" <tud...@gmail.com >>> >> <mailto:tud...@gmail.com>> wrote: >>> >> >>> >> Thanks very much Martin and Bruce. I guess I'd misread the Wiki >>> >> (my own fault, not the text's), and am glad to hear that the >>> >> longitudinal pipeline is in fact perfectly suitable for my >>> needs >>> >> here. >>> >> >>> >> Having run the first 2 steps (cross and base), I'm a bit >>> unclear >>> >> how the output so far has to be manually inspected. It says in >>> the >>> >> tutorial >>> >> <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial> >>> >> that you should load each subject's base volume + surfs in >>> >> freeview and then "move back and forth a few slices". However, >>> >> even just loading each base in this manner takes ~1 min on my >>> PC >>> >> (CoreDuo, 4GB, Ubuntu Virtualbox in Windows 7), and then moving >>> >> with PgUp/PgDn between all coronal slices (starting from the >>> >> default slice=128, going all the way posterior and then all the >>> >> way anterior) is excruciatingly slow. All of this would have to >>> be >>> >> repeated for all my 72 subjects - is there any way to optimise >>> >> this manual inspection? >>> >> >>> >> Also, if the surfs turn out to not follow the volume correctly, >>> >> presumably the thing to do is white surface correction + >>> >> re-running recon. But what should one do if, due to an >>> erroneous >>> >> averaging between timepoints, you see blurs/ghosts in your base >>> >> template? >>> >> >>> >> Many thanks! >>> >> Tudor >>> >> >>> >> >>> >> On 9 May 2014 21:33, Martin Reuter <mreu...@nmr.mgh.harvard.edu >>> >> <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: >>> >> >>> >> Hi Tudor, >>> >> >>> >> the longitudinal pipeline in FS is actually one of the best >>> on >>> >> the planet as far as I know :-). If there is any >>> contradictory >>> >> information on the wiki, can you point me to that so I can >>> see >>> >> what causes the misconception. Really: compared to >>> independent >>> >> processing, it significantly increases sensitivity. Also we >>> >> have designed it to be unbiased with respect to a single >>> time >>> >> point or directionality. It is quite mature by now. >>> >> >>> >> You should definitely use the longitudinal pipeline for the >>> >> analysis of your data. Now to your questions >>> >> >>> >> 1. QDEC: I am not too familiar with qdec. You can >>> definitely >>> >> try the 2-stage approach described on the wiki. There you >>> >> first compute a measure of change (e.g. hippocampal volume >>> >> change during your week) and then compare that measure >>> across >>> >> groups similar to a cross sectional volume/thickness >>> analysis. >>> >> You can also use our tools to run a linear mixed effects >>> model >>> >> if you want to do that (it is more involved and requires >>> you >>> >> to use matlab tools). In your case, you probably have 2 >>> time >>> >> points for all subjects and the time distance is probably >>> the >>> >> same for all subjects, so the 2-stage approach should be >>> fine. >>> >> >>> >> 2. The image processing is done via the longitudinal >>> pipeline >>> >> (three steps: cross, base, long), to prepare the data look >>> at >>> >> the description of the 2-stage model >>> >> http://freesurfer.net/fswiki/LongitudinalTwoStageModel >>> >> and also the longitudinal tutorial >>> >> >>> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial >>> >> >>> >> 3. At the recon all level in FS you get (after the 3 steps) >>> >> measurement for all time points. So you would compare those >>> >> results across time in the stats. >>> >> >>> >> Hope that helps, Martin >>> >> >>> >> >>> >> On 05/08/2014 08:14 AM, Tudor Popescu wrote: >>> >>> Sorry for the repeat, wasn't sure whether this was >>> received >>> >>> the first time. >>> >>> Tudor >>> >>> >>> >>> >>> >>> On 6 May 2014 19:55, Tudor Popescu <tud...@gmail.com >>> >>> <mailto:tud...@gmail.com>> wrote: >>> >>> >>> >>> Dear FS list, >>> >>> >>> >>> I have structural data from a learning study >>> >>> (pre&post-training scans, with 3 groups). Although the >>> >>> training was only one week, I'm guessing from an >>> analysis >>> >>> point of view, this still qualifies as longitudinal. I >>> >>> want to check for >>> >>> >>> >>> * the main within-subjects effect of time point >>> >>> (pre&post) >>> >>> * the main between-subjects effect of group >>> (treatment >>> >>> A, treatment B, control), >>> >>> * the time x group interaction >>> >>> >>> >>> I intend to look at thickness, surface area, volume, >>> and >>> >>> lGI. >>> >>> >>> >>> I read on the wiki >>> >>> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing> >>> >>> that FS is currently not optimal for longitudinal >>> >>> analyses. I intend my FreeSurfer analysis to >>> supplement a >>> >>> VBM analysis done in FSL. In case it is in fact a good >>> >>> idea to do this, my questions (not covered in the >>> >>> 'longitudinal' wiki page) are: >>> >>> >>> >>> 1) Can QDEC be used for such an analysis, and if so, >>> what >>> >>> would be different as compared to a cross-sectional >>> (no >>> >>> temporal/within factor) study? >>> >>> >>> >>> 2) Also, is the pre-processing stage any different? >>> >>> >>> >>> 3) In FSL, for longitudinal designs you do stats on >>> >>> images obtained as the difference between consecutive >>> >>> time points. Does this have to be done in FreeSurfer >>> as >>> >>> well, and if so, is it done at the recon-all level or >>> >>> only at the stats (QDEC) level? >>> >>> >>> >>> Thanks! >>> >>> >>> >>> Tudor >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Freesurfer mailing list >>> >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> -- >>> >> Martin Reuter, Ph.D. >>> >> >>> >> Instructor in Neurology >>> >> Harvard Medical School >>> >> Assistant in Neuroscience >>> >> Dept. of Radiology, Massachusetts General Hospital >>> >> Dept. of Neurology, Massachusetts General Hospital >>> >> Research Affiliate >>> >> Computer Science and Artificial Intelligence Lab, >>> >> Dept. of Electrical Engineering and Computer Science, >>> >> Massachusetts Institute of Technology >>> >> >>> >> A.A.Martinos Center for Biomedical Imaging >>> >> 149 Thirteenth Street, Suite 2301 >>> >> Charlestown, MA 02129 >>> >> >>> >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >>> >> Email: >>> >> mreu...@nmr.mgh.harvard.edu >>> >> <mailto:mreu...@nmr.mgh.harvard.edu> >>> >> reu...@mit.edu <mailto:reu...@mit.edu> >>> >> Web :http://reuter.mit.edu >>> >> >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> >> <mailto:Freesurfer@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. >>> >> >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > -- >>> > Martin Reuter, Ph.D. >>> > >>> > Instructor in Neurology >>> > Harvard Medical School >>> > Assistant in Neuroscience >>> > Dept. of Radiology, Massachusetts General Hospital >>> > Dept. of Neurology, Massachusetts General Hospital >>> > Research Affiliate >>> > Computer Science and Artificial Intelligence Lab, >>> > Dept. of Electrical Engineering and Computer Science, >>> > Massachusetts Institute of Technology >>> > >>> > A.A.Martinos Center for Biomedical Imaging >>> > 149 Thirteenth Street, Suite 2301 >>> > Charlestown, MA 02129 >>> > >>> > Phone: +1-617-724-5652 >>> > Email: >>> > mreu...@nmr.mgh.harvard.edu >>> > reu...@mit.edu >>> > Web : http://reuter.mit.edu >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@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. >> >> > <02-06-2014, 22.17.45.png><02-06-2014, 22.17.55.png><only LH > posterior.png><norm.png>_______________________________________________ > > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > --------------------------------- > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@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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