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 tudor3@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 fischl@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 nicks@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" <tudor3@gmail.commailto:tudor3@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 myneeds
here. Having run the first 2 steps (cross and base), I'm a bitunclear
how the output so far has to be manually inspected. It says inthe
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 myPC
(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 tobe
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 anerroneous
averaging between timepoints, you see blurs/ghosts in your base template? Many thanks! Tudor On 9 May 2014 21:33, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: Hi Tudor, the longitudinal pipeline in FS is actually one of the beston
the planet as far as I know :-). If there is anycontradictory
information on the wiki, can you point me to that so I cansee
what causes the misconception. Really: compared toindependent
processing, it significantly increases sensitivity. Also we have designed it to be unbiased with respect to a singletime
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 candefinitely
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 measureacross
groups similar to a cross sectional volume/thicknessanalysis.
You can also use our tools to run a linear mixed effectsmodel
if you want to do that (it is more involved and requiresyou
to use matlab tools). In your case, you probably have 2time
points for all subjects and the time distance is probablythe
same for all subjects, so the 2-stage approach should befine.
2. The image processing is done via the longitudinalpipeline
(three steps: cross, base, long), to prepare the data lookat
the description of the 2-stage model http://freesurfer.net/fswiki/LongitudinalTwoStageModel and also the longitudinal tutorialhttp://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 wasreceived
the first time. Tudor On 6 May 2014 19:55, Tudor Popescu <tudor3@gmail.com <mailto:tudor3@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 ananalysis
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 wikihttp://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
that FS is currently not optimal for longitudinal analyses. I intend my FreeSurfer analysis tosupplement 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 FreeSurferas
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.eduhttps://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: mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edu mailto:reuter@mit.edu Web :http://reuter.mit.edu
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A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
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<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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu