Freesurfer

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30132 discussions

Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
by Andrew C Yourich 25 Apr '12

25 Apr '12

Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well. Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not. Any other suggestions you all have would be appreciated. Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort(a)nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29 hi, have you fixed your problem? I still don't manage to make it work… thanks Alex ---------- Forwarded message ---------- From: Alexandre Gramfort <gramfort(a)nmr.mgh.harvard.edu> Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>, ayourich(a)uab.edu, Krish Subramaniam <krish(a)nmr.mgh.harvard.edu>, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can > answer. could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise > I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the > surfaces somewhere I can look at them and I'll take a look see the files in : /homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded that's the sample data we use for MNE. the log: $ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds. Alex 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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Fwd: Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 25 Apr '12

25 Apr '12

(sorry, here it is for the list again) ----- Mensagem encaminhada de Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ----- Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface Para: _andreia_(a)sapo.pt Hi Andreia, can you cc the list so others can answer? I just took a look and label_area is so old that is uses ?h.smoothwm without any ability to change it. I think there are probably other tools around that will do it, but someone else will know. If not I'll fix label_area to be less obstinate. cheers Bruce On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: > Hi Bruce, > > Thanks for the help! How do I know from which surface, i.e. pial or > wm is the command label_area getting the value? I compared V1 > surface area given in the BA.stats and the one I get with the > command, and the late is higher (V1 from BA.stats= 2081 and from > label_area = 2592.272). > > Now, imagine the follwing: I have no differences in cortical > thickness (CT) and surface area of this BA but the volume is > different (with p values near 0.04...). Also, other BA shows no > differences in CT neither in volume, but with differences showing up > in the surface area (with lower p value here). Since the values for > volume and surface are computed in different ways, can this account > for these odd results? > > Thanks! > Andreia > > > Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Andreia, >> >> yes, they will always shrink since the label contains every point that >> could possibly be in the BA, no matter how unlikely. I'll try to find time >> to automatically threshold the BAs so that they have the average area of >> the individual examples, but for now V2 is probably around .7 and MT around >> .4 I think. And yes, I would use ?h.sulc as the background gray scale. The >> volume of the BAs would be computed using both surfaces, but the surface >> area can be from either one. I think we use the white by default, but you >> can use label_area to measure on whatever surface you want. >> >> cheers >> Bruce >> >> >> On Mon, 23 Apr 2012, >> _andreia_(a)sapo.pt wrote: >> >>> (forgot to do answer all, here it goes for the list too) >>> >>> >>> Citando _andreia_(a)sapo.pt: >>> >>>> Hi Bruce, >>>> >>>> The ideia is to show one control subject vs. one patient inflated surface >>>> with BA surface (not volume, sorry) to show the difference >>>> (reduced surface >>>> area in one patient). Loading the relevant labels worked (I have the >>>> statistics shown in bar graphs, the images are only for visualizing the >>>> difference between controls and patients). When I threshold the labels in >>>> the subject's inflated surface they shrink a lot, is this supposed to >>>> happen? >>>> >>>> The BA are V1, V2 and MT. What is the thresghold for V2? >>>> >>>> And is it correct to load ?h.sulc in a gray scale to have the usual cortex >>>> representation, or I should do it other way? >>>> >>>> >>>> And getting back to my previous email: >>>> >>>> Another question is, how is the volume of the BA calculated? Is it >>>>>> from the surface-based stream? >>>>>> >>>>>> And, which surface area is the on in the output of the BA stats? Is it >>>>>> the pial or wm? >>>> >>>> Thanks, >>>> Andreia >>>> >>>> >>>> Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> >>>>> Hi Andreia >>>>> >>>>> sorry, I don't understand. What do you mean when you say you want to " >>>>> show the resulting Brodmann area (only 3 BA) volume in the inflated >>>>> surface of my subjects". Do you mean just to show what portion of the >>>>> surface is in each of 3 Brodmann areas? That you would do by loading the >>>>> relevant labels, although you will probably want to threshold them >>>>> differently (e.g. V1 you could threshold at .9 which is 90% and it would >>>>> have about the surface area of an individual, while MT would need to be >>>>> closer to .4 or .5). Or do you actually mean the volume of gray matter >>>>> within each BA? If the latter, it's just 3 numbers/subject, so I would >>>>> think you would want a scatter plot or something, not a map on the >>>>> surface. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm sorry if these questions have already been covered here, but I've >>>>>> looked into the archives and still can't do what I need (and since I'm >>>>>> running out of time for this task I decided to post here): >>>>>> >>>>>> I'm using version 5.0.0. >>>>>> >>>>>> I want to show the resulting Brodmann area (only 3 BA) volume in the >>>>>> inflated surface of my subjects to show the differences between >>>>>> patients and controls (for visualization purpose only). I've managed >>>>>> to overlay the volume in the curvature menu but this is for the entire >>>>>> cortex and I can't show the values bar. How can I show the volume of >>>>>> only 3 BAs and have the scale bar? >>>>>> >>>>>> Another question is, how is the volume of the BA calculated? Is it >>>>>> from the surface-based stream? >>>>>> >>>>>> And, which surface area is the on in the output of the BA stats? Is it >>>>>> the pial or wm? >>>>>> >>>>>> Thanks in advance, >>>>>> Andreia >>>>>> >>>>>> _______________________________________________ >>>>>> 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. >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ----- Fim de mensagem reenviada -----

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labels export
by Gabriel Gonzalez Escamilla 25 Apr '12

25 Apr '12

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Running Tracula -bedpostx and -path
by Richard Binney 24 Apr '12

24 Apr '12

Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather quicker than I expected and I expected it to at least output "all slices processed" and/or something after queing post Is there any reason to be concerned? Furthermore, in running the -path, the terminal window constantly outputting... ERROR: Degenerate spline segment 58 81 24 56 69 24 ...... ERROR: Degenerate spline segment ...... but it seems to continue on without exiting. Is there any reason to be concerned about this? what doe sit mean? Thanks for your help R

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mris_divide_parcellation
by Mario Ortega 24 Apr '12

24 Apr '12

Hi Freesurfer users, Does anyone have a method to divide aseg.mgz volumetric regions along a longitudinal axis? Or a simple split after finding a center of mass of an ROI? I found that mris_divide_parcellation only splits up regions from the surface based segmentation as found in the desikan killiany label file. Thanks, Mario

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Editing Talairach registration with shear
by Benjamin Matthew Deen 24 Apr '12

24 Apr '12

Hi all, I just ran a recon that produced a Talairach registration error. Viewing the registration in tkregister2, it became clear that it was in fact quite off. I tried to fix the registration manually, but there is a substantial and inaccurate shear component, and I can't seem to adjust shear in the tkregister2 controls (assuming I'm not missing something). Is there an easy solution to this issue? thanks, Ben

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How to convert a surface to volume space after using mris_preproc?
by Long 24 Apr '12

24 Apr '12

Hi all, I had a question when convert a surface to volume space. First, I converted a volume nifti data to fsaverage: mris_preproc --target fsaverage --hemi lh --iv data.nii bb_register.dat --out data.lh.mgh Then, I want to convert the data.lh.mgh to volume space, I tried mri_surf2vol, however, it needs register.dat. As I understood, the data.lh.mgh was already registered to fsaverage surface, so how can I get the required register.dat file? Thank you for your attention. Best, Xiangyu

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Re: [Freesurfer] your insight: parameter definition and --tnullmin necessary?
by Betina Ip 24 Apr '12

24 Apr '12

Dear Doug, Thank you for your excellent answers, they are very helpful. Please allow me to summarise and ask for additional clarification: 1) The main problem I'd like to solve is, as you spotted, whether the sequence will have required power to detect and effect (if there is one!). So, please disagree with me if this is incorrect, but one way to evaluate the potential of the sequence in terms of detecting an effect would be to plug the condition files directly into a Fsl FEAT analysis design matrix (FEAT>Stats>Full Model Setup> Efficiency), which would come out with an efficiency/estimability % to detect a statistically significant effect for a given comparison. The lower the effect required, the more efficient the design. 2) The second question is related to spacing of NULL trials. I would like to first run a univariate analysis and then run a multivariate analysis. You mentioned NULL trials would be 'helpful'- could you please clarify whether you mean having ANY null trials or having null trials between EACH trial would be helpful? My current design is allocating as much total null time as for any other condition (as recommended in freesurver list). This means that I do have some NULL trials, and they are randomly inserted in the sequence. However, most trials have no ITI between them. If I did force ITIs between EACH trial I would have to decrease number of trials for each condition type, which could lower the design efficiency. IF the problem of having carry-over effects of closely very spaced trials (i.e. majority of trials with no separation between trials) could be alleviated by rigorous first order counter-balancing within Optseq2 using the --focb option, is it necessary at all to add a null trial between EACH trial into the design? Thanks for your clarification. Best, Betina ________________________________ Hi Betina, see answers below doug On 04/23/2012 12:04 PM, Betina Ip wrote: > Dear Freesurfer list, > > I am using optseq2 for the first time and wanted to check with you whether my protocol makes sense, many thanks in advance for your insight. > > 1) I start by choosing the maximum scan duration equalling ~30 min: You might want to break this up into shorter chunks. It's totally up to you, you just don't need to have everything in a single run. > 2) set the psd window so it can capture the entire waveform of a 4 second event > 3) select equal amounts of trials for each of the 4 event types, I played around with it and 80 trials give me the greatest efficiency (2.72) and variance reduction factor average (54.37). Are these values acceptable? They are the best I could get tweaking the number of trials. You can't tell whether a VRF of 54 is good enough. You are asking a question about the power of your experiment, which optseq can't answer. If you don't have an effect, then no number of trials or efficiency will be good enough. Having said that, I usually shoot for a VRF of between 20 and 40, but that's just a rule of thumb. > > The command is here: > > ./optseq2 --ntp 440 --tr 4 --psdwin 0 20 \ > --ev evt1 4 80 \ > --ev evt2 4 80 \ > --ev evt3 4 80 \ > --ev evt4 4 80 \ > --nkeep 3 \ > --o gfatrial \ > --focb 10 \ > --nsearch 10000 > > A sample trial list is here: > > 0.0000 2 4.000 1.0000 evt2 > 4.0000 4 4.000 1.0000 evt4 > 8.0000 0 4.000 1.0000 NULL > 12.0000 3 4.000 1.0000 evt3 > 16.0000 3 4.000 1.0000 evt3 > 20.0000 2 4.000 1.0000 evt2 > … > > The other question I had concerns the position of null trials. Many trials are not separated by a NULL event, however studies of rapid event-related designs to report a minimum ITI, in this case the minimum seems to be 0? To assess the effect of forcing a minimum ITI on the sequence, I have run the search defining the --tnullmin to 4 sec (equal to 1 TR) however efficiency and VRFAvg drop to .79 and 16.07, obviously due to trade of between ntp and ntrials (ntp=440, ntrials=62). > > Are NULL trials between each event required at all if a standard FIR is used for the analysis? My aim is to first apply a univariate BOLD-analysis and subsequently a multivariate analysis to the dataset. Thanks for clarifying. They are not strictly necessary, however, they may be helpful. If you really don't want them as part of your design (eg, it would interfere with the psychology), then don't use them but make sure to optimize the FOCB more (I usually use 100 regardless). The disadvantage of not having the nulls is that there will probably be some non-linearity in that the second of two closely spaced trials will have a lower amplitude than if it occurred in isolation. This will hurt your power and might cause a false difference between conditions if they are not well counter-balanced. doug > > Betina > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 24 Apr '12

24 Apr '12

Hi again, We are trying to do the same as was done in Trachtenberg et al 2012 (Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT registration in FEAT with BBreg: "For group analysis, functional data were registered, via the high resolution anatomical image, to the Montreal Neurological Institute (MNI) standard brain. Functional data were aligned to the anatomical image initially using FMRIB's Linear Image Registration Tool, (FLIRT) ([Jenkinson and Smith, 2001] <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib27> and [Jenkinson et al., 2002] <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib28>), then optimized using the Boundary-Based Registration (BBR) approach (Greve and Fischl, 2009 <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib21>). Registration from anatomical to standard space was carried out using FMRIB’s Non-Linear Image Registration Tool (FNIRT)." That is, flirt from fmri --> brain, then initializing bbregister fmri --> brain by the previous flirt registration, then flirt and fnirt from brain --> standard space and finally fmri --> standard space and putting all these transformations together. However, our images are orientad as follows from top -> bottom (fmri, orig, 152MNI): http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a As shown in the previous communication, when we directly apply the images to the registration the results are oriented incorrectly, as the input images. Can you recommend a specific solution to overcome the orientation mismatch in these images which is compatible with the registration tasks? Thank you for your patience and help! All best E.H. Hi Erlend, while the images in the tkregister2 pics are oriented correctly the registration is way off. What images are you loading into fslview? You'll need to convert the orig.mgz into nii and load that to check the registration. doug On 04/22/2012 04:16 AM, Erlend Hodneland wrote: > Hi again, > > the registration looks fine in tkregister2, but is apparently wrong in > fslview (and also mricron). See the attached files (as link from > http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing > screenshots of fslview and tkregister2. How can this be explained, and > how can we visualize the correct orientation in fslview? > What does this misalignment influence any further processing with > fnirt and concatenation of the affine transformation fields? > > This is our command we run for bbregister: > > bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat > --init-fsl --t2 --o test.nii.gz > > where vol0001 is the first volume in the fmri sequence and is flipped > to align with LAS (as the highres). > > Thank you for your kind help, > > Erlend Hodneland > > ean that it is in the wrong orientation? It should be in > the same orientation as the anatomical. How does the reg look in > tkregister2? Note that fslview can display volumes in odd orientations > even when the orientation is correct. > doug > > On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > > Hi, > > > > we are trying to register fmri FEAT data (example_func.nii) to the > > anatomical scan (processed in Freesurfer) using bbregister to opt. > > the affine registration before running FNIRT. > > > > However, the orientation of the registered image is flipped around and > > is incorrect after applying bbregister. > > > > We have tried: > > > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat --init-header --bold --o example_func2highres-fs.nii > > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > > register.dat --init-fsl --bold --o example_func2highres-fs.nii > > 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat > > "myfeatdirectory" > > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > > (this one looks correct) > > followed by > > bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat > > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > > > 5) reorienting to match the highres: > > > > fslorient -swaporient example_func > > fslswapdim example_func x -y z example_func_swap (correct > > orientation) > > > > followed by > > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > > register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii > > > > with the output being flipped in wrong orientation for all options. > > > > We would greatly appreciate if you have any suggestions for how to > > overcome this problem! > > > > Cheers/Sincerly/All best > > > > Erlend Hodneland > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Edit Capability of Freeview
by Richard Binney 24 Apr '12

24 Apr '12

So shorlty after I sent that email I figured out how to do a little of what I spoke about... a) White matter (WM.mgz) edits - joining WM fingers in the WM.mgz or filling holes, etc......Should New WM voxels in WM.mgz should be = 255 (brush value)?? b) I can delete skull/dura......should I be replacing values in dura/skull voxels with 1 or 0 or what? Can I do cloning like in TKmedit such that I could replace small bits of skull-stripped cerebellum in the brainmask.mgz by cloning from the T1.mgz? In the voxel edits toolbar, what is the reference option for? I was hoping that it would be for cloning, but apparently not.... R

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