Freesurfer June 2013

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by A a 16 Jun '13

16 Jun '13

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Optseq optimizing event design
by fMRI 16 Jun '13

16 Jun '13

Dear Prof Douglas, I asked this before but I would like to understand what I am doing and also need your recommendation. I have three conditions : squeezes at three different levels. My aim is that I want to use spm to enter them as a one condition and then enter the parametric response as a covariate regressor. This will allow me to check the effect of using high low and mid forces using for example the first order effects. I am trying to find the best event design using optseq. I do not mind to make the stimuli close or far away from each other. What I have is tr 2.5 and ntp 174 so the length of the scanner is 435s. I tried different input: Optseq --ntp 174 --tr 2.5 --psdwin 0 20 2.5 --ev 1 3 20 --evc 2 3 20 --evc 3 3 20 --nkeep 1 --tnullmin 2 --nullmax6 The question that I have what are the inputs that I should change in order to get the best design that answer my question? I mean I thought that I should focus in tge nullmin and max. So in this. Case does increasing the null max make the design better. Also in term of the contrast should I look for it as a general term without including any contrast since I will enter them as one condition or should I see the effects of rest [1 1 1] Any tip or advice that I should look at and change? Lastly, if I would like to compare different designs, should I compare just the eff result ? Thanks AS

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Re: [Freesurfer] Fwd: Out of memory problem during selxavg3-sess
by Marcel Falkiewicz 16 Jun '13

16 Jun '13

Thanks Jacek for the advice, I'll try to upgrade to newer MATLAB version, maybe it will manage the memory better. I've got 64 bit versions of everything, so this doesn't really help. I've never considered a 800 timepoint timeseries as a large dataset, other software packages do not seem to be bothered by this, even SPM which is Matlab-based. Doug, I will try to split the dataset as you advised, it will help for sure, but given the fact that this problem occurs often, maybe dataset splitting should be automated in fsfast in order to avoid such problems in the future. Thanks again for your help guys. 2013/6/13 Jonca, Jacek <jacek.jonca(a)ttu.edu> > In the past (for other people) selxavg3 failed with as much as 16GBs > although as always much depends on your dataset. Most likely the problem is > not with the fact that you don't have enough memory but rather that not > enough memory is being allocated to Matlab. Are you running it on a 64-bit > machine with 64-bit version of Ubuntu installed and 64-bit version of > Matlab? If not this may be your best bet right now. In addition, as always > having most up-to-date version of both Ubuntu and Matlab may be helpful as > well. I noticed that you are running R2011a, that is a tad bit old. I think > that R2013a has been out for some time.**** > > ** ** > > Do you have access to a cluster where you can deploy freesurfer, Sunsite? > In my experience those tended to work better for running computationally > demanding analyses. I simply rsynced my remote directory with my laptop to > examine results from the laptop but run the actual anayses on the mainframe. > **** > > ** ** > > Cheers, > > Jacek**** > > **** > > [image: cid:image003.png@01CC924F.6F547760]**** > > ** ** > > Jacek Jońca-Jasiński, Ph.D. | The Graduate School | Texas > Tech University**** > > Administration Bldg 327 / 40D | 2625 Memorial Circle | Box 1030 > | Lubbock, TX 79409-1030**** > > ph.: 806.834.3348 | fax: 806.742.4038 | > http://www.gradschool.ttu.edu**** > > [image: Capture]**** > > ** ** > > ** ** > > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] *On Behalf Of *Marcel Falkiewicz > *Sent:* Thursday, June 13, 2013 1:19 PM > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Fwd: Out of memory problem during selxavg3-sess*** > * > > ** ** > > ** ** > > Hello,**** > > I know this problem has been discussed earlier, but I think in my case > the source of the problem might be quite different. I'm running FS 5.3.0 > and MATLAB R2011a on Ubuntu machine with 12 GB RAM. selxavg3-sess runs > perfectly for both hemis, but I get the following error when trying to run > it on subcortical volume: > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > /home/marcel/freesurfer/fsfast/toolbox/fast_selxavg3.m > /home/marcel/freesurfer/fsfast/toolbox/fast_ldanaflac.m > /home/marcel/freesurfer/matlab/MRIread.m > ------------------------- > outtop = /media/2TB/SDT_MRI/FS > Extension format = nii.gz > 1 DC_vs_HC.mat > 2 HI_vs_DC.mat > 3 HI_vs_HC.mat > 4 NAT_vs_PAL.mat > 5 NAT_vs_PAT.mat > 6 PAL_vs_NAT.mat > 7 PAL_vs_PAT.mat > nruns = 1 > autostimdur = > > > outanadir = /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni > Found 52644/537168 ( 9.8) voxels in mask > Creating Design Matrix > ... creation time = 0.007 sec > DoMCFit = 1 > ntptot = 851, nX = 19, DOF = 832 > Saving X matrix to /media/2TB/SDT_MRI/FS/AC1004/bold/sdt.sm8.mni/Xtmp.mat > XCond = 31.0456 (normalized) > Computing compensation for resdual AR1 bias > 1 -0.5 -0.500489 (t=0.097569) > 2 -0.25 -0.255326 (t=0.427178) > 3 0 -0.011955 (t=0.516085) > 4 0.25 0.229273 (t=0.839369) > 5 0.5 0.466983 (t=0.928175) > AR1 Correction M: 0.0147777 1.03322 > Computing contrast matrices > OLS Beta Pass > run 1 t= 0.0 > Global Mean 1120.98 > Global In-Mask Mean = 1120.98 (983.432) > Rescale Target = 100 > RescaleFactor = 0.0892077 > OLS Residual Pass > run 1 t= 0.0 > ??? Out of memory. Type HELP MEMORY for your options. > > Error in ==> fast_selxavg3 at 489 > rsserun = sum(rrun.^2); > > >> ------------------------------------------ > > **** > > I observed memory consuption with top(8) and noticed that around 11 GBs > are eaten after about 30 second of running OLS residual pass. Do you think > adding more memory to the PC would solve the problem, or is it some > MATLAB/FS-related bug?**** > > Best regards, > Marcel**** > > ** ** >

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Optseq - optimal parameters
by Ella Hinton 16 Jun '13

16 Jun '13

Hi all, I have been advised to use optseq to aid my event related fMRI design, specifically to help calculate stimulus order and timing. I've read the help in some detail but am still a little unclear on some of the appropriate values to input and indeed what values I am aiming for in the output. It'd be great if anyone can help out... Briefly, my study is a simple food cue reactivity study in which three different types of pictures (50 each) are presented for 3s each, in pseudo-random sequence. I now intend to include null events to optimise the spacing of the events to detect a difference between conditions, but also to provide a baseline for a 'sanity check' just in case. I am uncertain as to the value of psdwin and associated variables (PSD, min, max dPSD) - should I include a post-stimulus delay or should that be set to 0 as in most examples? Also what is the recommended psdwinMAX value for events of 3s? 12 or as much as 18 seconds to capture the whole haemodynamic response? Also I am not certain how to judge the resulting output. I understand I should maximise 'efficiency' but I can't find any advice as to what is a 'good' value of efficiency to aim for. Any advice here? Also should I be judging the sequence on any other values? So I have inputted the following and got a value of 2.586 for efficiency for the best sequence. Is this reasonable/sufficient? optseq2 --ntp 200 --tr 3 ---psdwin 0 12 3 --ev ev1 3 50 --ev ev2 3 50 --ev ev3 3 50 --nkeep 3 --o test6 --nsearch 10000 Many thanks in advance, Ella

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SPM ROI to Cortical Thickness
by xiangbo_2010 15 Jun '13

15 Jun '13

Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help!

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Conversion
by Anna Josefson 15 Jun '13

15 Jun '13

Dear FreeSurfer users! I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject. Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses. Then I would have to convert from freesurfer space to SPM space via the coordinates. And - I would also have to convert from .mgz to .nii data format. Does any have any tips on how to do this? Or a script? Kind Regards, Anna B. Josefson

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Group Analysis Error
by Nooshin Zadeh 15 Jun '13

15 Jun '13

Dear FreeSurfer Group I wanted to Group Analysis with qdec. I have MRIs of one patient in two different dates and I wanted to do group analysis on them to see the changes. I have "gender", "age", and "diagnosis". In qdec deme, when I make the analysis based on "thickness", I receive the attached error. I do not know what is the reason. Any help and advice would be appreciated. Thanks, Nooshin

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2013年6月15日 20:37:34 自动保存草稿
by xiangbo_2010 15 Jun '13

15 Jun '13

1 0

Installation Conflict
by Mark Plantz 14 Jun '13

14 Jun '13

Hello, I recently installed FreeSurfer on an OS x machine. After finishing the process, I received the following output: *Setting up environment for FreeSurfer/FS-FAST (and FSL)* *FREESURFER_HOME /Applications/freesurfer* *FSFAST_HOME /Applications/freesurfer/fsfast* *FSF_OUTPUT_FORMAT nii.gz* *SUBJECTS_DIR /Applications/freesurfer/subjects* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *grep: Command not found.* *wc: Command not found.* *MNI_DIR /Applications/freesurfer/mni* */usr/local/fsl/etc/fslconf/fslmachtype.sh: line 14: uname: command not found* *FSL_DIR /usr/local/fsl* */usr/local/Applications/freesurfer: No such file or directory.* Why can the grep, wc, of MNI commands not be found? Also, when I type the command: *$FREESURFER_HOME/subjects* I receive the following error: /Applications/freesurfer/subjects: Permission denied. Any ideas on how to solve this problem? Is it a licensing issue? I have already created the .license file. Best, Mark Plantz

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methods Q
by Joshua Lee 14 Jun '13

14 Jun '13

Hi Experts, I just wanted confirm my understanding that Freesurfer does not employ multi-atlas label fusion methods. Is this correct? Thanks, Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

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Freesurfer June 2013