Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Re: [Freesurfer] Recon-all difficulties off-site
by Nitenson, Adam 22 Jul '13

22 Jul '13

> > Hi Doug, > > The command runs a bit further now but then exits with errors. > Unfortunately this time there is no specific stated error. The last few > lines of the log are: > > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Tue Jun 4 13:22:08 EDT 2013 > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC > 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 EDT 2013 > > > > The only other section of the log that seems like it could be related to > an error is: > > Can't locate MNI/Startup.pm in @INC (@INC contains: > /gpfs/runtime/opt/perl/5.16.0/lib > /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /usr/local/lib64/perl5 > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > BEGIN failed--compilation aborted at > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > So, I'm not sure what it's not liking here. > > Thanks again, > Adam > > > On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> That dcmunpack command will put the data into a file called >> unpack3/MPRAGE/002/struct.nii >> It needs to be put into upack3/mri/orig/002.mgz >> doug >> >> >> >> >> On 06/04/2013 11:22 AM, Nitenson, Adam wrote: >> >>> Hi Doug, >>> >>> When I try the command as you suggested: >>> recon-all -all -s unpack3 >>> I get the following error: >>> >>> ERROR: no run data found in /gpfs/data/twhite/anitenso/** >>> FreesurferPractice/unpack3/**mri. Make sure to >>> have a volume called 001.mgz in /gpfs/data/twhite/anitenso/** >>> FreesurferPractice/unpack3/**mri/orig >>> >>> Do you know why I might be lacking that volume? This was not usually an >>> issue after running the two unpacksdcmdir commands (for MPRAGE and bold >>> runs). >>> >>> Thanks, >>> Adam >>> >>> >>> On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> Hi Adam, if the subject folder exists and you pass recon-all a -i >>> flag, >>> then it will exit with error saying that the data exist (otherwise it >>> would overwrite what is there). However, just because the subject >>> folder >>> exists does not mean that there is any data sitting in >>> subject/mri/orig. >>> Then it will tell you that it cannot find any data. >>> >>> Note that when you run recon-all, you need to tell it to do something >>> (eg, add the "-all" flag to do everything) >>> >>> doug >>> >>> >>> On 06/03/2013 03:21 PM, Nitenson, Adam wrote: >>> > Hello users, >>> > >>> > I am trying to get Freesurfer (5.2) working properly off-site and >>> am >>> > encountering errors I did not have while working at the Martinos >>> > center. We use the same Siemens 3T Tim Trio scanner at Brown, so I >>> > would hope the data is similar to work with. >>> > >>> > I have been using dcmunpack since unpacksdcmdir is not >>> identifying the >>> > DICOM files properly. I have successfully unpacked the >>> structural and >>> > bold scans using the command (entered from the raw scan data >>> folder: >>> > >>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 >>> -run 2 >>> > MPRAGE nii struct (I also tried using mgz instead of nii, >>> and also >>> > changed struct to other things as it appears to be a naming >>> argument) >>> > >>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 >>> -fsfast >>> > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii >>> f.nii -run >>> > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 >>> > bold nii f.nii >>> > >>> > (path) just being an abbreviate piece of the relevant pathway >>> > >>> > These generate the MPRAGE and bold folders in the subject folder as >>> > expected. I have difficulties with the next commands >>> (environment has >>> > been set). >>> > >>> > I try: >>> > recon-all -i <path to structural data> -s <subject name> -force >>> > recon-all -i (path)/FreesurferPractice/**unpack/MPRAGE/002 -s >>> unpack3 >>> > (I got an error about using -force so I omitted that from my >>> command) >>> > >>> > and get the following Error >>> > ERROR: You are trying to re-run an existing subject with (possibly) >>> > new input data (-i). If this is truly new input data, you >>> should delete >>> > the subject folder and re-run, or specify a different subject >>> name. >>> > If you are just continuing an analysis of an existing subject, >>> then >>> > omit all -i flags. >>> > >>> > Yet when I omit -i and just use "recon-all -s unpack3", I get >>> "ERROR: >>> > nothing to do" >>> > >>> > I tried a different tactic and used >>> > >>> > "recon-all -s unpack3 -autorecon1" as well as "recon-all >>> > -autorecon-all -s unpack3" >>> > >>> > which both created the various folders (bem, label, mri, surf, etc) >>> > but failed with >>> > "ERROR: no run data found in (path)/FreesurferPractice/** >>> unpack3/mri. >>> > Make sure to have a volume called 001.mgz in >>> > (path)/FreesurferPractice/**unpack3/mri/orig. If you have a >>> second run >>> > of data call it 002.mgz, etc." >>> > >>> > I have tried these commands in both bash and tcsh shells with >>> the same >>> > effect. So the problem, it seems, is that my "mri" file is >>> blank, and >>> > this was not a problem I had running these commands at Martinos. >>> Any >>> > idea what the issue might be? >>> > >>> > Best, >>> > >>> > Adam Nitenson >>> > Neuroscience Graduate Program >>> > Laboratory of Affective Neuroscience >>> > Brown University >>> > >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)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(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >

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beta weights from FS-Fast analysis
by Joseph Dien 17 Jul '13

17 Jul '13

I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta weights. Is there an index somewhere as to which beta weight is which? Or if not, how are they organized? 2) In order to extract the cluster, it looks like I would use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged with the number of the corresponding cluster. I could then use that to generate masks to extract the information I need for each cluster from beta.nii.gz. Is that correct? 3) The final information that I would need is the canonical hrf shape generated by FSFAST for a single event. I guess I could generate that by setting up a dummy analysis run with a single event of the desired duration and then look in the X variable in the resulting X.mat file? Sorry for all the questions! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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Re: [Freesurfer] Working with MEMPRAGE
by Kayle Sawyer 15 Jul '13

15 Jul '13

Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt <whatsdac(a)umich.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.02.1305091043500.13418(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> >>>> Thanks Bruce, >>>> >>>> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >>>> >>>> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >>>> >>>> jon >>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>> >>>>> Hi Jon >>>>> >>>>> yes, the subject and hemi need to be defined (they are required parameters) >>>>> Bruce >>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>> >>>>>> Hi all, >>>>>> combed through the mail archives to figure out how to work with multi echo >>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>> commands is the appropriate >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>>>> jon >>>>>>

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Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer
by Jeff Eriksen 14 Jul '13

14 Jul '13

Doug, Freeview looks like the best way to get what I want. Still trying to figure out how to mark a point in the 3D viewing window, but at least when I mark them in the 2D windows I get all the coordinates I need. Thanks, -Jeff Message: 5 Date: Fri, 04 Jan 2013 13:36:59 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <50E7214B.6010407(a)nmr.mgh.harvard.edu<mailto:50E7214B.6010407@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed tksurfer may be putting all 0s in the RAS field because the head surface does not match the cortical surface (tksurfer is very inflexible in this way). One way around it is to find the vertex number, then find the RAS for that vertex by converting the surface to ascii. freeview might do a better job than tksurfer. doug On 01/03/2013 10:38 PM, Jeff Eriksen wrote: FreeSurfer experts, I am trying to mark points on a surface in tksurfer, then obtain their original voxel coordinates. These are some of the problems I have encountered, and some of the instructions and examples I do not yet understand. -Jeff From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu%3E>> Date: Thursday, January 3, 2013 6:27 PM To: Jeff Eriksen <eriksenj(a)ohsu.edu<mailto:eriksenj@ohsu.edu> <mailto:eriksenj@ohsu.edu><mailto:eriksenj@ohsu.edu%3E>> Subject: Re: [Freesurfer] FW: how to obtain MRI coordinates of scalp surface points marked in tksurfer Can you cc the list so others can answer? Freeview can rotate....

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Discrepancy between surface data of Heschl's gyrus and its image
by Klein, Holger 10 Jul '13

10 Jul '13

Dear Freesurfers, I averaged 42 subjects with make_average_subject focusing on Heschl's Gyrus and finally got the image attached (for both atlases (Desikan = Atlas I, Destrieux = Atlas II). Gray matter surface calculations for Heschl's gyrus showed the following mean values (in mm^2): Atlas I lh = 439 (SD 60), rh = 323 (SD 46) Atlas II lh = 340 (SD 70), rh = 253 (SD 47) Heschl's gyrus depicted in the attached image looks considerably larger for Atlas II, but the surface analysis gives me smaller values for mean surface calculation (Atlas II < Atlas I) How can that be explained? Thanks in advance Holger

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Help with QDEC error
by Manish Dalwani 08 Jul '13

08 Jul '13

Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado

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Is there any way of finding out RESEL number in the GLM output?
by Glen Lee 08 Jul '13

08 Jul '13

Hello Freesurfer users, I'd hope to know the RESEL number in my group GLM analysis data. I can calculate the number of vertices and also see the fwhm.dat in the ouput GLM folder, but I wonder if there is anyway of finding out RESEL size if freesurfer also provides that info like SPM does. -Glen

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mri_glimfit paired analysis
by Gayane Aghakhanyan 08 Jul '13

08 Jul '13

Dear FreeSurfers I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS. Currently running paired analysis as described here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis After mri_glmfit \ --glmdir lh.paired-diff \ --y lh.paired-diff.thickness.sm05.mgh \ --fsgd paired-diff.fsgd \ --C mean.mtx \ --C age.mtx I've got an error "ERROR: you must use '--surface subject hemi' with surface data". Any idea how to fix it? Below is the full output: utente@RM-user:~/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis$ mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx gdfReadHeader: reading paired-diff.fsgd INFO: ignoring tag ,9 INFO: ignoring tag ,9 INFO: ignoring tag ,3 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 57 11.0454 Class Means of each Continuous Variable 1 Main 57.0000 INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis cmdline mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx sysname Linux hostname RM-user machine x86_64 user utente FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paired-diff.fsgd glmdir lh.paired-diff IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.paired-diff Loading y from /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh ERROR: you must use '--surface subject hemi' with surface data Thanks for yuo help Gayane

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Error for mri_glmfit contrast
by Catherine Bois 08 Jul '13

08 Jul '13

Dear Freesurfer experts, I am currently trying to do a cortical thickness group analysis with one factor, three levels . I have run mri_preproc and mri_surf2surf, and am now trying to run mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C contrast1.mtx --surf fsaverage lh --cortex --glmdir lh.group However, I keep getting this error; INFO: gd2mtx_method is doss Saving design matrix to lh.group/Xg.dat Normalized matrix condition is 1 Matrix condition is 7 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149953 voxels in mask Saving mask to lh.group/mask.mgh Reshaping mriglm->mask... search space = 74612.446501 MatrixReadTxT: could not scan value [2][1] The format of both the fsgd file and the contrast file is ASCII text My fsgd file is formatted as follows: GroupDescriptorFile 1 Title Group analysis Class HR Class Con Class ILL Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 HR Input EHRS_XXXX_2 Con Input EHRS_XXXX_2 Con Input EHRS_XXXX_2 ILL and my contrast file is; 1 -1 0 I do not understand why I keep getting this error. When I include the flag -no-contrasts-is-ok, the mri_glmfit does work. There are no commas in either file. This leads me to believe something is wrong with my contrast file? However I am not certain what this could be. Help would be greatly appreciated. Thank you very much, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

Parameterization Optseq
by Laura Dekkers 05 Jul '13

05 Jul '13

Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out? Our task consists of 3 runs of 72 trails each, in which participants are presented with a fixation cross that remains on the screen for a fixed duration of 1 sec, followed by one out of nine different stimuli that remains on the screen for a fixed duration of 4 sec. This gives a scan duration of 360 sec. We would then like to add 25% jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this results in 225 time points. However, Optseq yields an error if ntp is set to 225, ev duration set to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 ERROR: could not enforce tNullMax=6 (ntries=100000) You will need to reduce the number of time points or increase the number of presentations. However, reducing the number of time points makes Optseq to only insert null events of 1.0 or rarely 2.0 sec without much variation. Optimization with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and tnullmax to 6.0 does work. However, this renders Optseq to insert null events of a fixed duration op 1.0 sec, which is not what we want. Could you please advise us in how to set these parameters? Thank you in advance. Best regards, Laura Dekkers -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekkers(a)gmail.com

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Freesurfer June 2013