Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

References/materials for interaction analysis in freesurfer
by Bhavani Shankara Bagepally 12 Dec '11

12 Dec '11

Dear Sir/Freesurfer experts, We are working of genes and gene- gene interaction on cortical thickness using freesurfer. Please let me know if there any material/publications for validation of free surfer based analysis mainly on gene-gene interaction or any of the Interaction statistics using freesurfer. Many thanks in advance -- Dr. BHAVANI SHANKARA BAGEPALLY MBBS, (PhD in Clinical Neuroscience) NIMHANS, Bangalore, INDIA-560029 email: bshankara(a)gmail.com

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preprocessing error
by Maryam Vaziri Pashkam 11 Dec '11

11 Dec '11

Hi, I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I am receiving an error. I connect to the cluster using terminal and SSH connection in mac. the preprocessing is stalled in the middle with this error: ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 Can't connect? tcp_connect[connect]: Connection timed out ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out Can't connect? tcp_connect[connect]: Connection timed out It does not stop running and output an error. But rather keeps printing the last line and does not move forward. Any idea where the problem might be? Thanks, Maryam

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problem with visualizing hippo-subfields
by Tetiana Dadakova 10 Dec '11

10 Dec '11

Dear FreeSurfer list, I ran recon-all -bert -hippo-subfields, which finished without error. Now I try to open it with freeview using: cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt But get the following error: "Failed to load posterior_left_CA1.mgz". (posterior_left_CA1.mgz exists in bert/mri) Do you have an idea why it goes wrong? Thank you, Tanja.

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extracting time courses from fMRI
by Hellyer, Peter 09 Dec '11

09 Dec '11

Hi All, I'm trying to extract time courses from functional data I started by registering my motion corrected functional data to my segmentation using bbregister, then I used: mri_vol2surf --src Motioncorrectedfunctional.nii.gz --srcreg register.dat --out suface.mgz —hemi rh & mri_segstats --in surface.mgz --annot subject rh aparc --sum sum_output --avgwf Timecourse_output Is this a sensible thing to do? I'm not particually sure about the mri_vol2surf step.. Thanks in advance. Pete

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Re: [Freesurfer] tcl script question: labl_set_color
by Justin Baker 09 Dec '11

09 Dec '11

OK, right-clicking on the surface did in fact de-select the label (turning it all to a uniform color). Way to script a right-click? (I see left click...) Now that this is more or less working, I am looking to do something slightly different: i.e., combine the boundaries of one set of regions, one highlighed region, and an activation map. Is there a way to fill just one label and leave outlines for a different set of labels in the same image? Or alternatively set a different outline color for one label? As in my previous post, I am looking to do this via tcl script if possible. Thanks. On Mon, Dec 5, 2011 at 3:07 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > yes, just use the -tcl <script name> option, but don't but an "exit" > command at the end of the tcl script > > cheers > Bruce > > On Mon, 5 Dec 2011, Justin Baker wrote: > > Ah - in that case I have a total newbie question, since I primarily use >> tksurfer via command line: >> >> Is there a way to load up a case using the tcl script, but then leave it >> open rather than quit? >> This way I could try de-selecting with right-click. >> >> Thanks. >> >> On Mon, Dec 5, 2011 at 9:05 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> I think so, but I want to see if it fixes your problem before I go >> digging through the >> tcl code to see what it is >> On Mon, 5 Dec 2011, Justin Baker wrote: >> >> Is there a command to do this via tcl script? >> >> Justin >> >> On Sun, Dec 4, 2011 at 8:49 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> wrote: >> What happens if you right click on the surface then? >> >> >> >> On Dec 4, 2011, at 8:17 PM, Justin Baker < >> justintbaker(a)gmail.com> >> wrote: >> >> Hi Bruce, >> >> Thanks. Some progress! That resulted in the label border >> turning red, but the fill is still white. Any other >> thoughts? >> >> Cheers, >> Justin >> >> On Wed, Nov 30, 2011 at 2:54 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Justin >> >> try unselecting the label with: >> >> labl_select -1 >> >> cheers >> Bruce >> On Wed, 30 Nov 2011, Justin Baker wrote: >> >> >> I am trying to use tksurfer to >> script overlay of a label + >> functional map >> onto an fsaverage5 surface. >> >> In particular, I want to set the >> label to "fill" and color it red. >> >> I have: >> >> set labelstyle 0 >> labl_set_color 0 255 0 0 >> >> As you can see below, the output >> of label_print_list shows that the >> color of >> the label should be "255 0 0 " but >> it looks white in the output >> image. >> >> Am I missing something? Thanks >> >> ------------ >> subject is fsaverage5 >> hemi is lh >> surface is inflated >> >> Label 0 >> Name: >> lh.17Networks_LH_ContB_PFClv.**label, >> 109 vertices >> Structure: -1 Color: 255 0 >> 0 Visible: 1 >> Bounds: x -20.879234 >> 12.792567 y -4.000000 109.853737 z >> -4.033233 >> 4.040778 >> >> >> >> >> >> >> >> 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. >> >> >> >> >> >> >>

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[FreeSurfer]: mkanalysis-sess
by tapsya＠nmr.mgh.harvard.edu 09 Dec '11

09 Dec '11

Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info file (attached) where the parameters mcstem and nuisreg still point to -per-run (mcstem fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis fails. I have attached the analysis.info file in the email Thank you for your help again! -Tapsya Details: Machine: adapt nmr-dev-env (vs 5.1) preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so siemens -fsd bold -fwhm 5 set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt -stc siemens -force -fsd bold -tpef tpef.txt --------------------------------------------------------------------------- > >> I just ran this co > mmand and it completed successfully >> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm > 5 >> Is this what you ran? I'm also running it to generate the surfaces now, > but it does not seem to be complaining. >> doug >> >> Douglas N Greve wrote: >>> I'm currently running >>> preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm >>> 5 >>> and it seems to be going ok, I won't know until tomorrow whether this > is really working or not >>> doug >>> raij(a)nmr.mgh.harvard.edu wrote: >>>> Still no luck. mc-sess is stubbornly using -per-run despite that the > preproc-sess requests per-sess. This may be where things get on the > wrong >>>> track. -Tommi >>>>> Sorry, what I meant was for you to change the name and then run the > stream as usual. >>>>> doug >>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>> Done. I also made a backup of the registration. The entire >>>>>> directory at >>>>>> /space/adapt/1/users/raij/AVISI_FSFAST5.1/ >>>>>> is a copy of the actual data residing elsewhere (apart from the > Freesurfer >>>>>> recons) so feel free to change anything you need. -Tommi >>>>>>> I think I've found the problem, but it's going to be a bit >>>>>>> difficult to >>>>>>> fix. Can you change the name of your registration file to >>>>>>> register.dof6.dat and remove write permissions so that it does not >>>>>>> get >>>>>>> overwritten? >>>>>>> doug >>>>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>>>> Yes we have. It exits with the same error as below. -Tommi >>>>>>>>> Have you tried specifying your regfile with -regfile? >>>>>>>>> doug >>>>>>>>> raij(a)nmr.mgh.harvard.edu wrote: >>>>>>>>>> Hi Doug, >>>>>>>>>> Thank you for your help today! I tried running preproc-sess > again >>>>>>>>>> but >>>>>>>>>> it >>>>>>>>>> again exits with per-session related errors. However, the errors > are >>>>>>>>>> different than before so I think the changes you made were a > step to >>>>>>>>>> the >>>>>>>>>> right direction. This time >>>>>>>>>> preproc-sess \ >>>>>>>>>> -sf subjectname \ >>>>>>>>>> -df sessdir \ >>>>>>>>>> -mni305 \ >>>>>>>>>> -per-session \ >>>>>>>>>> -sliceorder siemens \ >>>>>>>>>> -fsd bold \ >>>>>>>>>> -fwhm 5 \ >>>>>>>>>> -surface $SUBJECT lhrh \ >>>>>>>>>> -noreg \ # I want to use my manually adjusted >>>>>>>>>> bold/register.dof6.dat >>>>>>>>>> file >>>>>>>>>> (1) mc-sess output is still saved with the per-run stem (pr) > despite >>>>>>>>>> that >>>>>>>>>> we defined -per-session. >>>>>>>>>> (2) stc-sess output is still saved with the per-run stem (pr) > despite >>>>>>>>>> that >>>>>>>>>> we defined -per-session. >>>>>>>>>> (3) rawfunc2surf-sess defaults to -per-run and then expects to >>>>>>>>>> find >>>>>>>>>> instem >>>>>>>>>> fmcpr.siemens >>>>>>>>>> (4) ERROR: cannot find >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. > Apparently the script looks for the registration file inside the > run >>>>>>>>>> directory (as it should for per-run analysis) instead of the fsd > <bold> >>>>>>>>>> where it should reside for a -per-session analysis. This forces >>>>>>>>>> the >>>>>>>>>> script >>>>>>>>>> to exit. >>>>>>>>>> I changed permissions so that you can write in the study >>>>>>>>>> directory. >>>>>>>>>> For details please see below. >>>>>>>>>> Thanks! >>>>>>>>>> -Tommi & Tapsya >>>>>>>>>> on machine avml >>>>>>>>>> nmr-dev-env (vs 5.1) >>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > setenv SUBJECT avml07 >>>>>>>>>> logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log > preproc-sess log file >>>>>>>>>> $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij >>>>>>>>>> setenv FREESURFER_HOME /usr/local/freesurfer/dev >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > Linux avml 2.6.32-131.12.1.el6.x86_64 #1 SMP Mon Sep 26 >>>>>>>>>> 10:13:43 BST >>>>>>>>>> 2011 >>>>>>>>>> x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07 > /usr/local/freesurfer/dev/fsfast/bin/preproc-sess >>>>>>>>>> -sf subjectname -df sessdir -mni305 -per-session -sliceorder > siemens >>>>>>>>>> -fsd >>>>>>>>>> bold -fwhm 5 -surface avml07 lhrh -noreg >>>>>>>>>> Mon Nov 14 20:07:57 EST 2011 >>>>>>>>>> instem f >>>>>>>>>> mc 1 f fmcpr >>>>>>>>>> stc 1 fmcpr fmcpr.siemens >>>>>>>>>> sm 0 >>>>>>>>>> mask 1 brain >>>>>>>>>> ---------------------------- Original Message >>>>>>>>>> ---------------------------- >>>>>>>>>> Subject: [FreeSurfer]: preproc-sess error >>>>>>>>>> From: tapsya(a)nmr.mgh.harvard.edu >>>>>>>>>> Date: Thu, November 10, 2011 1:41 pm >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> Cc: raij(a)nmr.mgh.harvard.edu >>>>>>>>>> -------------------------------------------------------------------------- > Dear Doug, >>>>>>>>>> We have encountered errors running preproc-sess (FSFAST v5.1) > command >>>>>>>>>> with >>>>>>>>>> the flag "-per-session". The command line is >>>>>>>>>> on machine adapt (same result on machine avml) >>>>>>>>>> cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 >>>>>>>>>> setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs > setenv SUBJECT avml07 >>>>>>>>>> nmr-std-env (=FS 5.1) >>>>>>>>>> preproc-sess \ >>>>>>>>>> -sf subjectname >>>>>>>>>> -df sessdir \ >>>>>>>>>> -mni305 \ >>>>>>>>>> -per-session \ >>>>>>>>>> -sliceorder siemens \ >>>>>>>>>> -fsd bold \ >>>>>>>>>> -fwhm 5 \ >>>>>>>>>> The error message: >>>>>>>>>> ... >>>>>>>>>> stc-sess Done >>>>>>>>>> avml07 To MNI305 ---------------- >>>>>>>>>> rawfunc2tal-sess -fwhm 5 -s avml07 -d >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1 -fsd bold > -stc >>>>>>>>>> siemens -update -subcort-mask >>>>>>>>>> ---------------- >>>>>>>>>> 1/1 avml07 >>>>>>>>>> 1/1 avml07 002 ---------------- >>>>>>>>>> "ERROR: could not determine file for >>>>>>>>>> /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/fmcpr.siemens" > Hence it looks like rawfunc2tal-sess is searching for -per-run > files (stem fmcpr*) rather than -per-session files (stem fmc*). > We tried to take control over the stems and added the following > lines: >>>>>>>>>> -mcin f \ >>>>>>>>>> -mcout fmc \ >>>>>>>>>> -stcin fmc \ >>>>>>>>>> -stcout fmcstc \ >>>>>>>>>> -smin fmcstc \ >>>>>>>>>> -smout fmcstcsm5 \ >>>>>>>>>> OR (modern naming conventions): >>>>>>>>>> -mcin f >>>>>>>>>> -mcout fmc >>>>>>>>>> -stcin fmc >>>>>>>>>> -stcout fmc.siemens \ >>>>>>>>>> -smin fmc.siemens \ >>>>>>>>>> -smout fmc.siemens.sm5.mni305.2mm \ >>>>>>>>>> However, these resulted in the same error. >>>>>>>>>> We also tried this on a more recent data set and received the >>>>>>>>>> same >>>>>>>>>> error. >>>>>>>>>> In summary, it appears that rawfunc2tal-sess (and in fact also > rawfunc2surf-sess) expect the stem fmcpr even when we use > per-session >>>>>>>>>> (where they should expect the stem fmc). >>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>> Best regards, >>>>>>>>>> Tapsya >>>>>>>>> -- >>>>>>>>> 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 >>>>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> -- >>>>>>> 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 >>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> -- >>>>> 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 >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> -- >> 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 >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> > >

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mri_surf2surf error - Return code 254
by John Griffiths 09 Dec '11

09 Dec '11

Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john

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Re: [Freesurfer] Event-Related design and jitter in stimulus onset
by Douglas N Greve 09 Dec '11

09 Dec '11

By default, optseq uses an internal clock synchronize to the TR (so events can only start on the TR). This can be changed by setting dPSD (eg, to 1). This would allow the NULL events to be multiples of 1 instead of 2. The PSD is specified in seconds. doug SHAHIN NASR wrote: > optseq2 --ntp 132 --tr 2 --tsearch 0.5 --ev C1 6 4 --ev C2 6 4 --ev C3 > 6 4 --ev C4 6 4 --ev C5 6 4 --ev C6 6 4 --ev C7 6 4 --ev C8 6 4 --ev > C9 6 4 --ev C10 6 4 --nkeep 10 --psdwin 10 16 --o Opt_Par_2nd > > > On Fri, Dec 9, 2011 at 2:03 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > What is your command line? > > > SHAHIN NASR wrote: > > Thanks Doug. > In my experiment, each trial (event) consists of 1 sec > stimulus presentation and 5 sec blank interval (TR=2). I have > also added a condition with just blank presentation which will > be repeated as much as other events. > > I have used optseq2 commands to generate the trial > sequence. But I faced two problem/questions: > > 1) Using this command, I expected to see a Null event > (other than my blank condition) with variable length > (irrespective of TR) between other trials. But to my surprise, > length of the Null event was always a multiplication of TR. Is > that correct? > > > 2) Also, for "psdmin psdmax" I wasn't sure if they are > number of TRs or number of seconds and what is a safe window > length when my stimuli are very simple visual objects (and no > cognitive task). > > Once again, thanks for your help. > > > > On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Shahin, there are several ways to answer this question. > If you > are going to analyze assuming a shape to the HRF, then the > actual > delay between stimuli is technically not important (though > 4s will > be good to avoid attenuation in the following stimulus). If > you're > using an FIR model of the HRF (no assumed shape), then I > usually > advise that you have, in total, as much time spent on > fixation (or > whatever your null stimulus is) as you have for any other > stimulus. You can use optseq to compute the actual schedule. > doug > > > SHAHIN NASR wrote: > > Hi Surfers, > > It is my first experience with Event-related > paradigms. In > my experiment, trials take minimum 6s (TR=2s). I wonder > what > is the optimum variable delay between trials to be able to > analyze data without any confound. > > Regards > > -- Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel: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> > FileDrop: > 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> > > > > > 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. > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_glmfit search space = 0
by Douglas N Greve 09 Dec '11

09 Dec '11

What are these asc files? Is this the input that you are having qdec load? If so, then there is at least one subject that has a 0 value at each vertex. The other 187 subjects may be non-zero. doug KYLE ROLLINS HANSEN wrote: > Doug- > Thank you for your response. The data set did not change between the two analyses. They both used the loading of the exact same .dat file. I think the error is in setting up and creating the new measures, and something went wrong in the process of creating the new measure entitled middle45.asc while it was done correctly for middle30.asc. That measurement is the only difference between the two analyses. Which file does mri_glmfit read in the case of creating a new measure? When I pull up the new measurement .asc files they look identical and don't have zero values for most of the values. Is there a different file the mri_glmfit command is running that would have those zeros in it? > Kyle Hansen > University of Utah > kyle.rollins.hansen(a)utah.edu > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, December 09, 2011 10:46 AM > To: KYLE ROLLINS HANSEN; freesurfer > Subject: Re: [Freesurfer] mri_glmfit search space = 0 > > Sorry, hit the send before I was ready. I was also going to point out > that mri_glmfit will zero-out a voxel unless it finds that all inputs > are non-zero (pruning). It looks like it could not find any voxels that > met this criterion. > doug > > Douglas N Greve wrote: > >> Did the data set change between the two analyses? The >> >> KingLab wrote: >> >> >>> Hello Doug- >>> In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! >>> Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. >>> middle30.asc >>> >>> lh-Avg-Intercept-middle30.asc ----------------------- >>> >>> Does the average middle30.asc differ from zero? >>> >>> 1.000 1.000; >>> >>> lh-Diff-Normal-AD-Intercept-middle30.asc ----------------------- >>> >>> Does the average middle30.asc differ between Normal and AD? >>> >>> 1.000 -1.000; >>> >>> ninputs = 188 >>> >>> Checking inputs >>> >>> nframestot = 188 >>> >>> Allocing output >>> >>> nframes = 188 >>> >>> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.648438 >>> >>> AvgVtxArea 0.399267 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> >>> $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >>> >>> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >>> >>> cmdline mri_glmfit --y >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >>> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >>> fsaverage lh --label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat >>> >>> >>> sysname Darwin >>> >>> hostname b417w74-106.med.utah.edu >>> >>> machine i386 >>> >>> user kinglab >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> labelmask >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> maskinv 0 >>> >>> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> IllCondOK 0 >>> >>> DoFFx 0 >>> >>> Creating output directory >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >>> >>> Matrix condition is 1 >>> >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> Found 149955 points in label. >>> >>> Pruning voxels by thr: 0.000000 >>> >>> Found 149953 voxels in mask >>> >>> Saving mask to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >>> >>> search space = 75250.1 >>> >>> DOF = 186 >>> >>> Starting fit and test >>> >>> Fit completed in 0.0740167 minutes >>> >>> Computing spatial AR1 on surface >>> >>> INFO: fwhmFromAR1: Fixing group surface area >>> >>> Residual: ar1mn=0.998860, ar1std=0.000986, gstd=11.981826, fwhm=28.215043 >>> >>> Writing results >>> >>> lh-Avg-Intercept-middle30.asc >>> >>> maxvox sig=1e+10 F=86188.1 at index 0 0 0 seed=1324082303 >>> >>> lh-Diff-Normal-AD-Intercept-middle30.asc >>> >>> maxvox sig=9.81891 F=46.013 at index 70329 0 0 seed=1324082303 >>> >>> mri_glmfit done >>> >>> ninputs = 2 >>> >>> Checking inputs >>> >>> nframestot = 2 >>> >>> Allocing output >>> >>> nframes = 2 >>> >>> Writing to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> reading group avg surface area 1041 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >>> >>> INFO: ignoring tag Creator >>> >>> INFO: ignoring tag SUBJECTS_DIR >>> >>> INFO: ignoring tag SynthSeed >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> >>> >>> ============================================================ >>> >>> Completed loading of analyzed data. >>> >>> >>> >>> Middle45.asc >>> >>> lh-Avg-Intercept-middle45.asc ----------------------- >>> >>> Does the average middle45.asc differ from zero? >>> >>> 1.000 1.000; >>> >>> lh-Diff-Normal-AD-Intercept-middle45.asc ----------------------- >>> >>> Does the average middle45.asc differ between Normal and AD? >>> >>> 1.000 -1.000; >>> >>> ninputs = 188 >>> >>> Checking inputs >>> >>> nframestot = 188 >>> >>> Allocing output >>> >>> nframes = 188 >>> >>> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.648438 >>> >>> AvgVtxArea 0.399267 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> >>> $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >>> >>> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >>> >>> cmdline mri_glmfit --y >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >>> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >>> fsaverage lh --label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle45.asc.mat >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle45.asc.mat >>> >>> >>> sysname Darwin >>> >>> hostname b417w74-106.med.utah.edu >>> >>> machine i386 >>> >>> user kinglab >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> labelmask >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> maskinv 0 >>> >>> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> IllCondOK 0 >>> >>> DoFFx 0 >>> >>> Creating output directory >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >>> >>> Matrix condition is 1 >>> >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> Found 149955 points in label. >>> >>> Pruning voxels by thr: 0.000000 >>> >>> Found 0 voxels in mask >>> >>> Saving mask to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >>> >>> search space = 0 >>> >>> DOF = 186 >>> >>> Starting fit and test >>> >>> Fit completed in 0.0002 minutes >>> >>> Computing spatial AR1 on surface >>> >>> INFO: fwhmFromAR1: Fixing group surface area >>> >>> WARNING: ar1 = nan <= 0. Setting fwhm to 0. >>> >>> Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 >>> >>> Writing results >>> >>> lh-Avg-Intercept-middle45.asc >>> >>> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >>> >>> lh-Diff-Normal-AD-Intercept-middle45.asc >>> >>> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >>> >>> mri_glmfit done >>> >>> ninputs = 2 >>> >>> Checking inputs >>> >>> nframestot = 2 >>> >>> Allocing output >>> >>> nframes = 2 >>> >>> Writing to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> reading group avg surface area 1041 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >>> >>> INFO: ignoring tag Creator >>> >>> INFO: ignoring tag SUBJECTS_DIR >>> >>> INFO: ignoring tag SynthSeed >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> >>> >>> ============================================================ >>> >>> Completed loading of analyzed data. >>> >>> Thank you! >>> >>> Kyle Hansen >>> >>> Research Assistant - AIAL >>> >>> University of Utah >>> >>> Hi Kevin, the problem is that once you threshold for >0, there are no >>> voxels that have non-zero values in all of the input subjects. Such >>> voxels are "pruned" because there is not a good model for them. The GLM >>> code does not do a different design at each voxels. In general, doing >>> such thresholding is bad statistically. If you really want to do it, run >>> it with --no-prune. >>> >>> doug >>> >>> kevin bickart wrote: >>> >>> >>>> Hi all, >>>> >>>> I am conducting a contrast of z (r) maps from 3 seed-based >>>> resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence >>>> of anticorrelations on the contrast results, I thresholded the z (r) >>>> maps at 0 before running mri_glmfit, thereby eliminating voxels with >>>> negative z (r) values. The command completed successfully but the >>>> resulting sig maps did not contain voxels with any values. I have >>>> attached the fsgd and contrast files and pasted the command and output >>>> below. Can anyone identify the problem here? >>>> Thanks, >>>> Kevin >>>> >>>> *Potentially problematic portion of output:* >>>> Pruning voxels by thr: 0.000000 >>>> Found 0 voxels in mask >>>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>>> search space = 0.000000 >>>> >>>> *Entire command and output: * >>>> [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] >>>> (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 >>>> _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd >>>> /autofs/homes/006/kbickart/AmySubNet_glm/pa >>>> ired3.fsgd doss --C >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir >>>> LR_Amy_lOFC2_glm2 >>>> gdfReadHeader: reading >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>>> Continuous Variable Means (all subjects) >>>> 0 roi1_vs_roi2_vs_roi3 0 0.707107 >>>> Class Means of each Continuous Variable >>>> 1 Class_081028_BC77WB 0.0000 >>>> 2 Class_081028_XE45TK 0.0000 >>>> 3 Class_081028_YY28TK 0.0000 >>>> .... >>>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >>>> cwd >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne >>>> r_YC >>>> cmdline mri_glmfit --y >>>> LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep >>>> --fsgd /autof >>>> s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired >>>> .mat --glmdir LR_Amy_lOFC2_glm2 >>>> sysname Linux >>>> hostname kreature >>>> machine x86_64 >>>> user kbickart >>>> FixVertexAreaFlag = 1 >>>> UseMaskWithSmoothing 1 >>>> OneSampleGroupMean 0 >>>> y >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn >>>> er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>>> logyflag 0 >>>> usedti 0 >>>> FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>>> glmdir LR_Amy_lOFC2_glm2 >>>> IllCondOK 0 >>>> ReScaleX 1 >>>> DoFFx 0 >>>> Creating output directory LR_Amy_lOFC2_glm2 >>>> Loading y from >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am >>>> yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>>> llINFO: gd2mtx_method is doss >>>> Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat >>>> Normalized matrix condition is 1 >>>> Matrix condition is 44.5 >>>> Pruning voxels by thr: 0.000000 >>>> Found 0 voxels in mask >>>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>>> search space = 0.000000 >>>> DOF = 177 >>>> Starting fit and test >>>> Fit completed in 0.0148667 minutes >>>> Computing spatial AR1 in volume. >>>> fMRIspatialAR1(): hit 0 voxels >>>> WARNING: no voxels in AR1 computation >>>> Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan >>>> Writing results >>>> paired >>>> maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 >>>> mri_glmfit done >>>> >>>> >>>> >>>> -- >>>> Kevin Bickart >>>> MD-PhD Student >>>> Department of Anatomy and Neurobiology >>>> Boston University School of Medicine >>>> >>>> >>>> live UP to it >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...(a)nmr.mgh.harvard.edu >>> 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> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >> > > -- > 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 > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Event-Related design and jitter in stimulus onset
by SHAHIN NASR 09 Dec '11

09 Dec '11

Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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