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30131 discussions

Doubt about paradigm file and event related paradigm
by Francisco Robles 27 Jan '09

27 Jan '09

Hi, I'm Francisco Robles, from México city. I am using FS-Fast to analyze some event-related fMRI. My problem is jow to use the paradigm file because I need to exclude some images from my analysis. The situation is that I have a paradigm of 3.5 secs of stimulus and a variable quantity of Null/fixation. But from those 3.5 secs of stimulus, I only want to analyze the last 1.75 secs. The opseqt file I've got goes like this: 0.0000 2 3.500 1.0000 var1 3.5000 4 3.500 1.0000 var3 7.0000 4 3.500 1.0000 var3 10.5000 3 3.500 1.0000 var2 14.0000 0 1.750 1.0000 NULL And I edited it to look like this but I really don't know if it is the right way to do it: 1.75 2 1.75 1 "var1" 5.25 4 1.75 1 "var3" 8.75 4 1.75 1 "var3" 12.25 3 1.75 1 "var2" 14.00 0 1.75 1 "NULL" So I put in the column of stimulus onset, the time point I want to analyze and in the duration column, only the quantity of time I want to analyze. But I've seen in mkanalysis-sess.new on wiki, that there is a flag -tpef [filename] for the command selxavg3-sess that allows to exclude certain files according to a time-point, but I don't know how to do it, how is the arrange of taht file, how many columns, how do I say to it that I only want the last 1.75 secs and not the hole 3.5 secs. I am really lost, if anyone can help mw I will appreciate it a lot. Thank you all in advance. _________________________________________________________________ Comparte fotos, juega y charla en Messenger. http://download.live.com/messenger

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Mean Curv
by Vina Goghari 27 Jan '09

27 Jan '09

Hello all, What is the mean curv in the stats files a measure of? Thanks kindly, Vina

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aseg.stats
by Kellen Mobilia 27 Jan '09

27 Jan '09

I would like to pose a brief question. Somehow in the process running brains through autorecon one of my subjects aseg.stats files became messed up and as far as I am able to tell everything else is intact. Is there a quick way to rebuild the data that is written to that file? Or do I have to re-run the autorecon sequence? Thanks Kellen

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memory alloc problem in mri_fwhm
by Krishna Srihasam 27 Jan '09

27 Jan '09

Hi, I am analyzing my fMRI data and I got a memory alloc problem in "mri_fwhm" The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from "freesurfer-Linux-rh9-stable-pub-v4.0.5". I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna

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preprocessing error
by jake＠nmr.mgh.harvard.edu 27 Jan '09

27 Jan '09

Hi, I am attempting to run the following command: preproc-sess -s CD_R01BTX_ctrl1_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 and am getting an error: >>>Tue Jan 27 16:33:44 EST 2009 >>>mcparams2exterg: finished >>>\n\n >>>Tue Jan 27 16:33:44 EST 2009 >>>mc-sess completed SUCCESSFULLY >>>CD_R01BTX_ctrl1_sess1 Smooth ------------------------ >>>Tue Jan 27 16:33:44 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox >>>spatialsmooth-sess -i fmc5 -o fmcsm5 -fwhm 5 -fsd bold -umask 2 -s >>>CD_R01BTX_ctrl1_sess1 -d /autofs/space/amaebi_035/users/ablood/R01_Botox >>>---------------------------------------- >>>------------------------------------------------ >>>------------------------------------------------ >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1 >>>Tue Jan 27 16:33:45 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>/space/amaebi/35/users/ablood/R01_Botox >>>RunList 016 017 018 019 020 021 >>>---------------------------------------------- >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>ipfsl -i 016/fmc5 -o 016/fmcsm5 -pct .1 -fwhm 5 -fmt bhdr >>>---------------------------------------------- >>>ERROR: cannot find /usr/pubsw/packages/fsl/4.1.2/bin/ip >>>ERROR: ipfsl failed >>>ERROR: spatialsmooth-sess failed Can anyone tell me what I am doing wrong? thanks!! Jake Bugr FREESURFER_HOME: /usr/local/freesurfer/stable3 >>>we have to use stable3 for specific reasons Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/amaebi/35/users/ablood/R01_Botox PWD: /space/amaebi/35/users/ablood/R01_Botox

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Re: [Freesurfer] possible memory allocation problem - make_average_volume
by Douglas N Greve 27 Jan '09

27 Jan '09

I don't think you'll need to run the surfaces again. --no-aseg is passed to make_average_volume from make_average_subject. Ruchika Shaurya Prakash wrote: > I just downloaded the latest version last week. Is there a change since then? > Also, I get the --no-aseg option with make_average_volume and not with > make_average_subject - but I am thinking that is probably okay since the > surfaces are already done. Do you think that I need to run the surfaces again? > > Thanks, > -Ruchika. > > > ---- Original message ---- > >> Date: Tue, 27 Jan 2009 15:01:20 -0500 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] possible memory allocation problem - >> > make_average_volume > >> To: Ruchika Shaurya Prakash <rprakash(a)uiuc.edu> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> >> Sorry, just run it with --no-aseg (for that you may need a new version). >> It probably ran the surfaces ok and then bonked on the volumes (and >> probably only on the aseg). >> >> doug >> >> Ruchika Shaurya Prakash wrote: >> >>> I do have this option - but that would mean that I would not get the >>> average for volumes? >>> >>> Also, if you take a look at the make_average_surface.log - that got >>> completed without any problems. So do I need to run the >>> make_average_subject command again? >>> >>> Thanks, >>> -Ruchika. >>> >>> On Jan 27, 2009, at 1:34 PM, Douglas N Greve wrote: >>> >>> >>>> Try running it with --no-vol. If you don't have this option, then you >>>> may need to upgrade. >>>> >>>> Ruchika Shaurya Prakash wrote: >>>> >>>>> Hello >>>>> >>>>> I am running the make_average script on 92 Ss and get the following >>>>> error message: >>>>> nframestat = 92 >>>>> Allocating output >>>>> mri_concat (63810) malloc: *** mmap(size=262144) failed (error >>>>> code=12) >>>>> *** error: can't allocate regions >>>>> *** set a breakpoint in malloc_error_break to debug >>>>> MRIalloc (256, 256, 256): could not allocate 262144 bytes for >>>>> 13929th slice >>>>> >>>>> >>>>> Following some of the threads, it seems like the problem is in >>>>> averaging the volumes and Doug had provided some scripts in the >>>>> following location, the link to which is not working anymore: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> Would it be possible to put the files back? I am using freesurfer v. >>>>> 4.1.0 and am attaching the make_average_surface.log and >>>>> make_average_volume.log files, in case there are some other issues. >>>>> Thanks for your help! >>>>> >>>>> -Ruchika. >>>>> = >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>> > > >

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possible memory allocation problem - make_average_volume
by Ruchika Shaurya Prakash 27 Jan '09

27 Jan '09

Hello I am running the make_average script on 92 Ss and get the following error message: nframestat = 92 Allocating output mri_concat (63810) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate regions *** set a breakpoint in malloc_error_break to debug MRIalloc (256, 256, 256): could not allocate 262144 bytes for 13929th slice Following some of the threads, it seems like the problem is in averaging the volumes and Doug had provided some scripts in the following location, the link to which is not working anymore: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Would it be possible to put the files back? I am using freesurfer v. 4.1.0 and am attaching the make_average_surface.log and make_average_volume.log files, in case there are some other issues. Thanks for your help! -Ruchika.

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mri_volcluster question
by Dave Brohawn 27 Jan '09

27 Jan '09

Hello, Does the frame flag refer to offsets? If so, would frame 5 be the same as offset 5 (6 seconds)? Thank you, Dave Brohawn

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Qdec Cluster Size
by nels5614＠umn.edu 26 Jan '09

26 Jan '09

Hello, I am wondering if there is an easy way to determine the size of a cluster of significant voxels resulting from a QDEC analysis? I have created a label and mapped the label to all of the subjects, but didn't know if there was a way to extract information about cluster size. Thanks, Miranda

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Statistic analysing for a mask
by Alexandru Hanganu 26 Jan '09

26 Jan '09

Dear Freesurfer users, We have an MNI mask and we want to apply this mask on a group of subjects for small volume correction. so we did the following steps: 1. cd $SUBJECTS_DIR/fsaverage/surf fslregister --s fsaverage --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat 2. cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh 3. cd $SUBJECTS_DIR/subjid/surf mri_surf2surf --s subjid --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh . . . Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 147410, nTrgMulti = 16432, MnTrgMultiHits = 2.25237 nSrc121 = 86069, nSrcLost = 0, nSrcMulti = 42416, MnSrcMultiHits = 2.31875 Saving target data 4. Next step was just for verifying, but we received an error (maybe it's not so important): cd $SUBJECTS_DIR/subjid/surf mri_segstats --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.fsaverage.ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg We want to determine the statistics only for this mask for the whole group of subjects (qdec, or mri_glmfit). If the mapping of our subjects thickness data was good, what should we do next in order to achieve our goal ? Thank you. Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.

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