Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

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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Minor issues with Freesurfer v4.0.4/rerunning on 4.2.0
by John Sheppard 26 Jan '09

26 Jan '09

Hey everyone, I have finished anatomical segmentations on a batch of brains, however this was done in Freesurfer 4.0.4 and I realized several of my subjects have issues previously described here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-August/008266.h…, with MRIScomputeWhiteVolume. I didn't get as massive error.log files but they were maybe up to 1mb in size. I understand should be corrected by re-running recon-all -segstats -wmparc for those using ?h.cerebral-white-matter in aseg.stats or wmparc.stats. In the latest release bugs were also fixed so that wmparc.stats and aseg.stats volumes should match up. Does this update only increase the volumes in wmparc.stats (we aren't using that data anyway, but we are using aseg.stats) but leave aseg.stats the same? There was also the potential for spikes to occur in pial surface near insula in 4.0.4, though I inspected the segmentations and did not notice this problem. Other than those things, is there any serious need to re-run autorecon2 or 3 after having processed them through 4.0.4 previously? Sorry if I missed anything previously discussed, I had a look at the update release notes and tried searching the mailing list archives. Thanks! John -- John Sheppard Undergraduate Student Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: john-sheppard(a)northwestern.edu Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201

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DODS/DOSS choice in patient/control study
by Burmicz, Ryzarda 26 Jan '09

26 Jan '09

Hello, We are looking at patients versus control group analysis. We have done a straight analysis and are now looking at covariates. DOSS produces similar results to a straight patient vs control analysis, in that some blobs are located in the same cortical regions. In the case of DODS, there is no similarity whatsoever to the straight analysis maps... which is why I am so stuck in deciding, because it really does impact on the results quite drastically. I understand the difference between DODS and DOSS - and I know the following question is not an easy one to answer, however we have sample sizes of 15 patient vs 15 control subjects and would like to know if that is great enough such that we are better off going for DODS. There is no reason to say that the patient cortical thickness - age relationship is any different in slope from that of normal ageing generally; however in certain cortical regions patients exhibit a thickening of the cortex, and thinning in other (albeit fewer) regions. Do you have any comments? I would have thought that our sample sizes are rather small, but would appreciate your input. I attach the comparison of patient vs control covaried for age under both DODS and DOSS to illustrate the differences. Thanks! Rysia Ryszarda Burmicz Research Assistant Centre for Neuroimaging Sciences PO89 Institute of Psychiatry

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Re: [Freesurfer] Freesurfer 4.0.5 Leopard
by Ming Hsu 26 Jan '09

26 Jan '09

Hi Nick, I was able to download 4.0.5, and everything runs fine on the desktop. However over ssh, qdec seems to crash the x server. The program would begin loading, and it appears for a second then the error: X connection to localhost:10.0 broken (explicit kill or server shutdown). After that I have to restart my laptop to run any X applications. BTW, the same thing seems to happen on 4.1. Thanks, Ming On Tue, 13 Jan 2009 07:34:49 -0800, Nick Schmansky wrote: > Ming, > You can get it here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable > notice there is one for intel and one for powerpc. > Nick -- Ming Hsu Department of Economics, and Beckman Institute for Advanced Science & Technology University of Illinois at Urbana-Champaign Office: (217) 244-1122

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Freesurfer January 2009