Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

A segmentation estimation?
by Dov Sadan 25 Jun '13

25 Jun '13

Hi there, I'm wondering if there's any parameter which can assess the correctness of the freesurfer's segmentation ( the aparc.a2009s+aseg.mgz file). --> Assuming the freesurfer's algorithm fitting/minimizing an objective function, right ? If so, where I can find the value of this fitted function ? (or RMS value ?) Thanks in advance, Dov

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Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh
by Yang, Zoe 25 Jun '13

25 Jun '13

Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html) We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt Is there anything else that we are missing and should run? Thanks!

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Must have compute capability 2 for GCAMORPH_ON_GPU CUDA device
by Clive Wong 25 Jun '13

25 Jun '13

Dear experts, I'm new to CUDA. I tried to use CUDA in my environment, it gives the message below: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.0 Runtime : 5.0 Acquiring CUDA device Using default device Must have compute capability 2 for GCAMORPH_ON_GPU CUDA device: Quadro NVS 420 I've checked that the Quadro NVS400 is of compute capability 1.1. and the script devicemanagement.c has blocked devices below compute capability 2. Is there any workaround to get it work? Or shall I compile the freesurfer from source code? If yes, how could I know how to setup the configuration? Thanks, Clive

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Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 (Douglas Greve)
by Maria Kharitonova 25 Jun '13

25 Jun '13

Hi, sorry I must have missed your response last week. Yes, I'm doing an identical analysis: comparing 2 groups of kids (controls and ADHD) in cortical thickness, controlling for age and demeaned ICV (nuisance). So all the parameters are the same. I'm attaching 3 screen shots: group differences using 5.0 before using Monte Carlo correction (lots of clusters), group differences before correction using 5.3 (few small clusters), and group differences using 5.0 after correction (frontal cluster). there was nothing sig. remaining after correcting for multi. comparisons using 5.3. I'm puzzled about why the differences are so large. I selected DODS in 5.0, so everything should be the same? Thanks! Maria On Tue, Jun 25, 2013 at 12:02 PM, Maria Kharitonova < maria.kharitonova(a)colorado.edu> wrote: > > Hi, sorry I must have missed your response last week. Yes, I'm doing an > identical analysis: comparing 2 groups of kids (controls and ADHD) in > cortical thickness, controlling for age and demeaned ICV (nuisance). So all > the parameters are the same. I'm attaching 3 screen shots: group > differences using 5.0 before using Monte Carlo correction (lots of > clusters), group differences before correction using 5.3 (few small > clusters), and group differences using 5.0 after correction (frontal > cluster). there was nothing sig. remaining after correcting for multi. > comparisons using 5.3. I'm puzzled about why the differences are so large. > I selected DODS in 5.0, so everything should be the same? > > Thanks! > Maria > > ****** > > Message: 10 > Date: Tue, 18 Jun 2013 23:34:10 -0700 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3 > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51C150E2.1080604(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Maria, can you elaborate on exactly what you have done? Is the data > the same and you are only changing the version of QDEC? What is the > nature of the difference? Can you send pics or stats? > doug > > > On 6/18/13 6:06 AM, Maria Kharitonova wrote: > > Hi, > > > > I'm learning how to use QDEC and was comparing results that it produces > under FresSurfer 5.0 vs 5.3. I know the 5.0 has an option for either DODS > or DOSS method of producing a design matrix, while the 5.3 only has DODS. > This suggests that results should be identical (or at least similar) across > versions if I select DODS. However, I'm getting very different results > based on the version I select: complete lack of differences across groups > in 5.3 and a predicted pattern of differences in 5.0 using DODS. I'd like > to understand where the differences are stemming from -- any ideas? > > > > Thanks in advance! > > Maria > > > > ******************************* > > > > Maria Kharitonova, Ph.D. > > Postdoctoral Research Fellow > > Laboratories of Cognitive Neuroscience > > Boston Children's Hospital > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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IndexError: list index out of range in post-processing of longitudinal data
by Sandra Preissler 25 Jun '13

25 Jun '13

Dear freesurfer users, we wanted to do longitudinal analyses for two different time points. So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepa…) The "Post-Processing Longitudinal Data" step does not work. (long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage ) After starting the process we get the following error message: Parsing the qdec table: ./qdec/long.qdec.table.dat Traceback (most recent call last): File "/opt/freesurfer/bin/long_mris_slopes", line 521, in <module> qdectable = LongQdecTable(options.qdec) File "/srv/freesurfer/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/srv/freesurfer/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range Weve already tried a lot of things, like removing subjects from the longitudinal qdec table, except for one subject, or deleting every command that was optional, but it still does not work. The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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freesurfer registration
by Parker, Christopher 25 Jun '13

25 Jun '13

Hi, I understand that the recon-all script registers and then averages two anatomical images (after bias field correction) if two are provided in the "orig" folder, before performing the other parcellation stages. I am writing a report and it might be good to mentioned what registration is used. I'm guessing this is a rigid registration using sum of squared differences cost function? Best, Chris

3 2

Matrix building
by Linn Mittlestein 25 Jun '13

25 Jun '13

Hello, I wondering if possible using fsgd files to do group analysis with two factors (one with 3 levels, one with 2 levels), with one covariate. On fsgd example list I cannot find this example? Kind Regards, Linn

2 1

Re: [Freesurfer] ribbon label volume mapping
by Colin Reveley 25 Jun '13

25 Jun '13

Doug - thanks that sounds well worth trying. the labels we have have arbitrary spatial resolution in the saggital plane, and 1mm gaps between saggital slices. In general in this project we are using an isotropic resolution of 0.25mm. To generate surfaces in freesurfer I have to downsample to 0.35mm (to fit into 256) in applying the procedure you suggest a) is it possible to use a volume with a dimension > 256? b) is it possible to use a non-isotropic resolution? playing around with non-isotropic resolutions, projection fractions and vote would yield different results. c) can mri_aparc2aseg output a volume > 256? 0.35 isotropic will be ok. we'd prefer 0.25 if we can. best Colin > ---------- Forwarded message ---------- > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > To: <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Sun, 23 Jun 2013 20:03:09 -0700 > Subject: Re: [Freesurfer] ribbon label volume mapping > > You could run mri_vol2surf at different projection fractions (and using > nearest neighbor interp). This will create a set of files, one for each > projection fraction. You can then run mri_concat with the --vote option to > get you the most frequently occurring label. You could then use > mris_seg2annot to create an annotation. > > If you want to go the other way, you will need to combine your labels into > an annotation (mris_label2annot), then convert that into a volume with > mri_aparc2aseg. > > doug > > > On 6/22/13 10:08 AM, Colin Reveley wrote: > > If one has a volume of integers, each representing a cortical area, > can one map that to the surface as a set of labels, in a smart way that > e.g. takes the mode of the voxels that lie on the vector between equivalent > white and pial nodes (ie uses curvature and thickness information, tacitly > or explicitly)? > > the labels are not exactly on the ribbon. There are many voxels outside > the ribbon that are non zero. Like caudate etc. > > and some voxels that are within the ribbon but are zero because the > label data is was/is non-isotropic originally (which is the problem we want > to solve in fact). > > that would be great. > > Now let's say you already have labels on a mesh. > > can you generate a ribbon volume of labels, i.e. the opposite operation > to what I enquire about above (opposite but not inverse operation)? > > This is work in rhesus. So my pipeline is very barebones indeed, really > just > > mri_normalize > ... > mri_tesselate > mri_inflate/smooth/sphere > mris_fix_topology <-noaseg -noaprc> > mris_make_surfaces <-naseg -noaparc> > > I only have access to what is generated by that sequence or what I can > subsequently generate. > I can generate a freesurfer like ribbon with mris_fill. > > My understanding of labels and data mapping in general in freesurfer is > very poor. > > Maybe adapting one of your matlab scripts might be an idea, if there is > not another way? > > many thanks, > > Colin, > Sussex > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

2 1

Monte Carlo simulation: Talairach coordinates
by Emily Boeke 25 Jun '13

25 Jun '13

Hi All, I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid." However, the .nii files I'm seeing look like I would expect them too. I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be? Thanks, Emily

2 1

problem with surface area regression
by wen.zhang55 25 Jun '13

25 Jun '13

Dear Freesurfer, I have checked the mail list, none could answer my problem. I added up the value of all vertxes in the .area or .area.pial files, find that brain size did not contribute much to that vertex-sum. However, some experiment used total brain volume as a regreesion coefficient to remove brain size effect. In these case, with the comparison of surface area in vertex-to-vertex, is it proper to use the above vertex-sum as the regression coefficient to remove different brain size? Thank you very much! Cowen 2013-06-24 wen.zhang55

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