Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

recon-all finished with errors
by Pedro Paulo de Magalhães Oliveira Junior 27 Mar '09

27 Mar '09

There is a researcher here who is getting this error in version 4.2.0, I have uploaded the 001.mgz to the ftp: ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=150,y=117, z=145, r=8362 iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073730580 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1073752625 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073753196 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=26 , nb = -1601994905 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1073752746 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1768967209 mri_watershed Error: GLOBAL region of the brain empty ! Darwin lim44-macpro.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br

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automatic subdivision of segmented subcortical structures
by Sungeun Kim 27 Mar '09

27 Mar '09

Hello, I am looking for any automated method to sub-divide segmented subcortical structures by FreeSurfer. Is there anyone who knows how to do this? Thanks in advance. -- Sungeun Kim.

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High resolution image of 0.8mm not rescaled to 1mm
by Rosa Steimke 27 Mar '09

27 Mar '09

Hi, Im trying to keep images at a resolution of 0.8 mm and used the –cm flag during the convertion. However i got an error message during talairach transformation in autorecon1. The logfile is attached. Do I need to use a flag here, too? I learned form the previous email that I have to also use the –noconform flag during mri-normalization and the –noaseg flag during autorecon2. Are there more things I will need to do? Kind regards. Rosa -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger01

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Qdec and error with ?h.aparc.a2005s.thickness
by Nasim Maleki 27 Mar '09

27 Mar '09

Dear Freesurfers, I get the following error message in Qdec (1.1) when I choose ? h.aparc.a2005s.thickness on the tutorial data: Loading data table /Applications/freesurfer/subjects/qdec/ stats_tables//lh.aparc.a2005s.thickness.stats.dat... Number of columns: 79 fsid column: 1 Number of factors: 78 Number of subjects: 40 ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/ vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x4418b10): Script: vtkTemp3 SetStatsImportItem lh.aparc.a2005s.thickness Returned Error on line 1: Uncaught exception: ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: lh_S_temporal_transverse_thickness Stack trace: Uncaught exception: ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: lh_S_temporal_transverse_thickness while executing "vtkTemp3 SetStatsImportItem lh.aparc.a2005s.thickness" How can I fix this? Thanks, Nasim

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Monte Carlos for Volume? (Part 2)
by Dave Brohawn 27 Mar '09

27 Mar '09

Hello, The mris_preproc command generates a concatenated group surface mgh file for easy use with the monte carlo analysis. Is there such a command to concatenate volume data for use with the monte carlo command for a group analysis? I wrote freesurfer earlier this week asking if you can use the output mgh files from preproc commands in the monte carlo commands. This doesn't seem likely, considering the mgh files have hemispheres specified. What would the input file be, and how do you create it? I would really appreciate an answer to this question, as I feel I have everything else I need to do a volume-based monte carlo analysis. Thank you very much, Dave Brohawn

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Re: [Freesurfer] Measuring cortical thickness with high resolution data
by Nick Schmansky 27 Mar '09

27 Mar '09

Falk, Is it possible to send me an example hires volume that you are working with? I'd like to send it through the stream myself so that I can fix the problems encountered (with using hires data) first-hand. You can upload the dicom or the 001.mgz file to me here: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote: > Hi Freesurfers, > > > > I’m trying to evaluate the usefulness of high resolution scans > acquired at 7T with an isometric voxel size of .6mm for the > measurement of cortical thickness. The inhomogeneities are taken care > of by dividing the scans with another scan of another sequence, so > they are not an issue anymore. > > > > My problem is that Freesurfer usually conforms the voxel size to 1mm > which is not desirable. I tried using the –cm and –noaseg flags for > the recon-all process to avoid the conformation and to skip the > subcortical segmentation, but another problem arises while using these > flags. > > > > The error I receive is occurring after the WM Segmentation and states > as follows: > > > > #-------------------------------------------- > > #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009 > > > > cp wm.mgz wm.seg.mgz > > > > > > mri_segment -keep brain.mgz wm.seg.mgz > > > > preserving editing changes in output volume... > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > computing class statistics for intensity windows... > > WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] > > GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] > > setting bottom of white matter range to 77.9 > > setting top of gray matter range to 89.4 > > doing initial intensity segmentation... > > using local statistics to label ambiguous voxels... > > using local geometry to label remaining ambiguous voxels... > > > > reclassifying voxels using Gaussian border classifier... > > > > removing voxels with positive offset direction... > > smoothing T1 volume with sigma = 0.250 > > removing 1-dimensional structures... > > thickening thin strands.... > > 20 segments, 4813 filled > > 10270 bright non-wm voxels segmented. > > 5589 diagonally connected voxels added... > > white matter segmentation took 2.4 minutes > > writing output to wm.seg.mgz... > > ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 > height=320. > > > > The dimensions of the data I’m trying to process is 320 x 320 x 224 > and is changed to 320 x 320 x 320 while using the –cm flag. It seems > the mri_segment process can’t handle any dimensions above 256 or I’m > missing another flag. > > > > Does someone has any ideas about that issue? > > > > Regards, > > Falk > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_fwhm problem
by Yigal Agam 27 Mar '09

27 Mar '09

Hi, I'm getting an NAN value for some surfaces but not for others. Any ideas? Both surfaces below were generated using an identical process. [yigal@schnook sph_sm20]$ pwd /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano010/bold/EMexec3/sph_sm20 [yigal@schnook sph_sm20]$ mris_fwhm --i e001-rh.bhdr --subject average7 --hemi rh average7 rh white Number of vertices 163842 Number of faces 327680 Total area 65350.234375 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.398861 AvgVtxDist 0.724276 StdVtxDist 0.238694 INFO: bvolumeRead: min = -0.473817, max = 0.363422 Polynomial detrending, order = 0 Computing spatial AR1 ar1mn = 0.995086, ar1std = 0.00271769, ar1max = 0.999702 avg vertex dist 0.724276 avg vertex dist 0.724276 fwhm = 12.150420 [yigal@schnook sph_sm20]$ pwd /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano016/bold/EMexec3/sph_sm20 [yigal@schnook sph_sm20]$ mris_fwhm --i e001-rh.bhdr --subject average7 --hemi rh average7 rh white Number of vertices 163842 Number of faces 327680 Total area 65350.234375 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.398861 AvgVtxDist 0.724276 StdVtxDist 0.238694 INFO: bvolumeRead: min = -0.749406, max = 1.43625 Polynomial detrending, order = 0 Computing spatial AR1 ar1mn = inf, ar1std = nan, ar1max = inf avg vertex dist 0.724276 avg vertex dist 0.724276 fwhm = nan

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Using FreeSurfer under severe morphological deformation
by Pedro Paulo de Magalhães Oliveira Junior 26 Mar '09

26 Mar '09

Attached there is a PDF with a slide that can be useful in some talk regarding surface based model soundness. Other examples can be found in: http://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br

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extracting data used in QDEC scatterplots
by Sam Torrisi 26 Mar '09

26 Mar '09

Hi, I would like to extract the thickness values displayed in the scatterplots in QDEC. Is there an existing method for exporting these values into a text file? Thanks, Sam University of California, Los Angeles

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FDR correction
by Lars M. Rimol 26 Mar '09

26 Mar '09

Hi, I have done an analysis involving three groups, so there are three pairwise comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple comparisons (across the vertices), so I use FDR. But since FDR determines the threshold basd on the actual p-values, I get 6 different tresholds: comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) There are lots of significant vertices in comparison 1 and nothing significant, after correction, in comparison 3. Is there anything wrong with using different tresholds here, and concluding that in comparison 1 there were extensive differences between the groups, whereas in comparison 3 there were none? I'm not sure if this is a problem, but I'm afraid some reviewers might have an issue with it. Across the hemispheres, I can choose a conservative threshold which covers both hemispheres, i.e. lower than both the FDR-adjusted treshold for lh and rh. But between the comparisons the tresholds differ even more, by a factor of 10 and 100. And if I choose the most conservative of all the adjusted thresholds, I'm afraid that I'll make a type II error in comparison 1. >From what I understand, the adjusted threshold for comparison 3 is more conservative because of the actual empirical data (the distribution of p-values), so that's an empirical argument for using a more conservative threshold there. And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole thing, would that be a better approach? And does Freesurfer use the Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all three p-maps? Thank you! -- yours, LMR

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