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30131 discussions

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

2 1

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

2 1

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

1 0

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

2 1

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

3 4

How to project fMRI activity of entire depth of cortex on to surface
by Wang, Xin 25 Mar '09

25 Mar '09

Hello, Freesurfer group, The mri_vol2surf only register the fMRI activity at a certain depth of cortex, as specisfied by -projecfrac, to the cortical surface. mri_surf2surf does the same thing. I want to identify any cortical region have activation during the task, therefore, I need to project fMRI activity of entire depth of cortex onto surface. Some regions may have activity in different depth of cortex, Ideally, the significent level of these regions reflect the peak of the activity cross entire depth or the sum of significense of entire depth. the --interp trilinear may do some toward my goal, but it elimit many activities compare to nearest. Thanks, Xin Wang

2 4

Monte Carlos for volume data?
by Dave Brohawn 25 Mar '09

25 Mar '09

Hello, Here is my bugr information, if you need. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090320 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd /autofs/space/ventzl_016/users Can you tell me if monte carlo simulations can be used for volume data? Josh Roffman and I are curious if clusters seen in the volume will pass monte carlo simulations. I have been working closely with Kara Dyckman, and we couldn't find a precedent for monte carlos involving volume data completed in the Manoach group, a freesurfer example, or a mention of it in the archives. I used an mgh file from the mris_preproc command below to complete monte carlos for surface data on the left hemisphere. mris_preproc --fsgd /autofs/space/ventzl_016/users/fsgd/qdec.fsgd --target fsaverage --hemi lh --sf /autofs/space/ventzl_016/users/Subject_files/All-18 --a newEMerror-tpx --c ASevASc_6s --out /autofs/space/ventzl_016/users/All-18/preproc/lh.ASevASc.All-18.gnr.mgh I examined a log created from this preproc command, and saw that mri_vol2surf was completed for each subject in the group, followed by a concatenate command to create the mgh file. Does this mean that the volume data is taken into account in this mgh file? Here is one of the ten monte carlos I ran for the surface data. The other nine differ only in the MCSIM #. mri_glmfit --y $SUBJECTS_DIR/All-18/preproc/lh.ASevASc.All-18.gnr.mgh --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --surf fsaverage lh --C $SUBJECTS_DIR/fsgd/All-18.mat --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01/lh_ASevASc_6_rfx_p05_f_MCSIM1 --fwhm 14.41 If the volume data was processed in the preproc to make the mgh file for both hemispheres, then do these monte carlos also take volume data into account? Do I run a mri_volcluster (as opposed to surfcluster) to assess volume clusters and see if they pass monte carlos with what I already have, then? Thanks for taking the time to read this through. I know this email is on the long side. Dave Brohawn

1 0

Measuring cortical thickness with high resolution data
by Falk Lüsebrink 25 Mar '09

25 Mar '09

Hi Freesurfers, Im 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 Im 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 cant handle any dimensions above 256 or Im missing another flag. Does someone has any ideas about that issue? Regards, Falk

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