Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Vertex size and vertex value export
by Dalwani, Manish 22 Feb '12

22 Feb '12

Hello Freesurfer's, What is the size of a vertex? Also, how do you define a vertex? Also, in the Qdec analyses, once you get a cluster and the maximum vertex, is there a way to export individual vertex value (for each subject)? Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado

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Cluster position
by Antonella Kis 22 Feb '12

22 Feb '12

Dear All, Is there a way that I can get my clusters location (segmentation and/or annotation) inthe MNI space if I know the MNI coordinates? Many thanks. AK

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memory and bus failure
by cloud.ctrl＠me.com 22 Feb '12

22 Feb '12

I have three scans that exit with errors that I cannot comprehend. The first two indicate memory and bus failures, so I thought maybe my computer had choked during processing, but after running again I received the same errors. The third is too cryptic for me to understand at all. Can anyone offer any advice for these? 1: BEST FITNESS (o)is 321.33384 mri =0.000 curv = 2.540 unmri = -331.493 ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) mris_topo_fixer(58671) malloc: *** mmap(size=534511616) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRISalloc(1142113, 468): could not allocate vertices Cannot allocate memory 2: searching scale 1 Z rot 65.8 searching scale 1 Z rot 66.1 searching scale 1 Z rot 66.3 global minimum found at slice 126.0, rotations (22.40, 59.33) final transformation (x=126.0, yr=22.402, zr=59.329): 0.472 -0.860 0.194 140.992; 0.795 0.510 0.328 -83.378; -0.381 -0.000 0.925 33.641; 0.000 0.000 0.000 1.000; Bus error 3: CORRECTING DEFECT 37 (vertices=32782, convex hull=6402) normal vector of length zero at vertex 95333 with 0 faces vertex 95333 has 0 face No such file or directory

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Trac-all -preproc cannot find cor-.info
by Martijn Steenwijk 22 Feb '12

22 Feb '12

Dear all, I'm trying to run trac-all (FS5.1, the updated trac-all) for a provided nii.gz DWI volume and it's bvals/bvecs. During the preprocessing mri_convert searches for dti/COR-.info, but cannot find it - see log below. Does anyone have a clue why it searches for this COR-.info file? Best, Martijn #------------------------------------- /usr/local/freesurfer51/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Feb 22 13:45:42 CET 2012 mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/raw.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/raw.nii.gz... TR=13000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.994366, -0.0972332, -0.0422076) j_ras = (-0.0971699, 0.995259, -0.00408943) k_ras = (-0.0424052, -3.49181e-05, 0.999101) writing to /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz... cp /haso/msteenwj/test_data/V3T/dti/bvecs_old /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs cp /haso/msteenwj/test_data/V3T/dti/bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals flip4fsl /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -2.39997 fslswapdim /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.nii.gz x y z /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.nii.gz INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvecs /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvecs mv -f /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/dwi_orig_flip.mghdti.bvals /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/bvals mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz mri_convert /haso/msteenwj/test_data/V3T/dti/ /haso/msteenwj/test_data/V3T/freesurfer/P1/dmri/b0mag.nii.gz corRead(): can't open file /haso/msteenwj/test_data/V3T/dti/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /haso/msteenwj/test_data/V3T/dti/... Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Feb 22 13:52:47 CET 2012

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Freesurfer and MATLAB
by Antonella Kis 22 Feb '12

22 Feb '12

Dear All, Is there a way that I can open my rh.aparc.stats files (saved in stats after recon-all) in MATLAB as a matrix? I would like to concatenate all the rh.aparc.stats files from all my subjects. Many thanks, Antonella

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Nearst Cortical Label (Annotation) for the CVS space
by Antonella Kis 22 Feb '12

22 Feb '12

Dear Doug, I wonder if you could get the chance to finish the work regarding the Nearest Cortical Label (Annotation) for the CVS space. Also, I have few questions and I will appreciate if anyone can help: 1) Can I get more clusters after I correct for multiple comparison than the number of clusters I have in the uncorrected results? Is this possible? 2)When I change the smoothing from fwhm 10 to fwhm 20 for example why I am loosing from my clusters (uncorrected results)? Also in this case my clusters show became larger no? 3) I found my significant clusters after multiple comparisons for the FA group analysis study and I would like to dilate all regions for a better visualization, using the dilM function of the FSL tool fslmaths.Can you please advise me how to do it if I have the significant clusters file permcsd.sig.cluster.mgh? 4) As I mentioned before,I completed my DTI group analysis at subcortical level on the CVS space and found clusters that survived by multiple comparisons. The results shows that FA is decreasing in patients vs. controls. I used then the same subjects to do a structural group analysis to compare the cortical thickness between the two classes. I found some clusters on the fsaverage but this time they different located then the clusters found in my DTI data. Is this right? I suppose it should be since I compare two different data sets for the same subjects: FA clusters on subcortical CVS space vs. structural data on the fsaverage. I still found that my cortical thickness is decreasing in patients vs. controls but is there any relation that I can established between the two studies? Can I merge my structural results with my subcortical results? I was reading about this on your webpage:http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastG… but I am not sure if in this case the structural analysis is using the same functional data set while in my case I have same subjects but structural data for the structural group analysis and DTI data for the subcortical analysis. Can you please make this a little clear for me? How can I run a structural analysis on my DTI data? Many thanks!Antonella

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tksurfer error
by Signe Bray 22 Feb '12

22 Feb '12

Hi, I have been experiencing an error with tksurfer. It occurs when I am trying to generate an occipital patch, following these instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I open a surface using: tksurfer <SUBJ> lh inflated -curv lh.curv Following the steps, when I click the surface and press the "Fill Uncut Area" button, tksurfer crashes with the following error: tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. I have also experienced this problem zooming out on a specific surface patch. I have seen this problem in different forms on the mailing list, but have not seen any solutions or workarounds: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19846.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.htmlhtt… My machine info: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-8-generic x86_64 --------------------------------------------------------------------- Thank you, Signe

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surface group analysis design matrix question
by Charlotte Bernard 22 Feb '12

22 Feb '12

Dear freesurfer users, I have a question about a design matrx. I have read all your explications about the FSDG file. But I am not sure I can construct the design which corresponds to my study! I have two groups: control and patients. I want to compare their cortical thickness. I have have one continue covariable (age) and three categorial covariable (gender, educational level and laterality). The educational level has five levels. Is it possible to construct such design matrix? Thanks for all, Charlotte

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weird relabeling with mri_convert
by David Grayson 21 Feb '12

21 Feb '12

Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David

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mri_vol2vol not downsampling when applying a morph and a rigid registration matrix
by Alex Kell 21 Feb '12

21 Feb '12

Hi Freesurfers, I am struggling to get mri_vol2vol to downsample when I apply an inverse morph and an inverse registration matrix. Specifically, I am bringing a volume in cvs_avg35 space back into an individual subject's functional space. I have already registered the subject's functional to their anatomical using bbregister and registered the subject's anatomical to cvs_avg35 space using mri_cvs_normalize. Here is the mri_vol2vol call that I am using to move a volume from cvs space to native functional space: mri_vol2vol --targ $roi_in_cvs_space \ --mov $func_vol_file \ --reg-final $bbreg_file \ --inv \ --inv-morph \ --m3z $morph_file \ --o $roi_in_native_func_space \ --interp nearest \ --noDefM3zPath This call seems to register the cvs space to the native functional space accurately -- the mask that I am projecting is in a reasonable position in the functional space. However, the voxel size for this output volume is not the same size as the functional voxels. The voxel size is still the same as the size in cvs space. (Or it could be the anatomical space, since both are 1 mm isotropic.) My question: How do I get mri_vol2vol to downsample? I have no problem getting mri_vol2vol to downsample from native anatomical to native functional by applying the inverse of the bbregister-generated matrix, but I am struggling to get the appropriate downsampling here. Any suggestions? And FYI: I'm using this version of freesurfer: freesurfer-Linux-centos4_x86_64-dev-20120104. Thanks in advance! Best, Alex Kell Kanwisher Lab Manager

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