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30086 discussions

mri_surfcluster
by Kelly Silva 19 Mar '10

19 Mar '10

Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly ________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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trio dicom files and mri_convert
by Paige Scalf 19 Mar '10

19 Mar '10

Hello, I've been trying to use mri_convert (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our Siemens Magnetom Trio. When I type: mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img DB*.IMA and Block1.img are the input and output files respectively, I get the output detailed below (the salient error seems to be that mri_convert can't find a useful transformation matrix). Can you tell me what I can do to correct this problem? Many thanks in advance, Paige Scalf mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info. INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = -1610546680 107 DICOM 3.0 files in list Found 107 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 107. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Date and time study date 20100318 study time 160300.312000 series time 162802.453000 acquisition time 162802.453000 Identification patient name DB_A0A1_318 manufacturer SIEMENS Dimensions number of rows 880 number of columns 960 number of frames 107 pixel width 2.13333 pixel height 2.13333 slice thickness 2.1 field of view 1877.33 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 25 repetition time 3000 inversion time not found echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -1027.46 -12.1727 952.833 last image position -1027.46 -12.1727 952.833 image orientation 1 0 0 0 -0.00174528 -0.999998 ------------------------------------------------- TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, 0.00174528, -0.999999) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: -2.133 -0.000 nan nan; -0.000 0.004 nan nan; 0.000 -2.133 nan nan; 0.000 0.000 0.000 1.000;

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mris_anatomical_stats question
by Bruehl, Hannah 19 Mar '10

19 Mar '10

Hi there, I have got 2 questions: 1) is there way to use mris_anatomical_stats to map back the label I have created onto all the subjects in my directory simultaneously? I know there is the "--subject" option but how do I then specify the directory for each individual subject? 2) I tried to do this for an individual subject and got the following error message: [LOE5145MAC:~] bruehh01% mris_anatomical_stats -l lh.CingulateKGvsPTSD.label -t lh.thickness -b -f 66/stats/lh.CingulateKGvsPTSD.stats 66 lh limiting computations to label lh.CingulateKGvsPTSD.label. using thickness file lh.thickness. reading volume /Users/bruehh01/Borderline_2/subjects/66/mri/wm.mgz... reading input surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.white... reading input pial surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.pial... reading input white surface /Users/bruehh01/Borderline_2/subjects/66/surf/lh.white... /Users/bruehh01/Borderline_2/subjects/66/label/lh.CingulateKGvsPTSD.label /Users/bruehh01/Borderline_2/subjects/66/label/lh.CingulateKGvsPTSD.label table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name Bus error Can anyone help? Thanks and greetz, hannah

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mri_aparc2aseg problems
by Alex Fornito 19 Mar '10

19 Mar '10

Hi all, Sorry if this is a re-post, but I¹m not sure if the first one got through. I¹m really stuck on a problem I was hoping to get help with. I¹m having trouble determining the correspondence between ROIs in a surface-based annotation and those in a volume-based annotation generated using mri_aparc2aseg. I have some custom-generated surface annotations and have been using a recently updated binary of mri_aparc2aseg which adds 10,000 to the values of left hemi annotation labels and 20.000 to the right hemi labels in the converted volume, to help distinguish the two hemisphere¹s rois. To check the correspondence between the surface and volume, I chose an roi 10386 from the volume. To check it on the surface I did the following in matlab: [v,l,ct]=read_anntotation('lh.fsavg_500_compact.aparc.annot'); new=zeros(size(v)); new(find(l==ct.table(386,5)))=1; % note the roi index should be 10,000 less that of the volume. F=write_wfile('386.w',new,v); I did this for both the fsaverage surface and a single subject surface, and compared it with the volume representation for the same single subject. The attached pic called vol386 shows the roi in blue, overlaid on the volume parcellation in greyscale. It is located in the left inferior temporal lobe. The attached surf386 pic however, indicates this region is in the retrosplenial cortex for both the single subject (left) and fsaverage (right). Am I missing something here? Have I misunderstood the correspondence between surface and volume rois? Thanks for your help, Alex ------------------------------------------ Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af397(a)cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: fornitoa(a)unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469

2 1

drawing adjacent labels with shared boundaries, and labels near the edge of a patch
by Lindsay Lewis 18 Mar '10

18 Mar '10

hi, I am trying to manually draw a "grid" of many small ROIs/labels on an occipital flattened surface patch in tksurfer, and am having 2 points of confusion: (1) I want my labels to be directly adjacent to each other, but since I am drawing manually, I am not sure how to use the boundary of one label to define the boundary of the adjacent label? (obviously, recreating the shared boundary manually each time will likely not be exactly identical - there could be some voxels accidentally left out between the two labels, or some voxels accidentally common to the two labels) (2) I have some labels I want to extend all the way to the edge of the patch. I keep doing my best to mark the vertex at the very edge, but I keep ending up marking a vertex not all the way at the edge, or slightly out in empty space beyond the patch. I am not sure how to mark the very edge of the patch. If anyone has any advice regarding how to address these two issues, I would very grateful! Many thanks.

2 1

Replicating qdec analysis with more than 2 continuous variables
by Laluz, Victor 18 Mar '10

18 Mar '10

Hello Freesurfer folks, I hope this question is simple to answer: Is there any way to do a surface-based group analysis, a-la qdec, without the limitation of 2 continuous variables? My goal is to analyze a thickness relationship with continuous variable X, which I have so far analyzed controlling for variable Y. However, I ALSO want to control for variable Z. As it is in qdec, it forces me to select only 2 of either X Y and Z. I have tried converting one of the variables to a discrete factor, but the results do not look the same at all. Any advice you can give will be very appreciated; and, as we are currently working under a deadline of sorts, the sooner someone might get back to me the better... as always, I really appreciate the help. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center 415-476-1680 : 415-476-1816 (fax)

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tksurfer and tcl scripting: looping over subjects
by Carrie Niziolek 18 Mar '10

18 Mar '10

Hello all, I've had great success using tcl scripts to loop over surfaces and overlays for a given subject. Are there scripting options for looping over subjects? The problem I see is that the call to tksurfer initializes the subject ("tksurfer subjid lh inflated -tcl myscript.tcl"), and I'm unsure how to change the subjid inside the tcl script. How can I invoke tksurfer inside a tcl script? I found another post asking the same question, but I couldn't find a response: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02344.html One workaround would be to do the loop from the shell, invoking a separate instance of tksurfer for each subject/hemisphere, but in that case I'm unsure how to quit tksurfer from the shell after each call (instead of winding up with dozens of tksurfers running simultaneously). Any advice would be appreciated. Many thanks, Carrie

2 1

research jobs in San Francisco, CA
by Brian Roach 18 Mar '10

18 Mar '10

Dear Freesurfer users, We are hiring for multiple positions in our San Francisco-based schizophrenia brain-imaging EEG research lab. Please visit the links below for additional details: <http://jobs-ncire.icims.com/jobs/1504/job>http://jobs-ncire.icims.com/jobs/1504/job http://jobs-ncire.icims.com/jobs/1505/job Thank you, Brian

1 0

Averaging cortical thickness maps
by Xiaojing Long 18 Mar '10

18 Mar '10

Hi, I have a question regarding how to average cortical thickness maps. I have a dataset with 10 MR brain images and I've run recon-all on each of them. So I've got thickness maps ?h.thickness for each subject. I wonder whether freesurfer provides a tool that can average the cortical thickness maps over the dataset. Thanks. Best, Xiaojing

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showing all slices in freeview
by ythomas 18 Mar '10

18 Mar '10

Hi, is it possible to show all slices (or every N slices) of a volume in freeview in a particular orientation (e.g. axial or coronal)? Thanks, Thomas

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