Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

fsgd file
by Jacobs H (NP) 11 Jul '12

11 Jul '12

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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Combining linear transformations
by Usman Khan 10 Jul '12

10 Jul '12

Hi FreeSurfer, I have two images. One MPRAGE (1x1x1mm) and a T1-weighted (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with hippocampal subfields on the MPRAGE and would now like to transform the posterior probability maps to the T1-weighted CBV space. I have been using 1) mri_vol2vol with --regheader to map the posterior_* subfield files to nu.mgz space 2) mri_robust_register to coregister the nu.mgz file to the T1-weighted CBV image Is there any way to combine the .reg and .lta files from (1) and (2) to transform the subfield posterior probability maps directly from their 0.5mm^3 space to the T1-weighted CBV space? I have been reluctant to create an intermediate volume between steps 1 and 2, as resampling the subfield probability maps into 1x1x1mm nu.mgz space will result in loss of resolution to the 0.68x0.68 (coronal) space in the T1-weighted CBV scan. Any help would be appreciated Usman

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Finding name of labels
by Sam Carpenter 10 Jul '12

10 Jul '12

Hi all, I have a simple problem that hopefully has a simple solution. I'm going through an annotation file, trying to find the names of select labels. In the tksurfer window at the bottom right it displays the name of the label file that the curser window is hovering over, BUT it only displays the first part of the name, does anybody know how to get the full name of a selected or highlighted label within a loaded annotation file? Thanks in advance. -Sam

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WM edit problems
by Charles Frank 10 Jul '12

10 Jul '12

Freesurfer experts, I am having problems generating a corrected wm boundary after editing the wm.mgz volume. After control points were placed and ran with the command autorecon2-cp, I noticed that the yellow line became overzealous and included gm in some of the slices. To fix this I followed the tutorial “fixing Non-white matter classified as white matter”. I fixed all the slices that had the problem in a certain area. However, after running autorecon2-wm and autorecon3 the edits to the wm.mgz volume remain and yellow line does not change....i.e. The edits that were made remained, but had absolutely no effect on the wm boundary. I am using version 5.0. I have included some screen shots of a certain area that was targeted correction. These shots are taken after the data was ran through autorecon2-wm and autorecon3. Any suggestions of what I'm doing wrong would be very appreciated. Thanks Chuck

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(no subject)
by Charles Frank 10 Jul '12

10 Jul '12

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no-aseg for make_average_subject
by Leon 10 Jul '12

10 Jul '12

Hi, FreeSurfer experts I want to generate an average surface and volume using make_average_subject command based on some of my non-human primate data, which do not have aparc.annot data. I wonder if it is possible with FS. From the archive, I found some emails entitled "no seg", in which a --no-seg switch was used and may help on solving this problem. However, from my FS v5.0, I could not find this switch in either the make_average_subject or make_average_surface/volume commands. Could someone tell me how I could turn on this switch and try if it will help to generate a surface without aparc.annot files? Thank you very much in advance! Leon

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nu_correct problem
by rega0026＠umn.edu 10 Jul '12

10 Jul '12

Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on most of my subjects, but for about 10 subjects, I got an error: nu_correct: Command not found I can see on the archive that several others have run into this problem, but I couldn't figure out from the archives what the solution is. I do have perl installed in usr/bin. Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry (612) 273-9825

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Using SPM transformation matrices as initial guess in talairach_avi
by Baudrexel, Simon 10 Jul '12

10 Jul '12

Hello, since I experienced a high rate of registration errors using talairach_avi in the conventional recon-all processing stream (more than 50% misregistration), I would like to incorporate SPM affine registration parameters (as provided in the seg_inv_sn.mat file obtained from the segmentation routine) as initial guess "to help" talairach-avi. Is there a possibility to do this? How do I have to adjust the transformation matrix that it can be handled by freesurfer? I also tried to circumvent the registration-problem using skull-stripped images, which unfortunately also did not improve the results (I think a template made from skull-stripped images has to be used in that case) Any help would be much appreciated Regards, Simon

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multiple correction
by Meng Li 09 Jul '12

09 Jul '12

Hi, freesurfer expert, I have three questions about the multiple correction. I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng

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the color range difference in the scale bar
by Leon 09 Jul '12

09 Jul '12

Hi, FreeSurfer experts I noticed that when I automatically draw the mapped results to the surface using tcl in tksurfer, the color range of the scale bar is not correctly displayed: it has mono blue or red color. This happens only when the range of the overlay is between 0 and 1. I then tested using the same data by opening the overlay in tksurfer GUI interface and then set the min and max in the view -> configure -> overlay, I find the color of the scale bar makes sense in this way (see the right one in the attached figure). I wonder if someone would help me on this. Did I do something wrong? The following is the tcl script I used to draw color bar automatically: I first calculated FS_TKFMAX for the overlay, which is 1 in this case xmax="1" FS_TKFMAX=${xmax} ; export FS_TKFMAX # load the overlay echo " set overlayflag 1 " > ${1}/${fold_base}${net_den}/script.tcl echo " set val ${1}/${fold_base}${net_den}/${hemi}.${meas}.mgh " >> ${1}/${fold_base}${net_den}/script.tcl echo " sclv_read_from_dotw 0" >> ${1}/${fold_base}${net_den}/script.tcl echo " set colscalebarflag 1 " >> ${1}/${fold_base}${net_den}/script.tcl echo " set fthresh 0 " >> ${1}/${fold_base}${net_den}/script.tcl echo "redraw" >> ${1}/${fold_base}${net_den}/script.tcl echo "save_tiff ${1}/${fold_base}${net_den}/${hemi}.${meas}_lateral.tif " >> ${1}/${fold_base}${net_den}/script.tcl tksurfer ${2} ${hemi} inflated -tcl ${1}/${fold_base}${net_den}/script.tcl Thank you very much in advance! Leon

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Freesurfer July 2012