Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

clusterwise correction, error message
by Sharmili 57 09 Nov '09

09 Nov '09

Dear all, i want to run clusterwise correction for group comparison. I use the following command. mri_glmfit-sim \ --glmdir /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/qdec/averagethichnessdiagnosisFWHM15rh \ --sim mc-z 10000 2 mc-z.abs.2 \ --sim-sign abs \ --overwrite I get the following error message: stem2fname:command not found Could anyone tell me,what's wrong? Thanks for your help sharmili _________________________________________________________________ http://redirect.gimas.net/?n=M0911xAktionswochen Das große Hotmail Gewinnspiel - jetzt Posteingang checken!

2 1

examples of amygdala and hippocampal region definitions
by Wouter Groen 09 Nov '09

09 Nov '09

Hi, a recently investigated hippocampal and amygdala volumes in a patient and control group using Freesurfer. The reviewers appreciate the method (Freesurfer's automated segmentation), but like to see an example of the anatomic definitions: "Please include examples of amygdala and hippocampal region definitions on delineated images, side by side with the gray scale images for several slices in orthogonal planes (sagittal and coronal at least)." I used T1 1x1x1 mm MR images, MPRAGE; TI 850 ms, TR 2250 ms, TE 3.68 ms, flip angle 15 deg, FoV 256x256x176 mm, voxel size 1.0x1.0x1.0 mm. Is there anyone who has some examples? I have been looking on the Wiki and in the published Freesurfer papers, but could not find it. It would help me a lot, Bye, Wouter Groen (The Netherlands) MD PhD _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

2 1

Question on pial surface intersecting wm limits and on qdec
by Hugo Ferreira 09 Nov '09

09 Nov '09

Dear all, I've two questions which I couldn't get answered in your wiki tutorials. I hope you can help me. - I have some processed images that have in the medial part of the brain intersection of the pial matter and the grey matter (see image in attachment). From the tutorial I could only learn about removing dura segmented as pial matter and filling in wm on lesions/ventricles. In my case if I delete voxels I'll loose wm/gm information is there anything I can do? - Also, there are cases where the pial matter does not cover the full gm, particularly at the base of the skull and at the temporal lobes (see attachment). What do you recommend me to do? One thing though is that the annotation seems to be ok (see attachs). So do I really have to correct for the pial and wm surface, as I'm asking above, as I'm interested in studying both cortical thicknesses and subcortical volumes of gm structures, wm and ventricles, or do not have to worry about it? Regarding QDEC, when preprocessing/preparing images for analysis do we have to have all the fsaverage folder together with all the subjects (lets say patients and controls), or can I have the fsaverage folder in two or more subfolders were I have segregated patient subjects and control subjects? This is to ask you also, do the fsaverage folder is changed by the qdec -cache processing or is it used only as a template for each subject (patient and control), and data is only created in patient/control individual subject folders? Many thanks and best regards, Hugo Ferreira

1 0

crop neck
by roberto toro 08 Nov '09

08 Nov '09

Dear Freesurfers, I have some mri volumes with too much neck, and I would like to crop them. I have been trying with mri_convert --cropsize, but it does not work. It seems that --cropsize is cropping around the center, so when I cut the neck I also cut the top of the head... I tried changing the center using -ic, but it doesn't seem to do anything... thank you in advance, roberto

1 0

masking out ROIs on the surface
by Mishkin Derakhshan 07 Nov '09

07 Nov '09

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin

3 5

label,vertex number
by Sharmili 57 07 Nov '09

07 Nov '09

Dear All, I've edited labels in tkmedit using the select voxel tool. I get the following text file,where the vertex numbers are missing. Could anyone tell me what's wrong about my procedure? Thanks!! Sharmili #!ascii label /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/HZM23/label/tfusiform.rh.label , from subject HZM23 vox2ras=TkReg 2356 -1 20.226 -73.900 17.357 76.000000 -1 26.376 -74.371 16.240 73.000000 -1 25.812 -74.475 16.531 96.000000 -1 22.978 -74.475 16.056 85.000000 -1 21.954 -74.177 16.214 80.000000 -1 20.823 -74.173 16.680 86.000000 -1 27.288 -73.821 15.230 75.000000 -1 26.925 -74.244 15.634 87.000000 -1 27.096 -74.204 13.384 82.000000 -1 26.832 -74.296 12.457 86.000000 -1 27.072 -74.564 10.434 83.000000 -1 28.889 -74.342 8.531 97.000000 -1 28.082 -74.475 8.909 97.000000 -1 28.956 -73.995 7.817 90.000000 -1 28.354 -74.134 8.128 88.000000 -1 20.325 -73.028 18.251 72.000000 -1 19.230 -73.321 18.180 72.000000 -1 21.970 -72.985 17.128 83.000000 -1 20.652 -73.330 17.735 88.000000 -1 19.734 -73.720 17.748 94.000000 -1 18.677 -73.793 17.285 76.000000 -1 25.286 -73.686 16.437 72.000000 -1 24.346 -73.645 16.264 83.000000 -1 27.364 -73.206 15.168 71.000000 -1 26.785 -73.293 15.804 92.000000 -1 27.543 -73.226 14.136 93.000000 -1 27.532 -73.228 13.247 91.000000 -1 27.181 -73.512 11.333 88.000000 -1 27.229 -73.676 9.754 86.000000 -1 27.549 -73.459 8.714 95.000000 -1 29.483 -73.407 7.581 98.000000 -1 27.974 -73.237 7.829 92.000000 -1 20.051 -72.119 19.058 80.000000 -1 18.987 -72.236 19.050 78.000000 -1 20.848 -72.230 18.407 77.000000 -1 19.446 -72.730 18.668 97.000000 -1 17.897 -72.272 18.081 78.000000 -1 22.060 -72.463 17.211 80.000000 -1 18.066 -72.863 17.693 90.000000 -1 17.553 -72.280 17.421 70.000000 -1 26.267 -72.892 16.014 80.000000 -1 24.721 -72.934 16.055 84.000000 -1 23.751 -72.489 16.140 89.000000 -1 22.844 -72.680 16.612 99.000000 -1 27.219 -72.189 15.053 81.000000 -1 26.721 -72.437 15.564 101.000000 -1 25.835 -72.298 15.741 95.000000 -1 24.973 -72.336 15.736 95.000000 -1 27.503 -72.341 14.454 89.000000 -1 27.622 -72.593 11.829 94.000000 -1 27.458 -72.810 10.571 78.000000 -1 27.490 -72.643 9.350 78.000000 -1 27.633 -72.404 8.397 88.000000 -1 29.394 -72.668 7.382 81.000000 -1 19.182 -71.629 19.505 100.000000 -1 18.234 -71.621 19.138 91.000000 -1 17.573 -71.190 19.172 77.000000 -1 21.054 -71.677 18.542 95.000000 -1 17.336 -71.497 18.316 83.000000 -1 21.689 -71.718 17.705 98.000000 -1 17.101 -71.716 17.351 90.000000 -1 23.489 -71.642 16.071 74.000000 -1 22.736 -71.573 16.593 95.000000 -1 22.081 -71.202 17.207 85.000000 -1 26.160 -71.728 15.256 75.000000 -1 25.246 -71.765 15.237 80.000000 -1 24.137 -71.575 15.473 75.000000 -1 23.170 -71.059 15.791 87.000000 -1 26.512 -71.330 14.675 97.000000 -1 25.636 -71.251 14.609 97.000000 -1 24.740 -71.271 14.578 98.000000 -1 23.924 -70.929 14.301 89.000000 -1 25.114 -71.047 14.065 90.000000 -1 23.723 -70.748 13.375 88.000000 -1 27.804 -71.610 12.687 85.000000 -1 27.811 -71.423 11.293 86.000000 -1 27.624 -71.678 10.027 91.000000 -1 27.504 -71.634 8.989 91.000000 -1 31.069 -71.465 7.555 82.000000 -1 30.016 -71.417 7.875 80.000000 -1 29.415 -71.200 7.909 88.000000 -1 27.392 -71.280 8.147 84.000000 -1 30.246 -72.113 7.333 82.000000 -1 29.080 -71.665 7.598 94.000000 -1 28.096 -71.441 7.623 90.000000 -1 20.155 -69.900 20.222 76.000000 -1 18.989 -70.283 20.429 69.000000 -1 18.396 -70.391 20.279 76.000000 -1 20.888 -70.221 19.459 77.000000 -1 19.518 -70.859 19.963 89.000000 -1 18.645 -70.964 19.976 82.000000 -1 17.709 -70.602 19.881 90.000000 -1 16.716 -70.225 19.547 86.000000 -1 15.966 -70.112 19.214 82.000000 -1 21.141 -70.538 19.068 85.000000 -1 17.136 -70.882 19.169 89.000000 -1 16.493 -70.740 18.709 101.000000 -1 21.773 -70.707 17.934 94.000000 -1 22.244 -70.306 16.462 87.000000 -1 23.264 -70.702 14.822 80.000000 -1 22.545 -70.351 15.280 101.000000 -1 22.195 -69.839 15.206 86.000000 -1 26.961 -70.899 14.082 82.000000 -1 26.086 -70.790 14.109 82.000000 -1 23.126 -70.569 13.745 81.000000 -1 22.478 -70.291 14.093 90.000000 -1 27.340 -70.664 13.159 71.000000 -1 26.390 -70.341 13.297 88.000000 -1 25.235 -70.600 13.392 83.000000 -1 23.063 -70.595 12.843 83.000000 -1 22.397 -70.345 13.076 90.000000 -1 27.570 -70.412 12.058 97.000000 -1 26.854 -69.926 12.478 79.000000 -1 25.621 -69.762 12.159 75.000000 -1 24.286 -70.510 12.326 83.000000 -1 23.232 -70.622 12.048 83.000000 -1 22.424 -70.433 12.140 95.000000 -1 27.631 -70.468 11.258 97.000000 -1 25.362 -69.636 11.203 82.000000 -1 23.532 -70.444 11.144 97.000000 -1 22.609 -70.455 11.218 102.000000 -1 21.892 -70.163 11.338 93.000000 -1 27.606 -70.752 10.500 93.000000 -1 27.259 -70.320 10.045 84.000000 -1 24.269 -70.074 10.149 93.000000 -1 22.878 -70.268 10.253 93.000000 -1 31.783 -70.160 8.907 86.000000 -1 31.350 -70.319 9.043 73.000000 -1 30.496 -70.386 9.145 75.000000 -1 27.446 -70.906 9.567 69.000000 -1 27.003 -70.374 9.239 89.000000 -1 22.744 -69.934 9.497 84.000000 -1 31.983 -70.489 8.284 73.000000 -1 29.649 -70.679 8.505 93.000000 -1 28.813 -70.462 8.269 75.000000 -1 27.284 -70.916 8.767 77.000000 -1 20.031 -69.468 20.453 67.000000 -1 19.332 -69.460 20.603 89.000000 -1 20.697 -69.562 19.920 94.000000 -1 17.206 -69.284 20.041 85.000000 -1 16.178 -69.382 19.514 95.000000 -1 22.277 -69.013 18.075 82.000000 -1 21.689 -69.600 18.629 99.000000 -1 22.386 -69.080 17.160 83.000000 -1 22.077 -69.704 17.479 88.000000 -1 22.359 -69.005 16.261 86.000000 -1 22.016 -69.430 14.458 89.000000 -1 26.939 -69.696 11.204 77.000000 -1 26.053 -69.524 11.007 73.000000 -1 31.805 -69.156 9.839 88.000000 -1 31.412 -69.212 10.040 77.000000 -1 25.759 -69.665 9.879 78.000000 -1 24.772 -69.804 9.860 84.000000 -1 22.224 -69.955 9.878 86.000000 -1 32.588 -69.306 9.028 89.000000 -1 30.959 -69.857 9.702 92.000000 -1 29.843 -69.694 9.583 93.000000 -1 28.988 -69.398 9.179 79.000000 -1 26.342 -69.972 8.993 84.000000 -1 25.443 -69.656 9.006 83.000000 -1 24.284 -69.649 9.156 86.000000 -1 22.185 -69.530 9.118 80.000000 -1 21.442 -68.983 9.179 83.000000 -1 29.084 -70.011 8.788 88.000000 -1 28.308 -69.721 8.422 85.000000 -1 27.428 -69.539 8.058 89.000000 -1 25.251 -69.245 8.608 97.000000 -1 24.091 -69.110 8.690 95.000000 -1 22.983 -69.018 8.536 95.000000 -1 22.029 -68.746 8.609 90.000000 -1 21.510 -68.427 8.755 89.000000 -1 21.115 -68.756 19.998 83.000000 -1 19.881 -68.696 20.658 91.000000 -1 18.094 -68.326 20.358 80.000000 -1 22.284 -68.177 19.159 74.000000 -1 21.543 -68.734 19.488 91.000000 -1 17.276 -68.212 19.957 89.000000 -1 23.274 -68.144 18.236 78.000000 -1 22.730 -68.309 18.564 92.000000 -1 24.155 -68.080 17.078 82.000000 -1 23.536 -68.256 17.542 91.000000 -1 22.848 -68.622 17.756 98.000000 -1 24.318 -68.194 16.140 79.000000 -1 22.850 -68.694 16.814 96.000000 -1 24.432 -68.057 15.163 83.000000 -1 22.700 -68.702 15.689 98.000000 -1 22.317 -68.954 15.455 86.000000 -1 24.540 -67.962 14.330 93.000000 -1 23.034 -68.515 14.610 98.000000 -1 24.256 -68.116 13.848 83.000000 -1 22.599 -68.653 13.631 99.000000 -1 23.087 -68.435 12.613 75.000000 -1 22.253 -68.756 12.556 87.000000 -1 21.772 -69.243 12.295 90.000000 -1 22.620 -68.380 11.744 81.000000 -1 21.995 -68.682 11.449 95.000000 -1 32.417 -68.316 9.840 79.000000 -1 31.012 -68.510 10.535 103.000000 -1 30.047 -68.644 10.430 81.000000 -1 21.312 -68.831 9.815 84.000000 -1 29.255 -68.740 9.846 93.000000 -1 21.302 -68.369 9.181 82.000000 -1 27.934 -68.700 8.597 94.000000 -1 27.131 -68.691 8.290 84.000000 -1 26.162 -68.623 8.295 85.000000 -1 25.085 -68.452 8.540 95.000000 -1 23.942 -68.306 8.576 95.000000 -1 22.854 -68.149 8.524 95.000000 -1 21.213 -68.225 20.160 72.000000 -1 20.539 -67.993 20.541 100.000000 -1 19.736 -67.768 20.669 89.000000 -1 18.881 -67.584 20.458 69.000000 -1 23.566 -67.251 18.928 88.000000 -1 21.966 -67.578 19.698 94.000000 -1 18.475 -67.200 20.128 89.000000 -1 16.925 -67.582 19.435 70.000000 -1 16.039 -67.844 19.291 76.000000 -1 25.347 -67.109 18.011 77.000000 -1 23.891 -67.480 18.487 69.000000 -1 16.385 -67.283 18.974 92.000000 -1 25.879 -67.089 17.198 83.000000 -1 24.571 -67.662 17.679 101.000000 -1 24.910 -67.849 16.843 89.000000 -1 26.389 -66.707 15.965 80.000000 -1 25.946 -67.167 15.497 83.000000 -1 25.110 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19.241 -66.330 20.021 90.000000 -1 17.578 -66.870 19.218 75.000000 -1 16.922 -66.985 18.890 86.000000 -1 26.044 -66.423 17.961 79.000000 -1 25.593 -66.674 18.111 92.000000 -1 24.517 -66.542 18.807 99.000000 -1 18.049 -66.353 18.844 95.000000 -1 26.630 -66.311 16.509 88.000000 -1 26.638 -66.203 15.270 89.000000 -1 26.510 -65.904 14.051 95.000000 -1 26.233 -66.492 14.329 76.000000 -1 25.956 -66.333 13.332 84.000000 -1 25.460 -66.926 13.135 79.000000 -1 25.240 -66.588 12.374 88.000000 _________________________________________________________________ http://redirect.gimas.net/?n=M0911xMSWin72 Windows 7 - jetzt upgraden!

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Postdoctoral offer - Neuroimaging - Paris (3 to 5 years)
by Olivier Colliot 07 Nov '09

07 Nov '09

Dear colleagues, The French government is offering a long-term postdoctoral position in the field of neuroimaging of Alzheimer's disease. The position is opened for 3-5 years with a competitive salary (50,000 to 60,000 euros). (please see attached document) Our team is looking for a researcher in the field of neuroimaging who would be interested in applying to this proposal, with the support of our lab. Experience in Alzheimer's disease is not a requirement. The laboratory (at the CRICM - Institute of Brain and Spine) is a recently established research center at the heart of the Pitié-Salpetriere hospital, the largest hospital in Europe. It is part of the University Pierre and Marie Curie (Paris 6), one of the leading French universities and includes over 200 researchers in neuroscience. If you are interested, please email me at olivier.colliot(a)upmc.fr Best regards Olivier Colliot -- Olivier Colliot COGIMAGE - CRICM +33 6 14 44 38 72 +33 1 42 17 85 20 http://cogimage.dsi.cnrs.fr/perso/colliot

1 0

whole brain vol and gray matter vol
by Ritobrato Datta 06 Nov '09

06 Nov '09

Hello After recon-all, if I want the whole brain vol and gray matter vol for the whole brain, which values should I be using and in which files in the stats folder ? Thanks Rito

2 1

aparcstats2table
by Dana W. Moore 06 Nov '09

06 Nov '09

Hi, I was very excited to read in the release notes that the aparcstats2table command had been updated so that the output will always be in the same order. This is an issue for me, as I have a spreadsheet that I like to paste new subjects into. However, I have just tried to do so, and was disappointed to find that the output was in a different order from my original spreadsheet. (This has all been done with v4.5.0, so it's not that I switched versions and then expected it to be in the same order.) Is there a command I can use to make it come out in the same order? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

1 0

(no subject)
by Zaman, Arshad 06 Nov '09

06 Nov '09

Please can you remove me from the email listing thanks, Arshad Zaman

1 0

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Freesurfer November 2009