[Freesurfer] stats
Dear Doug, I have a question: when I create the stats tables, there are two tables: lh.aparc.a2005s.thickness.stats and lh.aparc.thickness.stats which one is the right one if I want to get the thickness values of the significant clusters from the main effect (pat. / controls)? Thanks and best regards, Viola ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] nu_correct problem
Hello, I have got the following problem: if I want to load the qdec.table.dat, I get the following message: ERROR: 0xbfd96154 is invalid. Must have at least two levels. Attached is the table and the levels files. Do you know what is wrong? Best regards, Viola Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Nick Schmansky [ni...@nmr.mgh.harvard.edu] Gesendet: Dienstag, 10. Juli 2012 14:07 Bis: Christopher Bell Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] nu_correct problem Chris, This is an unusual error. I dont know why nu_correct would be found for some subjects but not others, if its being run on the same platform. I can only think this is a network issue. Is it replicable? nu_correct can be run from the command line. The intensity normalization issues in v5.1 are related to a change in 5.1 where talairach was run before nu_correct, which doesnt seem to work as well as when run before. this is being changed for v5.2. Nick I believe this post slipped through the cracks. Anyone have any thoughts on this nu_correct error. Some subjects ran fine, so it seems to be an intermittent problem and not an installation problem. Also, is this possibly related to the avi_talairach/intensity normalization issues being discussed in another post? Chris Bell University of Minnesota On Thu, May 31, 2012 at 12:13 PM, rega0...@umn.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferm wpatient controleID gender age diagnosis education TMT BDI BRMAS WMT wemam 45 patient 15 37 11 5 30 essem 40 patient 16 40 9 6 28 mefrm 35 patient 14 35 12 4 32 amkam 47 patient 15 36 10 7 30 wiebm 43 patient 16 31 11 3 31 webem 46 patient 15 40 12 4 29 gestm 41 patient 15 29 10 5 30 paxma m 37 patient 13 47 1 0 28 pchho w 32 patient 18 25 1 0 27 pcldo w 37 patient 15 23 20 0 33 phabe m 63 patient 16 43 4 0 34 phaho m 50 patient 17 31 26 0 34 phama m 49 patient 18 34 5 1 31 phewi w 33 patient 18 43 16 0 33 pirgr w 45 patient 14 48 21 0 31 pkiwe w 57 patient 17 58 20 0 27 pklhe m 60 patient 18 35 5 5 34 pklru m 65 patient 18 40 1 1 32 pmaha w 50 patient 15 28 0 0 33 pmobi w 61 patient 13 36 2 6 29 pvian w 40 patient 17 35 34 10 33 pyvbr w 33 patient 15 56 17 3 26 przlpu m 40 patient 13 40 26 0 27 franm
[Freesurfer] correction
Dear Freesurfers, could you please give me detailed information about the Bonferroni or clusterwise correction we can do in Freesurfer? How much iterations? Is that cluster- oder voxelwise? Is there anywhere a detailed description about the correction options? Best regards, Viola ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Masks
Dear Freesurfer-user, I have a general question: if I created a activation mask during a fMRI task with Brainvoyager software, which works with talairach space. Is it possible, and do you know how, to transform the Talairach space mask into the Freesurfer analysis? Thanks, Christian Dr. Viola Oertel-Knöchel Laboratory of Neuroscience Arbeitsgruppe Schizophrenie Department of Psychiatry, Psychosomatic Medicine and Psychotherapy University of Frankfurt Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Ruopeng Wang Gesendet: Di 25.01.2011 15:20 An: t...@ms36.hinet.net Cc: freesurfer Betreff: Re: [Freesurfer] color scale bar in freeview Hi, I can send you our latest development build if you want to give it a try. Please let me know what system you are running freesurfer on. Best, Ruopeng On 1/25/11 9:05 AM, Ruopeng Wang wrote: Hi, The current freeview release does not have that option. However, we've added the option in our development code. It should be available soon. Ruopeng On 1/25/11 3:47 AM, t...@ms36.hinet.net wrote: Dear Freesurfer experts, I use freeview to display the cortical thickness. Is it possible to change the color map in color scale bar ? how to make the color map such as use jet color ? thanks in advance JLH --- ?HiNet WebMail --- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mri_label2vol memory error
Dear all, can you tell me what command you use if you want to develop an average brain (myaverage)? Thanks, Viola Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Alex Fornito Gesendet: Do 22.10.2009 14:34 An: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Mri_label2vol memory error Hi again, I have noticed that the standard freesurfer annots have the same number of regions in each hemi. In my annot, I have different numbers; e.,g 1171 in the left and 1187 in the right. Is this what's causing the output of mri_aparc2aseg to label all right hemi cortical voxels with a 2000 (output below)? Is there a way around this; e.g., by running mri_aparc2aseg on a per hemi basis? I tried generating new annot-tables with either the same number of rois as my parcellation or with an arbitrarily high number (e.g., 5000) of rois, but this made no difference to the output. Thanks again, Alex On 21/10/2009 12:27, Alex Fornito forni...@unimelb.edu.au wrote: Hi again, After running the command, the output image seems to have the left hemi cortex parcellated, but the right is all assigned one intensity (2000). Is there something I'm missing? Output below. Thanks again, Alex mri_aparc2aseg --s fsaverage --rip-unknown --annot 1000_compact.aparc --volmask --o test.nii SUBJECTS_DIR /Users/alexfornito/Alex_Docs/MRI_data/freesurfer subject fsaverage outvol test.nii useribbon 0 baseoffset 0 RipUnknown 1 Reading lh white surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/lh.white.avg.area.mgh Reading lh pial surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/lh.pial reading group avg surface area 1041 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/lh.pial.avg.area.mgh Loading lh annotations from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa verage/label/lh.1000_compact.aparc.annot reading colortable from annotation file... colortable with 1171 entries read (originally /autofs/space/birn_044/users/chris tophe_atlas_rebuild/Simple_surface_labels2005.txt) Reading rh white surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.white reading group avg surface area 822 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/rh.white.avg.area.mgh Reading rh pial surface /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/surf/rh.pial reading group avg surface area 1043 cm^2 from file Reading in average area /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsavera ge/surf/rh.pial.avg.area.mgh Loading rh annotations from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsa verage/label/rh.1000_compact.aparc.annot reading colortable from annotation file... colortable with 1187 entries read (originally /autofs/space/birn_044/users/chris tophe_atlas_rebuild/Simple_surface_labels2005.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/alexfornito/Alex_Docs/MRI_data/freesurfe r/fsaverage/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 110 vertices from left hemi Ripped 90 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/alexfornito/Alex_Docs/MRI_data/freesurfer/fsaverage/mri /aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 337762 Used brute-force search on 0 voxels Writing
Re: [Freesurfer] How to flip a surface model?
Dear all, unfortunately, I have the problem with the creation of my average brain. The command is: make_average_subject subjects1 ... --out myaverage. During the creation of my average brain with freesurfer, I get the following ERROR message. getpwdcmd: command not found ERROR: format for rh.orig.avg.area.mgh not recognized. ERROR: make_average_surface Would you be so kind and help me with the solution for this problem? Thanks and yours sincerely, Viola -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N Greve Gesendet: Mi 21.10.2009 18:38 An: Jürgen Hänggi Cc: Freesurfer Mailinglist Betreff: Re: [Freesurfer] How to flip a surface model? I have some preliminary tools in development, but they are not ready to be released. There are some very tricky aspects to this that we need to make sure are correct. doug Jürgen Hänggi wrote: Dear FS experts We investigated patients with unilateral pain. For some patients, the pain was on the left side, for others it was on the right side. We would like to do a group analysis on cortical thickness maps vertex-wisely but we do not know whether it is possible to flip a surface model (e.g. the left cortical thickness map) so that we can pool patients with pain on the left with the patients who have pain on the right. Is there an easy way to do this? Thanks in advance Regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
