Re: [Freesurfer] lGI value aberrantly high
Dear Prapti, Which version of freesurfer do you use? Have you carefully checked that your surfaces are anatomically correct? (i.e. follow accurately the cortical mantle without gross abnormality) Marie Quoting Prapti Gautam prapti.gau...@anu.edu.au: Dear freesurfers, I have a problem running localGI in one subject. I previously got an error message that said that one of the vertex value was aberrantly high. The mris euler number on the subject was fine - but I relaunched the recon-all -autorecon2 -autorecon3 for the hemisphere in question and tried re-running the localGI command since this has been previously suggested as a fix to the problem. However, I get the same message (aberrantly high lGI value) even after re-running autorecon2 and autorecon3. Is there anything else I can try to complete lGI successfully? Thanks for your help, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 output aseg to test.nii On 20/10/2009 18:11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I just created a ribbon.mgz (link below). Copy this into fsaverage/mri and see if it works. doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ribbon.mgz Alex Fornito wrote: Thanks, that did the trick. The
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] lGI value aberrantly high
Prapti, Also beginning with version 4.5.0, the random number generator is at a fixed seed value, so re-running will result in exactly the same surface. For this particular lGI problem, you can try adding the flag -randomness to the end of the recon-all stream with -autorecon2 -autorecon3, and a slightly different surface vertex combination will result, which might allow -localgi to succeed. Nick On Thu, 2009-10-22 at 12:54 +0200, Marie Schaer wrote: Dear Prapti, Which version of freesurfer do you use? Have you carefully checked that your surfaces are anatomically correct? (i.e. follow accurately the cortical mantle without gross abnormality) Marie Quoting Prapti Gautam prapti.gau...@anu.edu.au: Dear freesurfers, I have a problem running localGI in one subject. I previously got an error message that said that one of the vertex value was aberrantly high. The mris euler number on the subject was fine - but I relaunched the recon-all -autorecon2 -autorecon3 for the hemisphere in question and tried re-running the localGI command since this has been previously suggested as a fix to the problem. However, I get the same message (aberrantly high lGI value) even after re-running autorecon2 and autorecon3. Is there anything else I can try to complete lGI successfully? Thanks for your help, Prapti ___ 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
Re: [Freesurfer] Mri_label2vol memory error
make_average_subject On Thu, 22 Oct 2009, Oertel, Viola wrote: 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
[Freesurfer] FSfast - excluding time points from my analysis
Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] optseq2 questions
Hi Doug, I reduced the total time points, however, I found the eff and VRF value all became smaller as the time points decreased, and I still got some null events more than 7s. If I set the time points as 470s, I got most 5-7 null events, except the last 35s null event, and then its eff is 0.007, and VRFAvg is 1.7. Compared with 500 time points (eff 0.01, VFRAvg 2.58), 470s is bad design. From one paper, I learned that exponential distribution produced less variance compared with unity distribution, and maybe optseq2 likes exponential distribution more, so can I use the 470s design without the last 35s null events? Is the value of eff and VFRAvg OK? .. .. 819.5 13.000 1. diamond 832.05.000 1. NULL 837.2 13.000 1. star 850.05.000 1. NULL 855.2 13.000 1. star 868.05.000 1. NULL 873.3 14.000 1. star 887.06.000 1. NULL 893.4 12.000 1. diamond 905.0 35.000 1. NULL On Tue, Oct 20, 2009 at 11:59 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think this is partially a bug in optseq and partially a problem with your design. You have a total amount of stimulation time = 12*9+13*8+14*8+12*9+13*8+14*8 = 648 sec. Your run lasts 500*2 = 1000 sec, so the total amount of fixation time is 1000-648 = 352 sec. You have 8*4+9*2 = 50 stimuli, so the average time between stimuli (ie, average null) will be 352/50 = 7.04s. Yet you have constrained optseq to give you nulls between 5 and 7 sec. You need to relax this constraint or reduce the total number of time points. doug 杨宏宇 wrote: Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2 events, which last for 12,13, and 14s. I found that the schedule documents I got had many null events more than 7s, however, I have set the maximam as 7s. In the sum logfile, I found that my script was recorded correctly, so could you please tell me the reason, and how to solve the problem? Many thanks, Hongyu Division on Addiction, Psychiatry Department, UT Southwestern Medical Center ___ 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
Re: [Freesurfer] FSfast - excluding time points from my analysis
Sent that earlier but seems like it didn't post. Sorry if it's a second posting. Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Re: [Freesurfer] optseq2 questions
Hi Doug, I figure out why this happened and how to solve the problem. Because My trials always lasted for 12,13,14s, and optseq2 believed that the baseline should last about 12-14s, which means null time should be as many as one task condition or the average of the task conditions. I set my trials as 5,6,7s, revised the time points, then I got very good sequence. I think now I need to do is to change the trial duration back and recode the time line. On Thu, Oct 22, 2009 at 10:31 AM, 宏宇 yanghy...@gmail.com wrote: Hi Doug, I reduced the total time points, however, I found the eff and VRF value all became smaller as the time points decreased, and I still got some null events more than 7s. If I set the time points as 470s, I got most 5-7 null events, except the last 35s null event, and then its eff is 0.007, and VRFAvg is 1.7. Compared with 500 time points (eff 0.01, VFRAvg 2.58), 470s is bad design. From one paper, I learned that exponential distribution produced less variance compared with unity distribution, and maybe optseq2 likes exponential distribution more, so can I use the 470s design without the last 35s null events? Is the value of eff and VFRAvg OK? .. .. 819.5 13.000 1. diamond 832.05.000 1. NULL 837.2 13.000 1. star 850.05.000 1. NULL 855.2 13.000 1. star 868.05.000 1. NULL 873.3 14.000 1. star 887.06.000 1. NULL 893.4 12.000 1. diamond 905.0 35.000 1. NULL On Tue, Oct 20, 2009 at 11:59 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I think this is partially a bug in optseq and partially a problem with your design. You have a total amount of stimulation time = 12*9+13*8+14*8+12*9+13*8+14*8 = 648 sec. Your run lasts 500*2 = 1000 sec, so the total amount of fixation time is 1000-648 = 352 sec. You have 8*4+9*2 = 50 stimuli, so the average time between stimuli (ie, average null) will be 352/50 = 7.04s. Yet you have constrained optseq to give you nulls between 5 and 7 sec. You need to relax this constraint or reduce the total number of time points. doug 杨宏宇 wrote: Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2 events, which last for 12,13, and 14s. I found that the schedule documents I got had many null events more than 7s, however, I have set the maximam as 7s. In the sum logfile, I found that my script was recorded correctly, so could you please tell me the reason, and how to solve the problem? Many thanks, Hongyu Division on Addiction, Psychiatry Department, UT Southwestern Medical Center ___ 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] fsaverage to mni152
Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] lGI value aberrantly high
Hi Marie, I'm using version 4.3.1. I've relaunched recon-all -all for the hemisphere, hopefully this will solve the problem, Thanks, Prapti -Original Message- From: Marie Schaer [mailto:marie.sch...@unige.ch] Sent: Thursday, 22 October 2009 9:54 PM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] lGI value aberrantly high Dear Prapti, Which version of freesurfer do you use? Have you carefully checked that your surfaces are anatomically correct? (i.e. follow accurately the cortical mantle without gross abnormality) Marie Quoting Prapti Gautam prapti.gau...@anu.edu.au: Dear freesurfers, I have a problem running localGI in one subject. I previously got an error message that said that one of the vertex value was aberrantly high. The mris euler number on the subject was fine - but I relaunched the recon-all -autorecon2 -autorecon3 for the hemisphere in question and tried re-running the localGI command since this has been previously suggested as a fix to the problem. However, I get the same message (aberrantly high lGI value) even after re-running autorecon2 and autorecon3. Is there anything else I can try to complete lGI successfully? Thanks for your help, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer segmentation label
in the segmentation, what does ventral dc stand for? thanks! -- Frida E. Polli, PhD Postdoctoral Fellow Brain Cognitive Sciences, MIT 43 Vassar St., Room 46-4033 Cambridge, MA 02139 email: fpo...@mit.edu tel: (617) 324 2897 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer segmentation label
ventral diencephalon. It's a grab-bag of a bunch of different structures in that region that we don't really have the contrast or resolution to see On Thu, 22 Oct 2009, Frida Polli wrote: in the segmentation, what does ventral dc stand for? thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSfast - excluding time points from my analysis
Use a time point exclude file. doug Maximilien Chaumon wrote: Hi Freesurfers, I would like to be able to regress out specific time points from my functionals using FSfast. I thought I should do it with the -extreg option to mkanalysis-sess but I don't know how to create the required extregstem_000.bfloat file. How can I create this file? Thanks, Max ___ 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
Re: [Freesurfer] optseq2 questions
I think your constraint of 5-7 null time is too tight for optseq, and you may still have too much time in your run to make 5-7 work. It's hard to say whether the VRFAvg is good enough or not. You are using sub-TR estimation during the optimization. If you are going to assume a shape to the HRF, then it's probably fine. If you are going to use an FIR, then you'd need about 7 runs or so. doug 杨宏宇 wrote: Hi Doug, I reduced the total time points, however, I found the eff and VRF value all became smaller as the time points decreased, and I still got some null events more than 7s. If I set the time points as 470s, I got most 5-7 null events, except the last 35s null event, and then its eff is 0.007, and VRFAvg is 1.7. Compared with 500 time points (eff 0.01, VFRAvg 2.58), 470s is bad design. From one paper, I learned that exponential distribution produced less variance compared with unity distribution, and maybe optseq2 likes exponential distribution more, so can I use the 470s design without the last 35s null events? Is the value of eff and VFRAvg OK? .. .. 819.5 13.000 1. diamond 832.05.000 1. NULL 837.2 13.000 1. star 850.05.000 1. NULL 855.2 13.000 1. star 868.05.000 1. NULL 873.3 14.000 1. star 887.06.000 1. NULL 893.4 12.000 1. diamond 905.0 35.000 1. NULL On Tue, Oct 20, 2009 at 11:59 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think this is partially a bug in optseq and partially a problem with your design. You have a total amount of stimulation time = 12*9+13*8+14*8+12*9+13*8+14*8 = 648 sec. Your run lasts 500*2 = 1000 sec, so the total amount of fixation time is 1000-648 = 352 sec. You have 8*4+9*2 = 50 stimuli, so the average time between stimuli (ie, average null) will be 352/50 = 7.04s. Yet you have constrained optseq to give you nulls between 5 and 7 sec. You need to relax this constraint or reduce the total number of time points. doug 杨宏宇 wrote: Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2 events, which last for 12,13, and 14s. I found that the schedule documents I got had many null events more than 7s, however, I have set the maximam as 7s. In the sum logfile, I found that my script was recorded correctly, so could you please tell me the reason, and how to solve the problem? Many thanks, Hongyu Division on Addiction, Psychiatry Department, UT Southwestern Medical Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- 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
Re: [Freesurfer] fsaverage to mni152
Use $FREESURFER_HOME/average/mni152.register.dat and mri_vol2vol with --inv Yigal Agam wrote: Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal ___ 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] Analysis using a custom template
Hi, I have a question regarding group analysis using a custom template. I have created a custom template using mris_make_template as described http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates I then registered all my study subjects (that have previously been run through recon-all) to this new template using mris_register and named the spherical registration ?h.sphere.reg for each subject. I want to conduct a group analysis of cortical thickness. So my question is do I need to rerun autorecon3 or any subset of it (e.g. ?h.avg_curv) that might affect my analysis or creation of the 'average subject'? All the best, Cathy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
