Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Rerunning aseg.stats
by Andrew Jahn 26 Oct '09

26 Oct '09

Hello, I recently ran a batch file which seemed to run fine for nearly all the participants. Yet, when I did an asegstats2table command on all the subjects, I received the following error for three of them: WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL11_2009E/stats/aseg.stats. proceeding to next file WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009C/stats/aseg.stats. proceeding to next file WARNING: cannot find /nfs/01/osu5323/freesurfer/freesurfer/subjects/JUL12_2009G/stats/aseg.stats. proceeding to next file I checked the status of /scripts/recon-all-status.log, and it said that recon-all finished without errors. Would I want to only rerun step 11 of the recon-all workflow, which is Aseg volumetric labeling and statistics? Thank you, -Andrew

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Problems converting annots
by Alex Fornito 26 Oct '09

26 Oct '09

Hi all, Sorry to keep pressing this issue, but I am really stuck and need to sort this out before I can progress. I have been generating some customised annotation files, generally with 500 or more ROIs. The parcellation is done on a per hemi basis, meaning that there will not always be the same number of rois in each hemi (e.g., left may have 540, right may have 603). I have tried using mri_label2vol to convert the annots into volumes, but I often run into memory problems (see second error below). On a recent posting, it was suggested that I use mri_aparc2aseg. This seemed to work, but only for one hemi. That is, I find that the left hemisphere is parcellated correctly, but the the entire right cortex is assigned just one intensity label (2000). I have tried using a label file with many more regions that there actually are (e.g., 5000), but this made no difference. I'm guessing the problem arises because I have a different number of regions in each hemi (?). The output for one trial is below. Can anyone suggest a workaround for this problem? Thanks, Alex ---------------------------- Mri_aparc2aseg error ---------------------------- 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 ------------------------------ mri_label2vol error ------------------------------ mri_label2vol --annot 1002593/label/fsavg_lh_500_compact.aparc.annot --identity --temp 1002593/mri/orig.mgz --subject 1002593 --hemi lh --o output.nii Number of labels: 0 Annot File: 1002593/label/fsavg_lh_500_compact.aparc.annot Template Volume: 1002593/mri/orig.mgz Outut Volume: output.nii Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: 1002593 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.25.2.3 2009/06/09 16:22:30 greve Exp $ Template RAS-to-Vox: -------- -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; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -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; INFO: loading surface /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.white nvertices = 143248 Reading thickness /work/imaging5/af397/twins/freesurfer/1002593/surf/lh.thickness Loading annotations from 1002593/label/fsavg_lh_500_compact.aparc.annot reading colortable from annotation file... colortable with 596 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2 005.txt) annotidmax = 595 Allocating Hit Volume (1392508928) voxels MRIalloc(256, 256, 256): could not allocate 131072 bytes for 22406th slice Cannot allocate memory

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exited with errors
by Ali Radaideh 26 Oct '09

26 Oct '09

Dear Freesurfer experts, I was running freesurfer in a normal way as usual but unfortunately I got the following error. This is the first time I see this error. Any ideas, please? Many thanks in advance Ali Reporting on 48 segmentations #-------------------------------------------- #@# Cortical ribbon mask rh Sun Oct 25 06:18:23 GMT 2009 /data_local/olivier/qCEST/study/freesurfer/subjects/subject02/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance subject02 mris_volmask.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Linux comp14 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sun Oct 25 06:18:25 GMT 2009 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Difference between t-test within 3 group ANOVA and separate t-test
by Alex Millner 23 Oct '09

23 Oct '09

Hi - Thanks for your help. I have 3 groups and am trying to run an ANOVA and series of t-tests. First, I ran mri_glmfit with two rows in my .mat file (1 -1 0, 1 0 -1) for the ANOVA. Then, before I ran into this webpage https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples, to do a follow up t-test between group 1 and group 2, I tried to mri_glmfit with a mat file of 1 -1 but it gave me an error because it was expecting any test to include all the subjects. So reran isxconcat-sess with subjects from just groups 1 and 2, and ran mri_glmfit with a mat file of 1 -1 Then I found the FSGD Examples webpage and realized I could perform all the tests in one command as long as I included a 0 in my mat file. So for the contrast between groups 1 and 2, I made a mat/mtx file with 1 -1 0. My question is, why are my results from these two similar analyses very different from each other? There are many more activations in the 1 -1 0 version than in the 1 -1 version and the activations that do exist are, for the most part, in different areas of the brain. Sorry to be ignorant of some of the statistics/analysis differences that are taking place here. I wondered why it was different and which was a more valid analysis. It seems like doing one analysis with all the tests is a better way to go then divided the data up, but I just wanted to check. Thanks again for your help, Alex Below are the mri_glmfit commands I used Directory PDSubsONLY = contains output of isxconcat-sess run on placebo and drug subjects only Directoy Analysis_Results = contains output of isxconcat-sess run all 3 subjects groups mri_glmfit --y PDSubsONLY_Results/RSF_v_NIF/tal.ces.nii --fsgd FSGD_Placebo_v_Drug.txt --C Placebo_v_Drug.mat --mask PDSubsONLY_Results/tal.mask.nii --glmdir Analysis_Results/tal.wrfx.RSF_v_NIF --nii --wls PDSubsONLY_Results/RSF_v_NIF/tal.cesvar.nii mri_glmfit --y Analysis_Results/RSF_v_NIF/tal.ces.nii --fsgd FSGD_Placebo_v_Drug_v_Control.txt --C mtx_files/placebo-drug.mtx --C mtx_files/placebo-control.mtx --C mtx_files/drug-control.mtx --C mtx_files/group_effect.mtx --C mt x_files/placebo-drug+control.mtx --C mtx_files/placebo+drug-control.mtx --mask Analysis_Results/tal.mask.nii --glmdir Analysis_Results/tal.wrfx.RSF_v_NIF --nii --wls Analysis_Results/RSF_v_NIF/tal.cesvar.nii Placebo_v_Drug.mat = 1 -1 mtx_files/placebo-drug.mtx = 1 -1 0 FSGD_Placebo_v_Drug.txt = contains only placebo and drug subjects FSGD_Placebo_v_Drug_v_Control.txt = contains placebo, drug and control subjects

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Analysis using a custom template
by Cathy Scanlon 22 Oct '09

22 Oct '09

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

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Re: [Freesurfer] optseq2 questions
by 杨宏宇 22 Oct '09

22 Oct '09

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? ...... ...... 819.0000 5 13.000 1.0000 diamond 832.0000 0 5.000 1.0000 NULL 837.0000 2 13.000 1.0000 star 850.0000 0 5.000 1.0000 NULL 855.0000 2 13.000 1.0000 star 868.0000 0 5.000 1.0000 NULL 873.0000 3 14.000 1.0000 star 887.0000 0 6.000 1.0000 NULL 893.0000 4 12.000 1.0000 diamond 905.0000 0 35.000 1.0000 NULL > > On Tue, Oct 20, 2009 at 11:59 AM, Douglas N Greve < > greve(a)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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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 >> >> >> >

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FSfast - excluding time points from my analysis
by Maximilien Chaumon 22 Oct '09

22 Oct '09

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

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freesurfer segmentation label
by Frida Polli 22 Oct '09

22 Oct '09

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: fpolli(a)mit.edu tel: (617) 324 2897

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lGI value aberrantly high
by Prapti Gautam 22 Oct '09

22 Oct '09

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

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How to flip a surface model?
by Jürgen Hänggi 22 Oct '09

22 Oct '09

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. ----------------------------------------------------------------------------

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