Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

wiki problem
by Liat Levita 10 Jun '08

10 Jun '08

I am sure you are aware of this problem, but since last week we have been unable to access the FreeSurfer wiki (http://surfer.nmr.mgh.harvard.edu/docs/index.html) Is it down for maintenance? and if so when will it be up again? I have just started using FreeSurfer, hence having major problems without the freesurfer wiki to guide me along. Thank you so much for you help. L

3 2

White Matter Regional Volumes
by hranilovich＠ucla.edu 10 Jun '08

10 Jun '08

My name is Jennifer as well, and I work in the same lab as Jennifer Bramen, who originally wrote to you, below. I am writing while she's out of town to follow up on your reply below. Mainly, I am a little confused by your suggestion to use asegstats2table command, because the resultant text file when this command is run on the wmparc.mgz file is not openable in excel - it has too many columns/is too large. Unfortunately, the --maxsegno flag is not helpful because the white matter volumes are the second half of the segmentations listed in the wmparc.mgz file. Thus, the --maxsegno command will only yield an output file that has none or some of the white matter volumes, rather than only the white matter volumes. Any suggestions? Thanks- Jennifer Hranilovich Quoting Jenni Pacheco <jpacheco(a)mail.utexas.edu>: Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 8:17 AM, Jenni Pacheco <jenni.pacheco(a)gmail.com> wrote: Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward. Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 7:04 AM, Bruce Fischl < fischl(a)nmr.mgh.harvard.edu> wrote: Hi Jen, Doug is out of town at the fBIRN meeting, and he's the one that will answer this so you might have to wait a bit. cheers, Bruce On Tue, 29 Apr 2008, Jennifer Bramen wrote: I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again. Jen Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h-<regionname>. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen

4 4

Topological defects in LGI
by Martin Kavec 10 Jun '08

10 Jun '08

Hi, I get the following warning followed by error in LGI calculation: ________________________________________________________ ... remeasuring lGI value for vertex iV = 6301. It may take a few minutes. WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high (lGI=48.6447)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file 'tmp-mris_compute_lgi/rh.pial_lgi.asc'! Linux antarctica 2.6.24-gentoo-r8 #1 SMP Sat May 17 14:07:35 CEST 2008 x86_64 Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz GenuineIntel GNU/Linux recon-all exited with ERRORS at Sun May 25 09:22:16 CEST 2008 ________________________________________________________ The suggested mris_euler_number gives: ________________________________________________________ mris_euler_number rh.pial euler # = v-e+f = 2g-2: 155756 - 467454 + 311636 = -62 --> 32 holes F =2V-4: 311636 != 311512-4 (-128) 2E=3F: 934908 = 934908 (0) total defect index = 64 ________________________________________________________ If I just rerun the LGI calculation, as suggested on the LGI web page, the calculation stops at exactly the same place. I am not sure, if I understand the execution correctly in this case, but while observing the commands, one of the first ones is removing the tmp-.... in the surf directory. Can anybody suggest me please, how to correct the defect in that particular vertex. The topological defect repair described on the web deals with dura matter pixels removal. Thanks in advance, Martin

5 9

ERROR in autorecon1
by p.s.bjerkan＠studmed.uio.no 10 Jun '08

10 Jun '08

Dear experts! Have a little problem that hopefully is easy to answer. When running autorecon1 with the 4.0.4 version I have the following ERROR (at the end of this excerpt): ________________________________________________________________ mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11745/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.11745/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Tue Jun 10 11:51:25 CEST 2008 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Tue Jun 10 11:51:25 CEST 2008 /home/batch/subjects/1030/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm /home/batch/subjects/1030/mri /home/freesurfer/freesurfer_4.0.4/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux Tue Jun 10 11:51:25 CEST 2008 -------------------------------------------- mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from nu.mgz... TR=2730.00, TE=3.93, TI=1000.00, flip angle=7.00 i_ras = (-1, 8.05145e-09, -3.11374e-08) j_ras = (-7.66902e-08, -2.80897e-09, -1) k_ras = (3.66e-08, 1, -5.54119e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 125.111; 0.000 -0.000 1.000 -71.398; -0.000 -1.000 -0.000 116.126; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Tue Jun 10 11:51:28 CEST 2008 /home/freesurfer/freesurfer_4.0.4/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Tue Jun 10 11:51:30 2008 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=127 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux millais.comp.neuro 2.6.23.8-63.fc8 #1 SMP Wed Nov 21 18:51:08 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Jun 10 11:51:30 CEST 2008 ________________________________________________________________ Seems that it´s a problem with the shared libraries. Think I remember that we had to deal with this kind of problem previously, but now exactly how... We have been running several other versions recently without changing things too much (I think). Anything apart from this that I have to be aware of? Thanks in advance! Petr S. Bjerkan Dept. of psychiatry University of Oslo

2 1

scuba bus error on MacBook
by akram＠nmr.mgh.harvard.edu 09 Jun '08

09 Jun '08

Hello all, We installed freesurfer on a brand new MacBook and downloaded some high resolution MRI data on the hard drive. we can open the volumes in tkmedit but not in scuba, it returns a Bus error. Any ideas? Thanks! Akram.

2 2

sub-voxel projections
by Ben Kennedy 09 Jun '08

09 Jun '08

Dear Freesurfer, I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of recorded sites that I want to project onto these surfaces and inflations. Is there any straightforward (but I'll take convoluted also) way to do this? Thanks, Ben K

3 11

cerebellar cortical volume
by Irene Mattisi 08 Jun '08

08 Jun '08

Hi everybody, some days ago Bruce wrote me that with FS it is possible to obtain measures of cerebellar cortical volume. I found these measures in the aseg.stats file. In this file what does "norm mean" stand for? is it the thickness? Then, does somebody know the command to obtain these measures? Thanks, Irene Mattisi

3 2

Editing Brain
by Lusineh Gharapetian 06 Jun '08

06 Jun '08

Hello, I have an epilepsy patient brain that has an abnormality I'm not sure how to fix. I have attached a few screenshots to clarify my question. When comparing the left vs right mesial-temporal area, notice that the white matter surface line on the left encloses a lot of dark space and has a lot of artificial fills on the wm.mgz volume. This subject appears to have had a hippocampal resection. However, the segmentation classifies some of the dark space as hippocampus. While I understand that FS is based off of healthy, full brains, and that is why it has filled in the missing white matter (etc.) in that section, I am trying to decide on the best way to edit this brain. Would you suggest deleting the artificial fills or leaving the brain as is? We are interested in both cortical and subcortical volumes. Thanks for your input! Lusineh

2 1

Gradient unwarp problem
by Inge Kasbohm Amlien 05 Jun '08

05 Jun '08

Hello list, we are looking into the possibility of adding the gradient unwarp tool (http://www.nbirn.net/tools/gradient_non_linearity/index.shtm) to our Freesurfer processing stream, but we are experiencing some problems with the output. Our physicist sent me what he believed was the sympathetic harmonics expansion for the Siemens Avanto, "coeff.grad". We are using mprages from said scanner. Following the readme: 1) set all environment vars, (ADDED not in readme: # setenv MATLAB_DIR $GRAD_UNWARP_DIR/matlab) 2) cd $GRAD_UNWARP_DIR 3) perl scripts/gradient_unwarp_converter.pl avanto/coeff.grad 4) create_displacement_table siemens avanto 5) grad_unwarp -i mpr1.mgh -o mpr1_uw.mgh -unwarp avanto The scripts run fine, and generate output, see attached screenshot and log. The output opens in tkmedit, but has intensity values ranging from about 28-30. Am I missing a step here? Any and all tips appreciated. Thank you, and kind regards, Inge Amlien Dept. of psychology University of Oslo Norway Attached: coeff.grad grad_unwarp_logfile.txt mpr1_uw.mgh.jpg grad_unwarp log file version: Version for distribution, 1.0, author: SC id: id pwd: pwd executable: /usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/scripts/grad_unwarp uname: uname -a date: date Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 Warning: Name is nonexistent or not a directory: /psyklab/local/eeglab/eeglab. Warning: Name is nonexistent or not a directory: /psyklab/local/eeglab/eeglab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >>>> >> >> GRADWARPPATH=/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables TABLE=/usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables/table.mat QuitOnError=1 Interp method is cubic INFO: loading mgh (mgz) format infile mpr1.mgh INFO: loading mgh (mgz) volume mpr1.mgh Beginning unwarping and/or resampling Full 3D unwarping... gradfilename is /usit/psi-brain/u1/Felles/labdata/lab-data/lab_tools/grad_unwarp/grad_unwarp_tables/avanto.gwv. Loading... Unwarp data loaded. slice 1/256 5.1e-05 slice 2/256 1.12689 slice 3/256 2.10518 slice 4/256 3.05796 slice 5/256 4.00608 slice 6/256 4.95446 slice 7/256 5.91948 slice 8/256 6.86984 slice 9/256 7.8175 slice 10/256 8.76374 slice 11/256 9.71455 slice 12/256 10.6598 slice 13/256 11.597 slice 14/256 12.5634 slice 15/256 13.5075 slice 16/256 14.4586 slice 17/256 15.4105 slice 18/256 16.3562 slice 19/256 17.3188 slice 20/256 18.2675 slice 21/256 19.2181 slice 22/256 20.164 slice 23/256 21.1119 slice 24/256 22.0761 slice 25/256 23.0236 slice 26/256 23.972 slice 27/256 24.9196 slice 28/256 25.8645 slice 29/256 26.8296 slice 30/256 27.7808 slice 31/256 28.7291 slice 32/256 29.6701 slice 33/256 30.6195 slice 34/256 31.5611 slice 35/256 32.5032 slice 36/256 33.4483 slice 37/256 34.395 slice 38/256 35.329 slice 39/256 36.2756 slice 40/256 37.2212 slice 41/256 38.1632 slice 42/256 39.111 slice 43/256 40.0735 slice 44/256 41.0182 slice 45/256 41.9631 slice 46/256 42.9138 slice 47/256 43.86 slice 48/256 44.806 slice 49/256 45.7543 slice 50/256 46.6898 slice 51/256 47.6285 slice 52/256 48.5789 slice 53/256 49.5268 slice 54/256 50.4915 slice 55/256 51.4393 slice 56/256 52.386 slice 57/256 53.3357 slice 58/256 54.2901 slice 59/256 55.2521 slice 60/256 56.1993 slice 61/256 57.1479 slice 62/256 58.0982 slice 63/256 59.0494 slice 64/256 60.0154 slice 65/256 60.9627 slice 66/256 61.91 slice 67/256 62.8575 slice 68/256 63.8069 slice 69/256 64.7726 slice 70/256 65.7184 slice 71/256 66.6661 slice 72/256 67.6116 slice 73/256 68.5513 slice 74/256 69.5043 slice 75/256 70.4383 slice 76/256 71.38 slice 77/256 72.3238 slice 78/256 73.2688 slice 79/256 74.2183 slice 80/256 75.1645 slice 81/256 76.1128 slice 82/256 77.0769 slice 83/256 78.0238 slice 84/256 78.974 slice 85/256 79.9211 slice 86/256 80.8692 slice 87/256 81.8363 slice 88/256 82.7843 slice 89/256 83.735 slice 90/256 84.6873 slice 91/256 85.6363 slice 92/256 86.5989 slice 93/256 87.5485 slice 94/256 88.4931 slice 95/256 89.4413 slice 96/256 90.3891 slice 97/256 91.3517 slice 98/256 92.2982 slice 99/256 93.247 slice 100/256 94.1918 slice 101/256 95.1394 slice 102/256 96.08 slice 103/256 97.0161 slice 104/256 97.9512 slice 105/256 98.8936 slice 106/256 99.841 slice 107/256 100.786 slice 108/256 101.726 slice 109/256 102.67 slice 110/256 103.614 slice 111/256 104.566 slice 112/256 105.513 slice 113/256 106.462 slice 114/256 107.396 slice 115/256 108.364 slice 116/256 109.313 slice 117/256 110.242 slice 118/256 111.183 slice 119/256 112.127 slice 120/256 113.07 slice 121/256 114.016 slice 122/256 114.963 slice 123/256 115.902 slice 124/256 116.848 slice 125/256 117.788 slice 126/256 118.734 slice 127/256 119.7 slice 128/256 120.648 slice 129/256 121.594 slice 130/256 122.542 slice 131/256 123.491 slice 132/256 124.455 slice 133/256 125.401 slice 134/256 126.344 slice 135/256 127.296 slice 136/256 128.246 slice 137/256 129.214 slice 138/256 130.163 slice 139/256 131.109 slice 140/256 132.053 slice 141/256 133.001 slice 142/256 133.965 slice 143/256 134.913 slice 144/256 135.862 slice 145/256 136.807 slice 146/256 137.755 slice 147/256 138.717 slice 148/256 139.667 slice 149/256 140.611 slice 150/256 141.559 slice 151/256 142.504 slice 152/256 143.468 slice 153/256 144.416 slice 154/256 145.369 slice 155/256 146.311 slice 156/256 147.245 slice 157/256 148.194 slice 158/256 149.145 slice 159/256 150.11 slice 160/256 151.061 slice 161/256 152.009 slice 162/256 152.954 slice 163/256 153.899 slice 164/256 154.842 slice 165/256 155.786 slice 166/256 156.728 slice 167/256 157.665 slice 168/256 158.608 slice 169/256 159.553 slice 170/256 160.496 slice 171/256 161.436 slice 172/256 162.401 slice 173/256 163.347 slice 174/256 164.299 slice 175/256 165.247 slice 176/256 166.198 slice 177/256 167.16 slice 178/256 168.108 slice 179/256 169.061 slice 180/256 170.01 slice 181/256 170.957 slice 182/256 171.923 slice 183/256 172.869 slice 184/256 173.818 slice 185/256 174.772 slice 186/256 175.718 slice 187/256 176.68 slice 188/256 177.626 slice 189/256 178.572 slice 190/256 179.52 slice 191/256 180.467 slice 192/256 181.409 slice 193/256 182.354 slice 194/256 183.302 slice 195/256 184.251 slice 196/256 185.197 slice 197/256 186.159 slice 198/256 187.104 slice 199/256 188.047 slice 200/256 188.989 slice 201/256 189.932 slice 202/256 190.87 slice 203/256 191.812 slice 204/256 192.784 slice 205/256 193.736 slice 206/256 194.677 slice 207/256 195.623 slice 208/256 196.589 slice 209/256 197.536 slice 210/256 198.485 slice 211/256 199.437 slice 212/256 200.384 slice 213/256 201.346 slice 214/256 202.295 slice 215/256 203.243 slice 216/256 204.191 slice 217/256 205.139 slice 218/256 206.102 slice 219/256 207.048 slice 220/256 207.996 slice 221/256 208.943 slice 222/256 209.892 slice 223/256 210.857 slice 224/256 211.804 slice 225/256 212.753 slice 226/256 213.702 slice 227/256 214.651 slice 228/256 215.616 slice 229/256 216.562 slice 230/256 217.513 slice 231/256 218.458 slice 232/256 219.406 slice 233/256 220.373 slice 234/256 221.322 slice 235/256 222.27 slice 236/256 223.217 slice 237/256 224.165 slice 238/256 225.128 slice 239/256 226.074 slice 240/256 227.02 slice 241/256 227.963 slice 242/256 228.926 slice 243/256 229.869 slice 244/256 230.814 slice 245/256 231.754 slice 246/256 232.708 slice 247/256 233.646 slice 248/256 234.595 slice 249/256 235.542 slice 250/256 236.48 slice 251/256 237.419 slice 252/256 238.373 slice 253/256 239.312 slice 254/256 240.251 slice 255/256 241.191 slice 256/256 242.131 Writing MGH (MGZ) output file mpr1_uw.mgh grad_unwarp ... done (246.344) >> >> Started at tir apr 15 17:14:41 CEST 2008 Ended at tir apr 15 17:18:51 CEST 2008 #*[ Script ****************************************************************\ # # Name : coeff_AS05_PT3.grad # # Author : BV_ICE # # Language : # # Description : Defines Legendre coefficients in spherical harmonics for # Gradient Coil AS05 # #****************************************************************************/ #* Changed: 08-May-2003; F. Hebrank, MREI-Phys *********************\ # # Requirement Key: # # Description : Creation: coefficients received from Peter Dietz, MRFG1 # #****************************************************************************/ #*] END: */ vision/AS05, Gradientsystem AS05, Gx,y,z = 40/28 mT/m win_low = 0, win_high = 0, win_algo = 0, win_dummy = 2; 0.25 m = R0, lnorm = 4? A(1,0) = B(1,1) = A(1,1) = 0; 0 = CoSyMode; Expansion in Spherical Harmonics ================================ NO. TYPE SPECTRUM AXIS 1 A( 3, 0) 0.00629 z 2 A( 5, 0) -0.15349 z 3 A( 7, 0) 0.04859 z 4 A( 9, 0) -0.00179 z 5 A(11, 0) -0.00440 z 6 A(13, 0) 0.00196 z 101 A( 3, 1) -0.02504 x 102 A( 3, 3) -0.00728 x 103 A( 5, 1) -0.05383 x 104 A( 5, 3) -0.00130 x 105 A( 5, 5) -0.00285 x 106 A( 7, 1) -0.01046 x 107 A( 7, 3) 0.00836 x 108 A( 9, 1) 0.01417 x 109 A( 9, 3) -0.00499 x 110 A(11, 1) -0.00517 x 201 B( 3, 1) -0.01427 y 202 B( 3, 3) 0.00459 y 203 B( 5, 1) -0.05697 y 204 B( 5, 5) -0.00196 y 205 B( 7, 1) -0.01356 y 206 B( 7, 3) -0.00930 y 207 B( 9, 1) 0.01451 y 208 B( 9, 3) 0.00516 y 209 B(11, 1) -0.00520 y 210 B(11, 3) -0.00198 y

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thalamus definition
by Anqi Qiu 03 Jun '08

03 Jun '08

Is there any reference for the anatomical definition of the thalamus? What nuclei are included in the thalamus delineated from FreeSurfer? Thanks! Anqi Qiu Center for Imaging Science Johns Hopkins University Email: anqi(a)cis.jhu.edu tel: 410-516-8103

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