Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

mri_label2label
by Ray Razlighi 10 Nov '15

10 Nov '15

Hi Guys, I'm trying to map the vertices of temporal pole in one subject into the space of another subject using mri_label2label. When I do it, the output doesn't have the same number of vertices and the other of the vertex are completely messed up. See below as the first few lines in the source and transferred labels along with the command execution. What I need to know is that where for example vertex number 129756 mapped to in the target surface space. I can't extract those information from these two files. Thanks a lot -------------------------------------------------------------------------------------------------------------------------------- Source Label file: aparc-lh-032.label #!ascii label , from subject FreeSurferClean vox2ras=TkReg 217 129756 -13.048 63.016 -1.943 0.0000000000 129757 -13.268 63.132 -1.961 0.0000000000 129767 -13.120 63.091 -2.173 0.0000000000 129768 -13.470 63.274 -2.293 0.0000000000 129870 -7.339 63.337 5.869 0.0000000000 129879 -7.347 63.505 5.024 0.0000000000 129888 -7.731 63.526 4.092 0.0000000000 129889 -8.111 63.407 3.205 0.0000000000 129893 -8.317 63.382 2.401 0.0000000000 129896 -7.864 64.313 1.332 0.0000000000 129897 -8.180 63.672 1.427 0.0000000000 129898 -12.359 64.295 1.105 0.0000000000 129899 -12.777 64.061 1.152 0.0000000000 129902 -7.780 64.251 0.861 0.0000000000 129903 -7.979 63.500 0.404 0.0000000000 129904 -11.492 64.276 0.155 0.0000000000 129905 -12.091 63.982 0.540 0.0000000000 129906 -13.264 63.628 0.557 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- Transfered Label file: aparc-lh-032-reg3.label #!ascii label , from subject FreeSurferClean2 vox2ras=TkReg 333 132988 -7.268 83.361 -2.195 0.0000000000 132714 -7.766 83.079 -2.603 0.0000000000 132259 -4.885 81.451 7.416 0.0000000000 132260 -5.354 81.986 6.795 0.0000000000 132609 -5.461 82.480 5.323 0.0000000000 132904 -5.190 83.525 4.692 0.0000000000 132903 -4.503 83.934 4.047 0.0000000000 133205 -3.592 84.944 3.299 0.0000000000 132913 -3.623 84.596 3.095 0.0000000000 133222 -6.863 84.768 1.300 0.0000000000 133223 -7.284 84.611 1.941 0.0000000000 133204 -3.445 84.969 2.831 0.0000000000 133211 -3.895 84.688 2.151 0.0000000000 133250 -6.409 84.885 -0.260 0.0000000000 133236 -6.568 84.963 0.611 0.0000000000 132934 -7.418 83.679 1.113 0.0000000000 133456 -3.481 85.560 2.366 0.0000000000 133470 -3.739 85.730 0.320 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- ray@athens-b8-e8-56-47-e6-54:~/Data/P00001613\> mri_label2label --srclabel FreeSurferClean/label/aparc-lh-032.label --srcsubject FreeSurferClean --trglabel FreeSurferClean2/label/aparc-lh-032-reg3.label --trgsubject FreeSurferClean2 --regmethod surface --hemi lh srclabel = FreeSurferClean/label/aparc-lh-032.label srcsubject = FreeSurferClean trgsubject = FreeSurferClean2 trglabel = FreeSurferClean2/label/aparc-lh-032-reg3.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/ray/Data/P00001613 FREESURFER_HOME /Applications/freesurfer Loading source label. Found 217 points in source label. Starting surface-based mapping Reading source registration /Users/ray/Data/P00001613/FreeSurferClean/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.white Reading target registration /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 217 nlabel points Performing mapping from target back to the source label 134519 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file FreeSurferClean2/label/aparc-lh-032-reg3.label 359 mri_label2label: Done ---------------------------------------------------------------------------------------------------------------------- -- Sincerely, Ray

3 6

mri_surf2surf - Interpolation
by Gardus III, John D 10 Nov '15

10 Nov '15

Hello all, I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv file containing the vertices of the pial surface mesh. I have values at roughly 100 vertices, leaving some 37000 with 'nan'. I then run an intra-subject surf2surf command in an attempt to interpolate between vertices for which I have values. The problem is that the NaNs pull the existing values down, resulting in a smearing/dilution of my outcomes. Is there any way to interpolate and make the intervening vertices purely a function of nearby vertices for which values exist? Thanks, John This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

3 5

Region specific stats
by Hassan bakhshi 10 Nov '15

10 Nov '15

Hi everyone, I could get all features from asegstats2table and aparcstats2table, Now I need stats by region, for example frontal lobe stats and etc. How can I get them??? Should I select by myself or there is an easy way?

2 1

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 10 Nov '15

10 Nov '15

Also, try removing the blank line at the end of wmh.levels, and make sure you have a carriage return at the end of long.qdec.table.txt. This may fix the 2nd error On 11/09/2015 10:38 PM, Heidi Foo wrote: > Dear Dr Greve, > > Thanks for your reply. I have already linked fsaverage to my > SUBJECTS_DIR but the error still persists. > > Attached is my qdec (long and cross) files. > > Thanks. > > Regards, > Heidi Foo > > > > On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > On 11/06/2015 09:35 PM, Heidi Foo wrote: > > Dear FreeSurfer experts, > > I am trying to compare between stable WMH group and rapid > progressed WMH group in regards to the cortical thickness as > well as volume changes in the gray matter. The nuisance > variable in my case is age. I ran my analysis using QDEC but > encountered a few problems: > > 1. There is error in analyze: couldn't open file > > It looks like it cannot find fsaverage. Link it to your > SUBJECTS_DIR if you have not already. > > 2. If this error doesn't appear, another one does. > QdecGlmDesign::Create: zero factors! > (Attached the screenshot of the errors for your perusal) > > please send the qdec file > > > I am hoping that you could give me a solution to my problems. > > Thank you so much. > > Regards, > Heidi > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 10 Nov '15

10 Nov '15

Are those the qdec files that generate the first error? That error implies that fsaverage is included as a subject in the qdec file. Is this possible? On 11/09/2015 10:38 PM, Heidi Foo wrote: > Dear Dr Greve, > > Thanks for your reply. I have already linked fsaverage to my > SUBJECTS_DIR but the error still persists. > > Attached is my qdec (long and cross) files. > > Thanks. > > Regards, > Heidi Foo > > > > On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > On 11/06/2015 09:35 PM, Heidi Foo wrote: > > Dear FreeSurfer experts, > > I am trying to compare between stable WMH group and rapid > progressed WMH group in regards to the cortical thickness as > well as volume changes in the gray matter. The nuisance > variable in my case is age. I ran my analysis using QDEC but > encountered a few problems: > > 1. There is error in analyze: couldn't open file > > It looks like it cannot find fsaverage. Link it to your > SUBJECTS_DIR if you have not already. > > 2. If this error doesn't appear, another one does. > QdecGlmDesign::Create: zero factors! > (Attached the screenshot of the errors for your perusal) > > please send the qdec file > > > I am hoping that you could give me a solution to my problems. > > Thank you so much. > > Regards, > Heidi > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

mri_surfcluster statistics and label question
by Yang, Daniel 10 Nov '15

10 Nov '15

Dear FreeSurfer experts, In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSu…) what is the statistics behind the Max? Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-statistics? Also, I notice that the annotation is picking only one of the anatomical regions in which the cluster is located. Is it possible to tell all the anatomical regions that a label has? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

3 4

Tracula bedpostx terminated
by denizzgursel 10 Nov '15

10 Nov '15

Dear Freesurfer experts, I am running tracula v5.3.0 on OpenSuse. I successfully ra n freesurfer reconstruction and trac-all-prep. However, when I try to run trac-all -bedp -c dmrirc_file, I get the following message: .... 47 s lices processed 48 s lices processed 50 s lices processed 53 slices processed Queuing post processing stage sw/freesurfer/5.3.0/bin/bedpostx_mgh: line440: 8026 Terminated ${subjdir}.bedpostX/monitor I am not running bedpostx on a cluster but locally. Any suggestions why it might be terminated? Thank you, -- D.

1 0

mri_glmfit fsgd and matrix problems
by Gay,Charles Wysaw 09 Nov '15

09 Nov '15

Hi Freesurfer group - I am receiving errors each time I try to run mri_glmfit. It appears to be the way I set up either the fsgd or mtx file. Any assistance would be greatly appreciated. Thanks, Chaz Hypothesis for the contrast in the mtx file: Is there an average affect of heat threshold regressing out the effect of gender and age? Command-line executed: mri_glmfit \--y lh.heatthreshold.thickness.10.mgh \--fsgd heatthreshold.fsgd dods \--C g1g2.heatthreshold.age.mtx \--surf fsaverage lh \--cortex \--glmdir lh.gender.heatthreshold.age.glmdir I seem to be getting 1 or 2 errors 1: gdfReadHeader: reading heatthreshold1.fsgd INFO: ignoring tag B113v1 INFO: ignoring tag B036V1 INFO: ignoring tag B015v1 INFO: ignoring tag B006v1 WARNING: gdfReadV1: class Male is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 HeatThreshold nan nan 1 Age nan nan Class Means of each Continuous Variable 1 Male nan nan 2 Female nan nan INFO: gd2mtx_method is dods Reading source surface /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold cmdline mri_glmfit --y lh.heatthreshold.thickness.10.mgh --fsgd heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir sysname Darwin hostname phhp-chazgay-mb.ad.ufl.edu machine x86_64 user chaz.gay FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh logyflag 0 usedti 0 FSGD heatthreshold1.fsgd labelmask /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.gender.heatthreshold.age.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.gender.heatthreshold.age.glmdir Loading y from /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.gender.heatthreshold.age.glmdir/Xg.dat Normalized matrix condition is 1e+08 Design matrix ------------------ -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.heatthreshold.thickness.10.mgh --fsgd heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir 2. The FSGD file (if using one) 3. And the design matrix above And 2 gdfReadHeader: reading heatthreshold.fsgd ERROR: gdfReadV1: Input line 1, subjid = B113v1 Found 242 variables, expected. 2 FSGDF Format Error: file = heatthreshold.fsgd, tag=Input I attached both the .mxt and fsgd files Thanks again, Chaz FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log

2 1

Error: dimension mismatch between source and mask
by Isabelle Deschamps 09 Nov '15

09 Nov '15

Dear FreeSurfer experts, After running the following command: recon-all -autorecon2 -autorecon3 -subjid S08_FS I get the following error: /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 ERROR: dimension mismatch between source and mask Darwin Isabelles-iMac.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s S08_FS exited with ERRORS at Mon Nov 9 18:56:20 EST 2015 I read in a post that it might be a problem with registration, so following a post found on the forum, I re-analyze this participant (from scratch) using: recon-all --autorecon1 -use-mritotal -subjid S08_FS then I ran recon-all -autorecon2 -autorecon3 -subjid S08_FS However, this did not solve the problem. Is there a workaround that I could use after the pial edits and running the -autorecon2 and 3? Thank you very much in advance, Isabelle

1 0

R: Re: R: Re: R: Re: R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 09 Nov '15

09 Nov '15

I have run cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary obtained ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.595 110577 865.93 11.8 39.4 -0.1 0.00620 0.00520 0.00720 1672 rostralanteriorcingulate after mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig. cluster.nii.gz --i Control21/rest/fc.seed.surf.rh/R_Seed/z.nii.gz --sum summaryfile_Control and summary file is: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 -2 1672 1672.0 Seg-002 -2.2757 2.2172 -6.4504 2.5762 9.0266 2 0 162170 162170.0 Seg0000 1.3956 1.6398 -7.0471 14.1452 21.1923 I have two raw. Which is the raw which contains the average z-score in the cluster? What's meaning Seg-002/0? Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 9-nov-2015 23.59 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: average z-score of each subject from a common cluster > > > >On 11/07/2015 07:29 PM, stdp82(a)virgilio.it wrote: >> Thanks. But what's meaning "colheader"? >Column header. The title of the column >> In my cache.th13.neg.sig.masked.nii.gz I have only a significant ROI. >> In the summary file there are five column and 5 different value of >> "mean". >> Which is the correct, expressing the mean z-score of the cluster? >The column labeled "Mean", probably the 6th column >> >> Stefano >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 6-nov-2015 23.07 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each subject >> from a common cluster >>> under the "Mean" column >>> >>> On 11/06/2015 07:46 AM, stdp82(a)virgilio.it wrote: >>>> I have run >>>> mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig. >> masked. >>>> nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum >>>> summaryfile >>>> >>>> and I have obtained 9 columns and 5 rows. >>>> I'm confused on results. Where is the mean z-score for cache. th13. >> neg. >>>> sig.masked.nii.gz? >>>> >>>> # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev >>>> Min Max Range >>>> 1 -4 7 7.0 Seg-004 -2.4544 0.5023 >>>> -3.2164 -1.7619 1.4545 >>>> 2 -3 153 153.0 Seg-003 -2.6662 1.4724 >>>> -6.2120 1.7587 7.9707 >>>> 3 -2 848 848.0 Seg-002 -2.4930 2.0088 >>>> -6.4504 2.3528 8.8032 >>>> 4 -1 1518 1518.0 Seg-001 -2.1416 1.6727 >>>> -6.4227 2.5420 8.9648 >>>> 5 0 161316 161316.0 Seg0000 1.4152 1.6218 >>>> -7.0471 14.1452 21.1923 >>>> >>>> Because my data are on surface mri_surfcluster should be helpful? >>>> >>>> Thanks. >>>> >>>> >>>> Stefano >>>> >>>> >>>>> ----Messaggio originale---- >>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>> Data: 3-nov-2015 19.55 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: average z-score of each subject from >> a >>>> common cluster >>>>> look in the summaryfile. Also, don't use --seg z.nii.gz. In the >>>> command >>>>> below, it works because you have --annot afterwards, but in >> general >>>> it >>>>> is not correct >>>>> >>>>> On 10/30/2015 04:22 PM, stdp82(a)virgilio.it wrote: >>>>>> Thanks. >>>>>> I have obtained: >>>>>> >>>>>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ >>>>>> >>>>>> cwd >>>>>> >>>>>> cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc >> -- >>>> i >>>>>> z.nii.gz --sum summaryfile >>>>>> >>>>>> sysname Darwin >>>>>> >>>>>> hostname iMac-di-Stefano.local >>>>>> >>>>>> machine x86_64 >>>>>> >>>>>> user Stefano >>>>>> >>>>>> UseRobust 0 >>>>>> >>>>>> Loading z.nii.gz >>>>>> >>>>>> Loading z.nii.gz >>>>>> >>>>>> Voxel Volume is 1 mm^3 >>>>>> >>>>>> Generating list of segmentation ids >>>>>> >>>>>> Found 22 segmentations >>>>>> >>>>>> Computing statistics for each segmentation >>>>>> >>>>>> 0 -7 2 2.000 >>>>>> >>>>>> 1 -6 110 110.000 >>>>>> >>>>>> 2 -5 255 255.000 >>>>>> >>>>>> 3 -4 518 518.000 >>>>>> >>>>>> 4 -3 1190 1190.000 >>>>>> >>>>>> 5 -2 1692 1692.000 >>>>>> >>>>>> 6 -1 4104 4104.000 >>>>>> >>>>>> 7 0 61577 61577.000 >>>>>> >>>>>> 8 1 42598 42598.000 >>>>>> >>>>>> 9 2 28146 28146.000 >>>>>> >>>>>> 10 3 14859 14859.000 >>>>>> >>>>>> 11 4 5845 5845.000 >>>>>> >>>>>> 12 5 1899 1899.000 >>>>>> >>>>>> 13 6 485 485.000 >>>>>> >>>>>> 14 7 116 116.000 >>>>>> >>>>>> 15 8 75 75.000 >>>>>> >>>>>> 16 9 74 74.000 >>>>>> >>>>>> 17 10 78 78.000 >>>>>> >>>>>> 18 11 65 65.000 >>>>>> >>>>>> 19 12 104 104.000 >>>>>> >>>>>> 20 13 45 45.000 >>>>>> >>>>>> 21 14 5 5.000 >>>>>> >>>>>> >>>>>> How I can know the meaning of this number? Where is z? >>>>>> >>>>>> I have tried also with: >>>>>> >>>>>> mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z. >> nii. >>>> gz >>>>>> --sum summaryfile --mask >>>>>> .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache. >> th13. >>>> neg.sig.masked.nii.gz >>>>>> --avgwfvol mrivol >>>>>> >>>>>> >>>>>> but I have problem with interpretation. >>>>>> >>>>>> >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>> Data: 30-ott-2015 16.17 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] average z-score of each subject from a >>>>>> common cluster >>>>>> >>>>>> >>>>>> >>>>>> On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: >>>>>>> Hi list, >>>>>>> I have two queries, please. >>>>>>> >>>>>>> I'd like to have the z-score from my rsfMRI data (seed- >>>> analyis). >>>>>>> 1) I have extract the z-score from the Vtx Max >>>>>>> >>>>>>> In details, after groups comparison analysis, I have opened >>>>>>> the cache.th13.pos.sig.cluster.summary contained in group. >> diff >>>>>>> folder and I have read the Vtx Max coordinates. >>>>>>> Next, I have open the z.nii.gz of each subject and I have >>>>>>> expected the z-score from the vertex which have the Vtx Max >>>>>>> coordinates. >>>>>>> >>>>>>> Is this procedure corrected? >>>>>> Yes >>>>>>> 2) z-score of each subject from a common cluster >>>>>>> >>>>>>> I would like to use the cluster which shows the group >>>> difference >>>>>>> (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I >> would >>>>>>> extract from it the average of the z-score which is >> contained >>>> in >>>>>>> each subject. >>>>>>> How should I do? >>>>>> Use mri_segstats passing the z map as the input (--i) and >> the >>>>>> cluster map as the seg. The output will be --sum. Run with >> -- >>>> help >>>>>> for more info >>>>>>> Thanks. >>>>>>> >>>>>>> >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard. >> edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>> edu/transfer/outgoing/flat/greve/ >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)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(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 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> _______________________________________________ >> 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 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer