Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

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

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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

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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 >

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Two recons with different vertex coordinates
by Reza Rajimehr 09 Nov '15

09 Nov '15

Hi, We have run recon-all twice on a single subject, both times without any error. Using a functional localizer, we have made a surface-based label for an ROI (FFA) in the ventral temporal cortex of the inflated surface from the first recon. When we visualize the same label on the inflated surface of the second recon, the label shows up as scattered points in the lateral parietal cortex! Why do we see such a huge difference in the vertex coordinates across the two recons of a single subject? Reza

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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

Thanks. But what's meaning "colheader"? 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? 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 >

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ROI
by UQAM 09 Nov '15

09 Nov '15

Hi I have created and saved labels for 2 regions in the anterior cingulate and corpus callosum in the left hemisphere and I would like to know if there is a way I can convert my .label files from the lh->rh without drawing them by hand in the other hemisphere. Thanks in advance, Best regards, Geneviève

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node coordinates
by André Schmidt 09 Nov '15

09 Nov '15

Dear experts, I defined 84 regions obtained from the aparc+aseg.mgz file as my nodes for later graph analysis. For visualization purposes, I want to assign each node the corresponding MNI coordinates. Can you please help me how I can do this? Is this documented somewhere? Many thanks for your help André

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MNI coordinates for regions in aparc+aseg.mgz file
by André Schmidt 09 Nov '15

09 Nov '15

Dear FS experts, I would like to know the MNI coordinates of my ROIs obtained from recon-all (aparc+aseg.mgz file). For example what for coordinates has number 10 (left thalamus)? Are the coordinates of each region listed somewhere? Many thanks for your help Best wishes André

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R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 09 Nov '15

09 Nov '15

I hope that this information are fine fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V 22926 22926.000000 Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 5-nov-2015 23.43 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS- FAST > >How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ? > >On 11/05/2015 04:47 PM, stdp82(a)virgilio.it wrote: >> Please see the file attached. >> Thanks >> >> Stefanofile >> >> ----Messaggio originale---- >> Da: greve(a)nmr.mgh.harvard.edu >> Data: 5-nov-2015 15.43 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST >> >> sorry, should have been >> >> fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log >> >> >> >> On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: >>> Hi Dough, >>> in summary: >>> I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri >>> thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the >>> MRS_MASK.mgz >>> and run: >>> fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - >>> cfg MRS_MASK.config >>> fcseed-sess -s Control22_FS -cfg MRS_MASK.config >>> >>> ...Writing to >>> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. fcseed- >>> sess.12305/avgwf.mgh >>> Segmentation fault >>> >>> Therefore, according with your suggestion, I have now run: >>> fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log >>> ERROR: cound not find session -cfg >>> >>> The doug.log is attached. >>> >>> Thanks, >>> >>> >>> Stefano >>> >>> >>> >>> >>>> ----Messaggio originale---- >>>> Da:greve@nmr.mgh.harvard.edu >>>> Data: 4-nov-2015 16.58 >>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST >>>> >>>> First, when running fcseed-config, don't give it the full path, just >>> the >>>> path relative to subject/mri (in this case only MRS_MASK.mgz) >>>> >>>> However, I don't think that is the problem. Please run >>>> >>>> fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log >>>> >>>> and send me doug.log >>>> >>>> >>>> >>>> >>>> >>>> On 11/04/2015 04:14 AM,stdp82(a)virgilio.it wrote: >>>>> Hi list, this error is still occurring: >>>>> >>>>> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz >>>>> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz >>>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK. mgz - >>> fsd >>>>> rest -mean -cfg MRS_MASK.config >>>>> fcseed-sess -s -cfg MRS_MASK.config >>>>> >>>>> During >>>>> >>>>> fcseed-sess -s subj -cfg MRS_MASK.config >>>>> >>>>> Voxel Volume is 64.5752 mm^3 >>>>> Generating list of segmentation ids >>>>> Found 1 segmentations >>>>> Computing statistics for each segmentation >>>>> 0 1 0 0.000 >>>>> MRIalloc(0, 1, 1): bad parm >>>>> Reporting on 0 segmentations >>>>> Computing spatial average of each frame >>>>> >>>>> Writing to /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp. >>>>> fcseed-sess.97908/avgwf.mgh >>>>> Segmentation fault >>>>> >>>>> I have read your previous message and you can check the MRS voxel >>>>> features. >>>>> MRS voxel mask is in subj directory where I have run recon all - >>> all. >>>>> data_type FLOAT32 >>>>> dim1 256 >>>>> dim2 256 >>>>> dim3 256 >>>>> dim4 1 >>>>> datatype 16 >>>>> pixdim1 1.000000 >>>>> pixdim2 1.000000 >>>>> pixdim3 1.000000 >>>>> pixdim4 0.010747 >>>>> cal_max 0.0000 >>>>> cal_min 0.0000 >>>>> file_type NIFTI-1+ >>>>> >>>>> >>>>> The features are same of other subject that runs fine. >>>>> data_type FLOAT32 >>>>> dim1 256 >>>>> dim2 256 >>>>> dim3 256 >>>>> dim4 1 >>>>> datatype 16 >>>>> pixdim1 1.000000 >>>>> pixdim2 1.000000 >>>>> pixdim3 1.000000 >>>>> pixdim4 0.010747 >>>>> cal_max 0.0000 >>>>> cal_min 0.0000 >>>>> file_type NIFTI-1+ >>>>> >>>>> Thank you very much. >>>>> >>>>> >>>>> Stefano >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da:stdp82@virgilio.it >>>>>> Data: 16-ott-2015 23.15 >>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL >>>>>> >>>>>> I'd like to open with FSLview the sig.nii.gz which is produced by >>>>>> selxavg3-sess. >>>>>> If I use mri_surf2vol, which is the template to added in -- >>> template? >>>>>> It should be in Tailairach space? Where can I find the template >>> that >>>>> I >>>>>> should added? >>>>>> Thanks, >>>>>> >>>>>> Stefano >>>>>> >>>>>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >>>>>> data_type FLOAT32 >>>>>> dim1 27307 >>>>>> dim2 1 >>>>>> dim3 6 >>>>>> dim4 1 >>>>>> datatype 16 >>>>>> pixdim1 1.000000 >>>>>> pixdim2 1.000000 >>>>>> pixdim3 1.000000 >>>>>> pixdim4 1100.000000 >>>>>> cal_max 49.1815 >>>>>> cal_min -12.3855 >>>>>> file_type NIFTI-1+ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Stefano >>>>>> >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da:greve@nmr.mgh.harvard.edu >>>>>>> Data: 29-set-2015 22.09 >>>>>>> A:<freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>>>>>> >>>>>>> Do you mean surface-based analysis? You'd have to put them back >>>>> into >>>>>> the >>>>>>> volume using mri_surf2vol, write them out as nifti and then run >>>>>> fslview >>>>>>> on them >>>>>>> >>>>>>> On 09/29/2015 11:17 AM,stdp82(a)virgilio.it wrote: >>>>>>>> Hi list, >>>>>>>> >>>>>>>> I would like to import FS-FAST results (conjunction maps) >>> in >>>>>> FSL, >>>>>>>> opening them by fslview. >>>>>>>> Could you provide me any suggestion? >>>>>>>> >>>>>>>> Thank you very much >>>>>>>> Best regards, >>>>>>>> >>>>>>>> >>>>>>>> Stefano >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>> >>>>> _______________________________________________ >>>>> 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 >> >> >> >> >> >> _______________________________________________ >> 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 >

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Drawing a circle around a vertex on a surface
by Reza Rajimehr 09 Nov '15

09 Nov '15

Hi, I want to draw a circle around a vertex on the smoothwm or pial surface, with a particular radius (e.g. 10 mm), fill the circular region and save it as a label file, then repeat this for all the vertices on the surface. I need this for doing a searchlight analysis. Does anyone have a script/code for it? I know that mris_pmake (using Dijkstra's algorithm) can be used for this purpose, but I don't know exactly how to make it to work in a script for drawing circular ROIs. Thanks for any help! Reza

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Freesurfer November 2015