Re: [Freesurfer] LME design matrix for changes in 1 group
External Email - Use Caution Hi Martin, I ran longitudinal pipeline on all time points so I have one template. For the GLM approach I first calculated pc1 for baselineVs placebo (either day1 or day2) and got the lh(rh).bl-pl.thickness-pc1.fwhm10.mgh then calculated pc1 for bl vs drug and got lh(rh).bl-drug.thickness-pc1.fwhm10.mgh. How should I look at the difference of difference now? should I stack them together and then create fsgd? Regarding the LME approach I made the design file and followed the steps in tutorial , so I calculated with 2 and 1 random effect and length(dvtx) is smaller than 80% of length(lhcortex), so I assume that I should go for 1 random effect (lhstats_1RF) and CM.C = [0 0 0 1] then: F_lhstats = lme_mass_F(lhstats_1RF,CM); dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); And now the dvtx is empty. Am I doing the right steps? Is there anything else you suggest? Best regards, Amirhossein Manzouri On Mon, Jan 30, 2023 at 7:59 PM amirhossein manzouri wrote: > Thanks Martin. I assume in GLM approach I should calculate change for > session 1 and 2 and then 3 and 4 and then run difference of difference. > We actually randomized the order so half day1 is plcebo and half drug. So > I just need to be caretabout the design for LME. > BR > > On Mon, 30 Jan 2023 at 17:09, Reuter, Martin,Ph.D. < > mreu...@mgh.harvard.edu> wrote: > >> Hi Amirhossein, >> >> So you have session 1 , placebo , session 2 >> Another day session 3, drug, session 4 ? >> >> Again if this is for all subjects, easiest is to subtract session 2 from >> 1, and 4 from 3, to get thickness/volume differences for each condition. >> Then compute the difference of the differences and run a GLM testing for >> difference from zero. >> >> An LME approach could be: >> Column of 1 >> Column of time (zero for session 1 and 3, one for session 2 and 4) >> Column of day (zero for session 1 and 2, one for session 3 and 4) >> Column of drug (zero for session 1,2,3 and one for session 4) >> >> The last one is the interesting one. But I would discuss this with a >> bio-statistician. I develop methods for image analysis and this could be >> wrong (or sub-optimal). >> >> Best, Martin >> >> >> >> On 30. Jan 2023, at 16:40, amirhossein manzouri >> wrote: >> >> >> >> Thanks a lot Martin for the information. >> We have actually 2 sessions of placebo for each subject. How do you >> suggest to do the analysis including that data? >> BR >> >> On Mon, 30 Jan 2023 at 16:30, Reuter, Martin,Ph.D. < >> mreu...@mgh.harvard.edu> wrote: >> >>> Hi Amirhossein, >>> >>> - If you have two time points for all participants, >>> - and the time difference is the same for all >>> you can simply subtract the thickness (or volume) values per participant >>> and run a regular GLM. LME is a little overkill here. >>> >>> >>> In LME, you have one column of ones, and one of the time (which is 0 and >>> t alternating ) , this is not the time difference! The first time point is >>> at time 0 and the second at time t (in hours or days whatever). If the time >>> really does not matter, you can also put 0 and 1. >>> >>> You can run the model with no random effect or with one random effect. >>> The wiki >>> https://secure-web.cisco.com/1Ey4MhXIG_R2LHA5sT7HL2EJPi4egIFFk0CvQ42MPwbI9wb0GQML9h127BSXU9YP00g6FQ3lOo53JKDfMyyKW-gKwDM5807-3MgE9x_IGeMj-9fZ-gmYbeSuu7gzp8XwqIcMEsWBxQVV69nGwtp_GjHIaAajNBxqP4Ke4wkCH-us3y2bZWcR3Az1JpaOq4CA0sttiTArjpszVtLFCwz2UhKTmw6vzBkC3wrRxafQK0ra2r9AezZGOKP4BsmsxVRQpZ3hD-AQEguntv7jazFE1bkJKGeWbE9dklYI0F80nDpYtsGlZyJnJpfSdUr3fdcXZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels >>> <https://secure-web.cisco.com/1CSHB-5Ru-H_vm7bj0aIPjdrfuSN8LCdCPwMAtUeig065FbJHQSap5C8AvEn_6ceCs_21nSgcls3Pi-hX-gLtpA81R1NcrWukVV8tRbO66bjHACvq9NFfjtu6qX53752X_OIMrKu6TQc1AnyPMzj6VWoDyk-ojaL4txDORLwU1SVWTJo9VOchHuCdUMIcGnWMP_kDLmSBnAYZxkmhITpLs4pY9k9FGZqcf4Tf3dk8b-P_tqUBwdjlZD2yMAEur9MIZuFKScaSEGaVk4CBsqbUPnc1DFns7_Ew-goF7LAcc_pDWLzg0X3WPQpFD1qTcmuGT12wVNaZWKvHSXSAGjA56A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels> >>> describes how to compare those models, also how to compute significance. >>> >>> You probably have more columns (also if you do the GLM) e.g. the amount >>> of drug that was given, or who got the drug and who got placebo. Otherwise >>> you cannot check for a drug effect. That column would be the one you are >>> interested in. >>> >>> Without a placebo group, you will find
Re: [Freesurfer] LME design matrix for changes in 1 group
External Email - Use Caution Thanks Martin. I assume in GLM approach I should calculate change for session 1 and 2 and then 3 and 4 and then run difference of difference. We actually randomized the order so half day1 is plcebo and half drug. So I just need to be caretabout the design for LME. BR On Mon, 30 Jan 2023 at 17:09, Reuter, Martin,Ph.D. wrote: > Hi Amirhossein, > > So you have session 1 , placebo , session 2 > Another day session 3, drug, session 4 ? > > Again if this is for all subjects, easiest is to subtract session 2 from > 1, and 4 from 3, to get thickness/volume differences for each condition. > Then compute the difference of the differences and run a GLM testing for > difference from zero. > > An LME approach could be: > Column of 1 > Column of time (zero for session 1 and 3, one for session 2 and 4) > Column of day (zero for session 1 and 2, one for session 3 and 4) > Column of drug (zero for session 1,2,3 and one for session 4) > > The last one is the interesting one. But I would discuss this with a > bio-statistician. I develop methods for image analysis and this could be > wrong (or sub-optimal). > > Best, Martin > > > > On 30. Jan 2023, at 16:40, amirhossein manzouri > wrote: > > > > Thanks a lot Martin for the information. > We have actually 2 sessions of placebo for each subject. How do you > suggest to do the analysis including that data? > BR > > On Mon, 30 Jan 2023 at 16:30, Reuter, Martin,Ph.D. < > mreu...@mgh.harvard.edu> wrote: > >> Hi Amirhossein, >> >> - If you have two time points for all participants, >> - and the time difference is the same for all >> you can simply subtract the thickness (or volume) values per participant >> and run a regular GLM. LME is a little overkill here. >> >> >> In LME, you have one column of ones, and one of the time (which is 0 and >> t alternating ) , this is not the time difference! The first time point is >> at time 0 and the second at time t (in hours or days whatever). If the time >> really does not matter, you can also put 0 and 1. >> >> You can run the model with no random effect or with one random effect. >> The wiki >> https://secure-web.cisco.com/1WKlQ0u9JEMPReF063WyLOTyVSO-47TES55AV1uo84axCXL0kE1Z5uE8xmrCOrlheB9Om3Da_FWdm7ktpek1AmfgLGoEwfjyWPw6T3WFBwwEGQPaxXCu6fBhHaOM20lPohVTYDzNNpnqdLo0ll07K3ilVb52yVueNvhlIOGszB6w-Bt4QWdTOvBHhVxmBlWQAdxi2fHYJwbtjm_y2Hb3qX94xJiF8aK1bVRRBVOWSy9PDEKEicWY18BwHVnHa8NmUdAJM-uiURRvVNdt57zKntQJXQeqYEpC2FSDfvIONjZLCp3vnUtALZSaw4z2KOVAAU1_i0sp4B_GGtG5CkFdVyg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels >> <https://secure-web.cisco.com/1CSHB-5Ru-H_vm7bj0aIPjdrfuSN8LCdCPwMAtUeig065FbJHQSap5C8AvEn_6ceCs_21nSgcls3Pi-hX-gLtpA81R1NcrWukVV8tRbO66bjHACvq9NFfjtu6qX53752X_OIMrKu6TQc1AnyPMzj6VWoDyk-ojaL4txDORLwU1SVWTJo9VOchHuCdUMIcGnWMP_kDLmSBnAYZxkmhITpLs4pY9k9FGZqcf4Tf3dk8b-P_tqUBwdjlZD2yMAEur9MIZuFKScaSEGaVk4CBsqbUPnc1DFns7_Ew-goF7LAcc_pDWLzg0X3WPQpFD1qTcmuGT12wVNaZWKvHSXSAGjA56A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels> >> describes how to compare those models, also how to compute significance. >> >> You probably have more columns (also if you do the GLM) e.g. the amount >> of drug that was given, or who got the drug and who got placebo. Otherwise >> you cannot check for a drug effect. That column would be the one you are >> interested in. >> >> Without a placebo group, you will find difference across time, but you >> will not know if they are from the drug or from the fact that people are >> familiar with the scanner (less head motion) or more annoyed by the scanner >> (more head motion) or more tired, or more dehydrated, or rehydrated if you >> give the drug with water, or simply a time-of-the-day effect, or scanner >> heats up etc. >> >> Some of these confounders are problematic anyway, as the drug can have a >> sedative effect (less motion?) or was given with water (re-hydration). The >> second can be controlled by giving placebo with the same amount of water. >> Disentangling motion from drug effect (due to the possible correlation) >> would only be possible if you separately measure motion or take fMRI or >> diffusion motion estimates as a proxy for motion during T1. >> >> >> Head motion reduces grey matter estimates: >> doi.org >> <https://secure-web.cisco.com/1Gxeqs4jJ99OuR4by9bss7f3j35AVnLoFz3XximPcl4CqxGfEA2sLpbIhDtoXRFDGBiHMnODrMWCNdNy-5vQ_hKlNVmMnPSO2WEjvxo2UALdotWZMx3RR9olNrX4XX1zOpcZtcRH0mUft385Fn5hYsfqyUACXdEORwRYWQd4-550qgRH_RbP7ubFCgtYLTPHbYa4RauCEhEZvvzikMY8dthIQpWkuxPQ5Vhsp7-vq_WpzFfmPEVzMqLcStIiHuHBHeZCqpsTbnX2LAV7-TDgxvcCbkfSoq0WAswm
Re: [Freesurfer] LME design matrix for changes in 1 group
pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long> > <http://secure-web.cisco.com/1t9KdLgaaOX0ZM8q84nAgqzxuwxzOE7mU6W8L9Xf2vgU34gxEtyG2Zcx557UOSHgoNdN49Uy--wXidOihtVmF9VBDcwIi6GXK4c-fI6xsd0VLgD1yc30AOeIMNBdY-WvgV-sepvsAql3Tdi9OKH248IzQH0t-cXbj3q_HlbowpgfWh6Zbzw9dGMuZUpftxn6Gp-Ycq8od7JVV4DikAMkhj2y-8JdyHdUSU3JJkETfUVntjuAVBZ5AN_y-1pI39bu3w95rTUrH9BhH2ic1xtlG1hASibJjoDsnj87lYMrp6h4urWndK0g1UHCj-Scz0voeCsI6nuyoAYkEJEZLjFog8g/http%3A%2F%2Fwww.ajnr.org%2Fcontent%2F36%2F12%2F2277.long> > > > Best, Martin > > > > On 30. Jan 2023, at 15:18, amirhossein manzouri > wrote: > > > > Hi, > I have 2 sessions of data acquired in the same day for each participant > before and after the drug intake. I wonder how to analyse this with LME > tool. I create design matrix X in 2 columns, first all ones and second the > time differences(which are the same) and wonder if I need to only run the > model with one random effect like > > lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3); > > And what would be the next steps to get the stats and sig.mgh > > Best regards, > Amirhossein Manzouri > > > > > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1Soma_Jv2D3v65EVhiRlp3N_lY_u17jLzODtOQXfB7cHB9AoOVsWBj7Sx_fCSSakWrw2FdgBvujP5xEEAFhkoYCg3PuTGXU3E7E6JIZV0SQvNByoAlfytRkTOjXCN00A5cGYp7XhK-7MluC4bGYaDlCEpFgQkZ2M84H_GbNqmYfts9oUL2iW1d8dT4OYDFmoYI9IrWcwPXwa7fPwHWnzKPgrYkAAzp7h41ek8EnvFSKJmpqFkY2DwpLUVsZVbyuzhWEsPejDyVuaGO9dukoWJUyukOTXfkciTHx2IAUvUDXuy9kL0Vnkt9KAPMV99scdcwAktivS7eubS4m8i-LafPg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . > -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] LME design matrix for changes in 1 group
External Email - Use Caution Hi, I have 2 sessions of data acquired in the same day for each participant before and after the drug intake. I wonder how to analyse this with LME tool. I create design matrix X in 2 columns, first all ones and second the time differences(which are the same) and wonder if I need to only run the model with one random effect like lhTh0_1RF = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3); And what would be the next steps to get the stats and sig.mgh Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis
External Email - Use Caution Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open file No such file or directory mri_surfcluster: could not read surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white No such file or directory I wonder if you found the reason and solution? Best regards, Amirhossein Manzouri On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 11/27/2018 06:46 AM, C.P.E. Rollins wrote: > > External Email - Use Caution > > Hi Douglas, > > > > Thanks a lot for your answers. > > > > 1) For the permutations, would you recommend using this for > > controlling for MC in cortical thickness analyses too? > Yes > > Why is it recommended to use permutation simulation as opposed to Z > > Monte Carlo simulation for an LGI analysis? > Because the spatial correlations are very high (which makes MCZ less > accurate) > > > > 2) I've attached here the output from ls -Rl > > $FREESURFER_HOME/subjects/fsaverage. > It looks like there is a difference in where you think FREESURFER_HOME > is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the > attached file says it is in /applications/freesurfer/freesurfer_6.0.0. > Which one is it? > > > > > > Thanks again, > > Colleen > > > > On 2018-11-23 16:26, C.P.E. Rollins wrote: > >> Dear Freesurfer Developers, > >> I have a 2-part question: > >> 1) I was advised to use permutation to control for multiple > >> comparisons in an LGI analysis, would you mind elaborating how to do > >> this in command line (in terms of command and parameters)? > >> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache > >> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error > >> (attached). I was wondering if you might have any advice? The file > >> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can > >> view it in freeview. > >> > >> Many thanks, > >> Colleen > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit
I see , so volumes are also surface based. On Tue, 20 Feb 2018 at 23:16, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > so this is thickness data? Hippocampus is a volume-based structure and > so not represented on the surface > > > On 02/20/2018 05:13 PM, amirhossein manzouri wrote: > > Hi , > > This is the output of long_mris_slopes! > > > > On Tue, 20 Feb 2018 at 23:10, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast > > output, then use the aseg.mgz in fsaverage/mri.2mm > > > > > > > > On 02/16/2018 05:24 AM, amirhossein manzouri wrote: > > > Hi, > > > To make the mask: > > > mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh > > > > > > Run glmfit: > > > > > > cmdline mri_glmfit.bin --osgm --glmdir > > > lh.testretest.volume-rate.fwhm10_LHipp --y > > > lh.testretest.volume-spc-10.stack.mgh --mask > fsaverage/mri/Lhipp.mgh > > > --surf fsaverage lh > > > sysname Linux > > > FixVertexAreaFlag = 1 > > > UseMaskWithSmoothing 1 > > > OneSampleGroupMean 1 > > > y > > > > > > > /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh > > > logyflag 0 > > > usedti 0 > > > mask fsaverage/mri/Lhipp.mgh > > > maskinv 0 > > > glmdir lh.testretest.volume-rate.fwhm10_LHipp > > > IllCondOK 0 > > > ReScaleX 1 > > > DoFFx 0 > > > Creating output directory lh.testretest.volume-rate.fwhm10_LHipp > > > Loading y from > > > > > > > /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh > > > ... done reading. > > > Saving design matrix to > > lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat > > > Computing normalized matrix > > > Normalized matrix condition is 1 > > > Matrix condition is 1 > > > ERROR: dimension mismatch 1 between y and mask > > > > > > Best regards, > > > Amirhossein Manzouri > > > > > > > > > > > > On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > Can you send your glmfit command line and terminal output? > > > > > > > > > > > > > > > On 02/15/2018 07:21 AM, amirhossein manzouri wrote: > > > > > > Hi , > > > I did longitudinal analysis and now I made masks for > > > Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz > > > using mri_binarize .I use the masks with mri_glmfit for > > > volume_rate_stack but I get "dimensions mismatch 1 between > y > > > and mask" error . > > > I wonder: > > > 1) How can I run analysis in subcortical volumes? > > > 2) Is it possible to run mri_glmfit on the whole brain > > not lh > > > and rh separately ? > > > > > > Best regards, > > > Amirhossein Manzouri > > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > <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> > > > <http://www.nmr.mgh.harvard.edu/facility/
Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit
Hi , This is the output of long_mris_slopes! On Tue, 20 Feb 2018 at 23:10, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast > output, then use the aseg.mgz in fsaverage/mri.2mm > > > > On 02/16/2018 05:24 AM, amirhossein manzouri wrote: > > Hi, > > To make the mask: > > mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh > > > > Run glmfit: > > > > cmdline mri_glmfit.bin --osgm --glmdir > > lh.testretest.volume-rate.fwhm10_LHipp --y > > lh.testretest.volume-spc-10.stack.mgh --mask fsaverage/mri/Lhipp.mgh > > --surf fsaverage lh > > sysname Linux > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 1 > > y > > > /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh > > logyflag 0 > > usedti 0 > > mask fsaverage/mri/Lhipp.mgh > > maskinv 0 > > glmdir lh.testretest.volume-rate.fwhm10_LHipp > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory lh.testretest.volume-rate.fwhm10_LHipp > > Loading y from > > > /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh > > ... done reading. > > Saving design matrix to lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat > > Computing normalized matrix > > Normalized matrix condition is 1 > > Matrix condition is 1 > > ERROR: dimension mismatch 1 between y and mask > > > > Best regards, > > Amirhossein Manzouri > > > > > > > > On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Can you send your glmfit command line and terminal output? > > > > > > > > > > On 02/15/2018 07:21 AM, amirhossein manzouri wrote: > > > > Hi , > > I did longitudinal analysis and now I made masks for > > Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz > > using mri_binarize .I use the masks with mri_glmfit for > > volume_rate_stack but I get "dimensions mismatch 1 between y > > and mask" error . > > I wonder: > > 1) How can I run analysis in subcortical volumes? > > 2) Is it possible to run mri_glmfit on the whole brain not lh > > and rh separately ? > > > > Best regards, > > Amirhossein Manzouri > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <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/ > > <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 > > <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 > gr...@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/ > > -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit
Hi, To make the mask: mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh Run glmfit: cmdline mri_glmfit.bin --osgm --glmdir lh.testretest.volume-rate.fwhm10_LHipp --y lh.testretest.volume-spc-10.stack.mgh --mask fsaverage/mri/Lhipp.mgh --surf fsaverage lh sysname Linux FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh logyflag 0 usedti 0 mask fsaverage/mri/Lhipp.mgh maskinv 0 glmdir lh.testretest.volume-rate.fwhm10_LHipp IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.testretest.volume-rate.fwhm10_LHipp Loading y from /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh ... done reading. Saving design matrix to lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 ERROR: dimension mismatch 1 between y and mask Best regards, Amirhossein Manzouri On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Can you send your glmfit command line and terminal output? > > > > > On 02/15/2018 07:21 AM, amirhossein manzouri wrote: > >> Hi , >> I did longitudinal analysis and now I made masks for Hippocampus and >> amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the >> masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch >> 1 between y and mask" error . >> I wonder: >> 1) How can I run analysis in subcortical volumes? >> 2) Is it possible to run mri_glmfit on the whole brain not lh and rh >> separately ? >> >> Best regards, >> Amirhossein Manzouri >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > > > 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@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] Using masks from aseg.mgz with mri_glmfit
Hi , I did longitudinal analysis and now I made masks for Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch 1 between y and mask" error . I wonder: 1) How can I run analysis in subcortical volumes? 2) Is it possible to run mri_glmfit on the whole brain not lh and rh separately ? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Paired t-test for correlation analysis on two time points
Of course. Just another question to make sure I understand your answer correctly. What you suggested with the fsgd file and contrast is the same as running Qdec on the two time points as two groups and ROI as variable in the dec table and then select the ROI as continuous and group as discreet with DODS, right? Best regards, Amirhossein Manzouri On Fri, Feb 19, 2016 at 4:28 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > I think so. Just make sure you don't try to draw conclusions from the ROI > or area around it. > > > On 2/19/16 2:02 AM, amirhossein manzouri wrote: > > Yes, I extracted the mean thickness of the ROI label from each timepoint > to use it as a continuous variable and study the correlation of whole brain > thickness with this region, is this ok? > > On Friday, 19 February 2016, Douglas N Greve < <gr...@nmr.mgh.harvard.edu> > gr...@nmr.mgh.harvard.edu> wrote: > >> Hmmm, I think I'm more confused. what do you mean by "mean thickness of >> ROI from longitudinal group comparison"? You are looking at how the >> thickness across cortex correlates with the mean thickness in your ROI? >> >> On 02/18/2016 05:50 PM, amirhossein manzouri wrote: >> >>> I just wanted to clarify a bit more to see if makes more sense now ? >>> >>> On Thursday, 18 February 2016, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> Hi Amirhossein, I can't tell from below if you have a question or >>> not >>> >>> On 02/18/2016 05:32 PM, amirhossein manzouri wrote: >>> >>> Hi and thanks, tp1 is before and tp2 after treatment, and the >>> measurement is the mean thickness of ROI from longitudinal >>> group comparison, so we basically want to see effect of >>> treatment on cortico cortical correlation. >>> >>> On Thursday, 18 February 2016, Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>> wrote: >>> >>> so you want to test whether the cross-sectional slope changes >>> across time? That is unusual, but you can do it by >>> specifying two >>> classes in the FSGD file, one for each time point. Also >>> specify a >>> variable which is your measurement. Then create a contrast >>> 0 0 1 >>> -1. This will test whether the slopes change between >>> "groups", >>> where a "group" is the given time point. This analysis >>> does not >>> make sense to me, but that is how to do it. >>> doug >>> >>> On 02/18/2016 12:16 PM, amirhossein manzouri wrote: >>> >>> Hi, >>> We would like to run paired t-test on longitudinal within >>> group data for correlation analysis of one measurement >>> and >>> cortical thickness, not cortical thickness comparison >>> at the >>> respective time point . >>> I found the paired analysis and read that but in fact >>> we need >>> to see if correlation between our measure and CTH >>> differs from >>> time point one to time point 2. So the question will >>> does the >>> thickness and measure1 correlation differs between time >>> point1 and tp2? >>> >>> >>> >>> Best regards, >>> Amirhossein Manzouri >>> >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://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> >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>
Re: [Freesurfer] Paired t-test for correlation analysis on two time points
I just wanted to clarify a bit more to see if makes more sense now ? On Thursday, 18 February 2016, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Hi Amirhossein, I can't tell from below if you have a question or not > > On 02/18/2016 05:32 PM, amirhossein manzouri wrote: > >> Hi and thanks, tp1 is before and tp2 after treatment, and the measurement >> is the mean thickness of ROI from longitudinal group comparison, so we >> basically want to see effect of treatment on cortico cortical correlation. >> >> On Thursday, 18 February 2016, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> so you want to test whether the cross-sectional slope changes >> across time? That is unusual, but you can do it by specifying two >> classes in the FSGD file, one for each time point. Also specify a >> variable which is your measurement. Then create a contrast 0 0 1 >> -1. This will test whether the slopes change between "groups", >> where a "group" is the given time point. This analysis does not >> make sense to me, but that is how to do it. >> doug >> >> On 02/18/2016 12:16 PM, amirhossein manzouri wrote: >> >> Hi, >> We would like to run paired t-test on longitudinal within >> group data for correlation analysis of one measurement and >> cortical thickness, not cortical thickness comparison at the >> respective time point . >> I found the paired analysis and read that but in fact we need >> to see if correlation between our measure and CTH differs from >> time point one to time point 2. So the question will does the >> thickness and measure1 correlation differs between time >> point1 and tp2? >> >> >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 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. >> >> >> >> -- >> Best regards, >> Amirhossein Manzouri >> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Paired t-test for correlation analysis on two time points
Hi and thanks, tp1 is before and tp2 after treatment, and the measurement is the mean thickness of ROI from longitudinal group comparison, so we basically want to see effect of treatment on cortico cortical correlation. On Thursday, 18 February 2016, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > so you want to test whether the cross-sectional slope changes across time? > That is unusual, but you can do it by specifying two classes in the FSGD > file, one for each time point. Also specify a variable which is your > measurement. Then create a contrast 0 0 1 -1. This will test whether the > slopes change between "groups", where a "group" is the given time point. > This analysis does not make sense to me, but that is how to do it. > doug > > On 02/18/2016 12:16 PM, amirhossein manzouri wrote: > >> Hi, >> We would like to run paired t-test on longitudinal within group data for >> correlation analysis of one measurement and cortical thickness, not >> cortical thickness comparison at the respective time point . >> I found the paired analysis and read that but in fact we need to see if >> correlation between our measure and CTH differs from time point one to time >> point 2. So the question will does the thickness and measure1 correlation >> differs between time point1 and tp2? >> >> >> >> Best regards, >> Amirhossein Manzouri >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > > > 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. > -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Paired t-test for correlation analysis on two time points
Hi, We would like to run paired t-test on longitudinal within group data for correlation analysis of one measurement and cortical thickness, not cortical thickness comparison at the respective time point . I found the paired analysis and read that but in fact we need to see if correlation between our measure and CTH differs from time point one to time point 2. So the question will does the thickness and measure1 correlation differs between time point1 and tp2? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Using ROIs in SPM
Hi Doug, I solved the problem by using: bbregister --s subject --mov func_denoised/vol.nii --bold --init-spm --reg register.dat mri_label2vol --label mask.label --reg register.dat --temp func_denoised/vol.nii --o mask.nii Best regards, Amirhossein Manzouri On Mon, Jul 27, 2015 at 7:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What are the two T1 images? The command line below will take a label in 152 space and transfer it to mni305 space. I'm not sure what you are actually trying to achieve. doug On 07/23/2015 10:44 AM, amirhossein manzouri wrote: Hi, I found group differences based on T1 images with 8 channel coil in QDEC and for fMRI in SPM I have used T1 images from 32 channel coil for the same subjects . Now I want to use the regions that I found in QDEC for fMRI analysis . Would you please let me know how can I transfer the labels between two T1 images in a way that I end up in the same regions. I am using the following now but the coordinates are not correct in the T1-32 ch: mri_label2vol --label 1001_1/label/lh.transversetemporal.label --reg ../../average/mni152.register.dat --temp /Applications/spm8/canonical/avg152T1.nii --o lh.transversetemp_1001.nii Best regard s Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 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@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@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.
Re: [Freesurfer] Huge difference ini area for the same subject
Hi Doug, As you can see in the image I attached the average area is different for the same set by two different editor. I wonder if there is any reason for this? Best regards, Amirhossein Manzouri On Mon, Jul 27, 2015 at 9:16 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Hi Doug, Yes, one set of subjects by two editors and no difference in thickness but huge difference on the area between two sets. Actually I want to see f there is any difference between editors for the same set of subjects. On Monday, July 27, 2015, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: sorry, I'm not sure I understand. Can you elaborate what you did? Same set of subjects edited independtly by two editors? Then you look for a difference within the subjects and you don't find it with editor 1 but you do find it with editor 2? On 07/27/2015 07:24 AM, amirhossein manzouri wrote: Hi, Two people has done recon-all and edits for the same subjects in FS version 5.1 . In the qdec comparing same group which has been edited by two persons , we found no significant change in Cth but there is a pattern of area difference on both hemispheres showing significant decrease in middle area and increase on frontal and occipital. Do you have any idea what can be the reason for this?The first recon-all and edits and qcache have been done in 2012 and the second in 2015! Attached is the sample screenshot. Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Huge difference ini area for the same subject
Hi Doug, Yes, one set of subjects by two editors and no difference in thickness but huge difference on the area between two sets. Actually I want to see f there is any difference between editors for the same set of subjects. On Monday, July 27, 2015, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: sorry, I'm not sure I understand. Can you elaborate what you did? Same set of subjects edited independtly by two editors? Then you look for a difference within the subjects and you don't find it with editor 1 but you do find it with editor 2? On 07/27/2015 07:24 AM, amirhossein manzouri wrote: Hi, Two people has done recon-all and edits for the same subjects in FS version 5.1 . In the qdec comparing same group which has been edited by two persons , we found no significant change in Cth but there is a pattern of area difference on both hemispheres showing significant decrease in middle area and increase on frontal and occipital. Do you have any idea what can be the reason for this?The first recon-all and edits and qcache have been done in 2012 and the second in 2015! Attached is the sample screenshot. Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Using ROIs in SPM
Hi, I found group differences based on T1 images with 8 channel coil in QDEC and for fMRI in SPM I have used T1 images from 32 channel coil for the same subjects . Now I want to use the regions that I found in QDEC for fMRI analysis . Would you please let me know how can I transfer the labels between two T1 images in a way that I end up in the same regions. I am using the following now but the coordinates are not correct in the T1-32 ch: mri_label2vol --label 1001_1/label/lh.transversetemporal.label --reg ../../average/mni152.register.dat --temp /Applications/spm8/canonical/avg152T1.nii --o lh.transversetemp_1001.nii Best regard s Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] (no subject)
Hi FS, MR images of two of my subjects in a group have been acquired with different T1 protocol from the rest. All the subjects has been acquired with sagittal 1mm iso : Width: 230.00 mm (256) Height: 230.00 mm (256) Resolution: 1.113 pixels per mm Pixel size: 0.90x0.90 mm and these two with coronal iso: Width: 220.00 mm (256) Height: 220.00 mm (256) Resolution: 1.164 pixels per mm Pixel size: 0.86x0.86 mm Now I want to use these images in group analyses with Q-dec. Does Freesurfer Freesurfer automatically reformat/reconstruct the T1 images independent of their acquisition protocol? OR Do I need to reformat the images before running recon-all and then use in the Qdec? If so, which program do you recommend to use? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Apply ROI Label from first time point to longitudinal template
Thanks Martin, Yes, the label is from Qdec in first time point space I have done the following: 1) mri_label2label --srclabel rh_roi --srcsubject fsaverage --trgsubject 1003_1.long.temp_1003 --trglabel rh_roi --regmethod surface --hemi rh (For all the subj_1.long.temp_subj and subj_2.long.temp_subj) 2) mris_anatomical_stats -l rh.roi -t rh.thickness -b -f $subs/stats/rh.parsopercularis.stats $subs rh And at the end when I am trying to extract the thickness from each subject I get the following error: amir% aparcstats2table --hemi lh --subjects `cat list5.txt` --parc transversetemporal --meas thickness --skip --tablefile lh.Cth.roi.txt SUBJECTS_DIR : /Applications/freesurfer/subjects/longBO Parsing the .stats files Skipping /Applications/freesurfer/subjects/longBO/1003_1.long.temp_1003/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1005_1.long.temp_1005/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1003_2.long.temp_1003/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1005_2.long.temp_1005/stats/lh.transversetemporal.stats Building the table.. Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 388, in module rows, columns, table = sanitize_table(options, pretable) File /Applications/freesurfer/bin/aparcstats2table, line 303, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range The lh.tranverstemporal.stats looks like this: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2015/05/27-11:57:08-GMT # generating_program mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # cmdline mris_anatomical_stats -l lh.transversetemporal.label -t lh.thickness -b -f 1003_1.long.temp_1003/stats/lh.transverstemporal.stats 1003_1.long.temp_1003 lh # sysname Darwin # hostname Cerebro.local # machine x86_64 # user amir # # SUBJECTS_DIR /Applications/freesurfer/subjects/longBO # anatomy_type surface # subjectname 1003_1.long.temp_1003 # hemi lh # AnnotationFile lh.transversetemporal.label # AnnotationFileTimeStamp 2015/05/27 12:22:37 # Measure Cortex, NumVert, Number of Vertices, 134133, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 89551.4, mm^2 # NTableCols 10 # TableCol 1 ColHeader StructName # TableCol 1 FieldName Structure Name # TableCol 1 Units NA # TableCol 2 ColHeader NumVert # TableCol 2 FieldName Number of Vertices # TableCol 2 Units unitless # TableCol 3 ColHeader SurfArea # TableCol 3 FieldName Surface Area # TableCol 3 Units mm^2 # TableCol 4 ColHeader GrayVol # TableCol 4 FieldName Gray Matter Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader ThickAvg # TableCol 5 FieldName Average Thickness # TableCol 5 Units mm # TableCol 6 ColHeader ThickStd # TableCol 6 FieldName Thickness StdDev # TableCol 6 Units mm # TableCol 7 ColHeader MeanCurv # TableCol 7 FieldName Integrated Rectified Mean Curvature # TableCol 7 Units mm^-1 # TableCol 8 ColHeader GausCurv # TableCol 8 FieldName Integrated Rectified Gaussian Curvature # TableCol 8 Units mm^-2 # TableCol 9 ColHeader FoldInd # TableCol 9 FieldName Folding Index # TableCol 9 Units unitless # TableCol 10 ColHeader CurvInd # TableCol 10 FieldName Intrinsic Curvature Index # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.transversetemporal.label 1759 1138 3029 2.424 0.552 0.101 0.026 11 2.0 Best regards, Amirhossein Manzouri On Thu, May 28, 2015 at 6:40 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Amirhossein, where exactly is your label. If it is in the first time point, then how did it get there? I think it is probably in fsaverage space (where the first time points were mapped to perform your QDEC analysis). In that case use mri_label2label from fsaverage to the individual base spaces for all subjects. Best, Martin On 05/27/2015 04:32 PM, Douglas N Greve wrote: Use mri_label2label. Run it with --help to get more info doug On 05/27/2015 05:08 AM, amirhossein manzouri wrote: Hi All, I have created two ROIs from first time point Qdec group comparison. I need to use this ROI labels to extract the thickness from tp1 and tp2 registered to base (template) subjects(from longitudinal pipeline). Would you please let me how can I convert the label from 1st time point space to longitudinal template space? Best regards, Amirhossein Manzouri -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital
Re: [Freesurfer] Apply ROI Label from first time point to longitudinal template
Thanks Doug, I am trying to extract mean thickness from the ROI but I get the following error : amir% aparcstats2table --hemi lh --subjects `cat list5.txt` --parc transversetemporal --meas thickness --skip --tablefile lh.Cth.roi.txt SUBJECTS_DIR : /Applications/freesurfer/subjects/longBO Parsing the .stats files Skipping /Applications/freesurfer/subjects/longBO/1003_1.long.temp_1003/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1005_1.long.temp_1005/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1003_2.long.temp_1003/stats/lh.transversetemporal.stats Skipping /Applications/freesurfer/subjects/longBO/1005_2.long.temp_1005/stats/lh.transversetemporal.stats Building the table.. Traceback (most recent call last): File /Applications/freesurfer/bin/aparcstats2table, line 388, in module rows, columns, table = sanitize_table(options, pretable) File /Applications/freesurfer/bin/aparcstats2table, line 303, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range The lh.tranverstemporal.stats looks like this: # Table of FreeSurfer cortical parcellation anatomical statistics # # CreationTime 2015/05/27-11:57:08-GMT # generating_program mris_anatomical_stats # cvs_version $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ # mrisurf.c-cvs_version $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # cmdline mris_anatomical_stats -l lh.transversetemporal.label -t lh.thickness -b -f 1003_1.long.temp_1003/stats/lh.transverstemporal.stats 1003_1.long.temp_1003 lh # sysname Darwin # hostname Cerebro.local # machine x86_64 # user amir # # SUBJECTS_DIR /Applications/freesurfer/subjects/longBO # anatomy_type surface # subjectname 1003_1.long.temp_1003 # hemi lh # AnnotationFile lh.transversetemporal.label # AnnotationFileTimeStamp 2015/05/27 12:22:37 # Measure Cortex, NumVert, Number of Vertices, 134133, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 89551.4, mm^2 # NTableCols 10 # TableCol 1 ColHeader StructName # TableCol 1 FieldName Structure Name # TableCol 1 Units NA # TableCol 2 ColHeader NumVert # TableCol 2 FieldName Number of Vertices # TableCol 2 Units unitless # TableCol 3 ColHeader SurfArea # TableCol 3 FieldName Surface Area # TableCol 3 Units mm^2 # TableCol 4 ColHeader GrayVol # TableCol 4 FieldName Gray Matter Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader ThickAvg # TableCol 5 FieldName Average Thickness # TableCol 5 Units mm # TableCol 6 ColHeader ThickStd # TableCol 6 FieldName Thickness StdDev # TableCol 6 Units mm # TableCol 7 ColHeader MeanCurv # TableCol 7 FieldName Integrated Rectified Mean Curvature # TableCol 7 Units mm^-1 # TableCol 8 ColHeader GausCurv # TableCol 8 FieldName Integrated Rectified Gaussian Curvature # TableCol 8 Units mm^-2 # TableCol 9 ColHeader FoldInd # TableCol 9 FieldName Folding Index # TableCol 9 Units unitless # TableCol 10 ColHeader CurvInd # TableCol 10 FieldName Intrinsic Curvature Index # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd lh.transversetemporal.label 1759 1138 3029 2.424 0.552 0.101 0.026 11 2.0 Best regards, Amirhossein Manzouri On Wed, May 27, 2015 at 10:32 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Use mri_label2label. Run it with --help to get more info doug On 05/27/2015 05:08 AM, amirhossein manzouri wrote: Hi All, I have created two ROIs from first time point Qdec group comparison. I need to use this ROI labels to extract the thickness from tp1 and tp2 registered to base (template) subjects(from longitudinal pipeline). Would you please let me how can I convert the label from 1st time point space to longitudinal template space? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo
[Freesurfer] Apply ROI Label from first time point to longitudinal template
Hi All, I have created two ROIs from first time point Qdec group comparison. I need to use this ROI labels to extract the thickness from tp1 and tp2 registered to base (template) subjects(from longitudinal pipeline). Would you please let me how can I convert the label from 1st time point space to longitudinal template space? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Fw: longitudinal statistics LGI
Hi Jorge,
Which direction does this contrast show? con pat is redis or vice versa?
I mean how can one interpret the result?
Best regards,
Amirhossein Manzouri
On Sat, Mar 28, 2015 at 3:46 PM, jorge luis jbernal0...@yahoo.es wrote:
Hi Amirhossein
You need another column in your design matrix to encode the group. That
new column is 0 for control's row and 1 for patient's rows. the contrast to
test for population group differences is then [0 0 1].
-Jorge
--
*De:* amirhossein manzouri a.h.manzo...@gmail.com
*Para:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu
*CC:* jorge luis jbernal0...@yahoo.es
*Enviado:* Jueves 26 de marzo de 2015 10:50
*Asunto:* Re: [Freesurfer] Fw: longitudinal statistics LGI
Hi Jorge,
I have read the previous posts and applied it for my analysis which is
longitudinal study go control and patient groups. I have a control group
(n=19) with 2.87 ± 0.3 years time difference between scans. and patient
group (n=16) who have 1.31 ± 0.6 years time difference. I followed your
instructions first in each group separately , for example in control group
I have read the data:
1-Read your label eg.:
*lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); *
2-Read the data file eg.:
*[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');*
Then X which is 38x2 double , first column is all ones and second is 0 and
time difference every one row for each subject , so I want to see thickness
change so I used :
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
*lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);*
Having first column as all ones and second the time difference , I made
the contrast to look at thickness changes within group:
*CM.C = [1 0];*
4-Perform vertex-wise inferences eg.:
*F_lhstats = lme_mass_F(lhstats1, CM);*
5-Save results eg.:
*fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); *
*Would you please let me know if the approach is correct ? and if I want
to add the patient group should I do the same just change the contrast ?*
*Best regards,*
Best regards,
Amirhossein Manzouri
On Fri, Mar 13, 2015 at 5:52 PM, Jon Alan Wieser wie...@uwm.edu wrote:
--
*From:* Jon Alan Wieser
*Sent:* Tuesday, December 30, 2014 8:11 PM
*To:* jorge luis
*Cc:* Kristin Elizabeth Maple
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jorge,
Following your instructions, so far we have done the following:
1-Read your label
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept
term and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
lhstats3 = lme_mass_fit_vw(X, [1 2 6], lhY, ni, lhcortex);
%intercept_time_gender
lhstats4 = lme_mass_fit_vw(X, [1 2 7], lhY, ni, lhcortex);
%intercept_time_age
lhstats5 = lme_mass_fit_vw(X, [1 2 3 6 ], lhY, ni, lhcortex);
%intercept_time_cannabis_gender
We displayed the lREML data on the surface models in matlab. In some
cases,(when there were 3 or more effects ( i.e. 1 2 6) ) the lreml values
had real and imaginary values, so I displayed the ABS value of the lreml
We need to know the following:
1. How do we model this:
Intercept, time, age, gender, Alcohol, other drugs vs.
Intercept, time, age, Gender, Alcohol, Other drug, cannabis
2. Correct for multiple comparisons
3. Open these in Freesurfer, significance maps using tksurfer ( P
0.05)
Is it only visual, or is there a significance test between the two models
4. How do we get a map that demonstrates the unique effect of
cannabis
5. What Contrast matrix do we use for the LME_mass_F program
Thanks
Jon
--
*From:* jorge luis jbernal0...@yahoo.es
*Sent:* Wednesday, December 17, 2014 9:25 AM
*To:* Freesurfer support list; Jon Alan Wieser
*Cc:* Krista Lisdahl Medina; alicia.thomas@gmail.com
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the
following way: First, the intercept term (which is a column of ones);
second, the time covariate; third, any time-varying covariates (eg.
cannabis use); fourth, the group covariates of interest (eg. a binary
variable indicating whether the subject is a patient or control) and their
interactions with the time-varying covariates; finally any other nuisance
time-invariant covariate (eg. gender). So your design matrix is comprised
by the following columns:
1. Intercept (a column of ones)
2. Time since baseline
3. cannabis use (time
Re: [Freesurfer] Fw: longitudinal statistics LGI
Dear Jorge,
Thanks for the reply , when I run *lhstats1 = lme_mass_fit_vw(X, [1 2],
lhY, ni, lhcortex); *Matlab says that it doesn't converge in 99% !
Another question is about the approach you suggested in the FreeSurfer
website,
[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere,lhRe,lhTh0,lhcortex,2,95);
The second step lasts forever without any response from Matlab, should it
take long time? or can I change some parameters or should I stick to your
method?
Best regards,
Amirhossein Manzouri
On Sat, Mar 28, 2015 at 3:46 PM, jorge luis jbernal0...@yahoo.es wrote:
Hi Amirhossein
You need another column in your design matrix to encode the group. That
new column is 0 for control's row and 1 for patient's rows. the contrast to
test for population group differences is then [0 0 1].
-Jorge
--
*De:* amirhossein manzouri a.h.manzo...@gmail.com
*Para:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu
*CC:* jorge luis jbernal0...@yahoo.es
*Enviado:* Jueves 26 de marzo de 2015 10:50
*Asunto:* Re: [Freesurfer] Fw: longitudinal statistics LGI
Hi Jorge,
I have read the previous posts and applied it for my analysis which is
longitudinal study go control and patient groups. I have a control group
(n=19) with 2.87 ± 0.3 years time difference between scans. and patient
group (n=16) who have 1.31 ± 0.6 years time difference. I followed your
instructions first in each group separately , for example in control group
I have read the data:
1-Read your label eg.:
*lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); *
2-Read the data file eg.:
*[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');*
Then X which is 38x2 double , first column is all ones and second is 0 and
time difference every one row for each subject , so I want to see thickness
change so I used :
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
*lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);*
Having first column as all ones and second the time difference , I made
the contrast to look at thickness changes within group:
*CM.C = [1 0];*
4-Perform vertex-wise inferences eg.:
*F_lhstats = lme_mass_F(lhstats1, CM);*
5-Save results eg.:
*fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); *
*Would you please let me know if the approach is correct ? and if I want
to add the patient group should I do the same just change the contrast ?*
*Best regards,*
Best regards,
Amirhossein Manzouri
On Fri, Mar 13, 2015 at 5:52 PM, Jon Alan Wieser wie...@uwm.edu wrote:
--
*From:* Jon Alan Wieser
*Sent:* Tuesday, December 30, 2014 8:11 PM
*To:* jorge luis
*Cc:* Kristin Elizabeth Maple
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jorge,
Following your instructions, so far we have done the following:
1-Read your label
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept
term and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
lhstats3 = lme_mass_fit_vw(X, [1 2 6], lhY, ni, lhcortex);
%intercept_time_gender
lhstats4 = lme_mass_fit_vw(X, [1 2 7], lhY, ni, lhcortex);
%intercept_time_age
lhstats5 = lme_mass_fit_vw(X, [1 2 3 6 ], lhY, ni, lhcortex);
%intercept_time_cannabis_gender
We displayed the lREML data on the surface models in matlab. In some
cases,(when there were 3 or more effects ( i.e. 1 2 6) ) the lreml values
had real and imaginary values, so I displayed the ABS value of the lreml
We need to know the following:
1. How do we model this:
Intercept, time, age, gender, Alcohol, other drugs vs.
Intercept, time, age, Gender, Alcohol, Other drug, cannabis
2. Correct for multiple comparisons
3. Open these in Freesurfer, significance maps using tksurfer ( P
0.05)
Is it only visual, or is there a significance test between the two models
4. How do we get a map that demonstrates the unique effect of
cannabis
5. What Contrast matrix do we use for the LME_mass_F program
Thanks
Jon
--
*From:* jorge luis jbernal0...@yahoo.es
*Sent:* Wednesday, December 17, 2014 9:25 AM
*To:* Freesurfer support list; Jon Alan Wieser
*Cc:* Krista Lisdahl Medina; alicia.thomas@gmail.com
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the
following way: First, the intercept term (which is a column of ones);
second, the time covariate; third, any time-varying covariates (eg
[Freesurfer] Measuring Brain torque
Dear Freesurfer Experts, I wonder if there is anyway in FS to measure the brain torque or if you have any experience with other tools regarding this? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Fw: longitudinal statistics LGI
Hi Jorge,
I have read the previous posts and applied it for my analysis which is
longitudinal study go control and patient groups. I have a control group
(n=19) with 2.87 ± 0.3 years time difference between scans. and patient
group (n=16) who have 1.31 ± 0.6 years time difference. I followed your
instructions first in each group separately , for example in control group
I have read the data:
1-Read your label eg.:
*lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); *
2-Read the data file eg.:
*[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');*
Then X which is 38x2 double , first column is all ones and second is 0 and
time difference every one row for each subject , so I want to see thickness
change so I used :
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
*lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);*
Having first column as all ones and second the time difference , I made the
contrast to look at thickness changes within group:
*CM.C = [1 0];*
4-Perform vertex-wise inferences eg.:
*F_lhstats = lme_mass_F(lhstats1, CM);*
5-Save results eg.:
*fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); *
*Would you please let me know if the approach is correct ? and if I want to
add the patient group should I do the same just change the contrast ?*
*Best regards,*
Best regards,
Amirhossein Manzouri
On Fri, Mar 13, 2015 at 5:52 PM, Jon Alan Wieser wie...@uwm.edu wrote:
--
*From:* Jon Alan Wieser
*Sent:* Tuesday, December 30, 2014 8:11 PM
*To:* jorge luis
*Cc:* Kristin Elizabeth Maple
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jorge,
Following your instructions, so far we have done the following:
1-Read your label
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept
term and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
lhstats3 = lme_mass_fit_vw(X, [1 2 6], lhY, ni, lhcortex);
%intercept_time_gender
lhstats4 = lme_mass_fit_vw(X, [1 2 7], lhY, ni, lhcortex);
%intercept_time_age
lhstats5 = lme_mass_fit_vw(X, [1 2 3 6 ], lhY, ni, lhcortex);
%intercept_time_cannabis_gender
We displayed the lREML data on the surface models in matlab. In some
cases,(when there were 3 or more effects ( i.e. 1 2 6) ) the lreml values
had real and imaginary values, so I displayed the ABS value of the lreml
We need to know the following:
1. How do we model this:
Intercept, time, age, gender, Alcohol, other drugs vs.
Intercept, time, age, Gender, Alcohol, Other drug, cannabis
2. Correct for multiple comparisons
3. Open these in Freesurfer, significance maps using tksurfer ( P
0.05)
Is it only visual, or is there a significance test between the two models
4. How do we get a map that demonstrates the unique effect of
cannabis
5. What Contrast matrix do we use for the LME_mass_F program
Thanks
Jon
--
*From:* jorge luis jbernal0...@yahoo.es
*Sent:* Wednesday, December 17, 2014 9:25 AM
*To:* Freesurfer support list; Jon Alan Wieser
*Cc:* Krista Lisdahl Medina; alicia.thomas@gmail.com
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the
following way: First, the intercept term (which is a column of ones);
second, the time covariate; third, any time-varying covariates (eg.
cannabis use); fourth, the group covariates of interest (eg. a binary
variable indicating whether the subject is a patient or control) and their
interactions with the time-varying covariates; finally any other nuisance
time-invariant covariate (eg. gender). So your design matrix is comprised
by the following columns:
1. Intercept (a column of ones)
2. Time since baseline
3. cannabis use (time-varying if varies over time for each subject
during the follow-up time)
4. alcohol use (time-varying if varies over time for each subject during
the follow-up time)
5. drug use over time (time-varying if varies over time for each subject
during the follow-up time)
6. gender
7. age at baseline
There is no GUI for setting up the models. Here is an outline of the
basic steps (with only three time points you shouldn't need more than two
random effects):
1-Read your label eg.:
*lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); *
2-Read the data file eg.:
*[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');*
3-Fit a vertex-wise lme model with two random effects for the
intercept term and time eg.:
*lhstats1
Re: [Freesurfer] treatment effect compare to controls
Hi Martin, Thanks for your instructions. In my analysis when we look at Two Stage Model results within our control group , we see increase in thickness (thickening) more than decrease (thinning), where we expect to see the thinning effect. Is there any explanation for this? I have 19 controls with 2 to 3 years difference between tp1 and tp2. Best regards, Amirhossein Manzouri On Mon, Feb 23, 2015 at 5:25 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi, yes, the first is to stack all the data into a single file (on your study average, usually that is fsaverage). The second steps smoothes the data. You can use different smoothing levels, depending on your data. Usually 10 or 15 is a good number. The data will automatically be taken from the sub1t1.long.tempsub1 etc directories (this is signaled by the --qdec-long flag. The qdec table needs to be in the longitudinal format, that means the first column is the subject id (sub1-t1) the second column the base name (tempsub1) column headers are fsid fsid-base …. usually the third column is time from baseline (in years), but can be any time variable that you want to use in the LME. There is an example of the longitudinal qdec table here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel I'll probably add that to the lme page so it is easier to find. Best, Martin On Feb 23, 2015, at 4:54 AM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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@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.
Re: [Freesurfer] treatment effect compare to controls
Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape ___ Freesurfer mailing list Freesurfer@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] treatment effect compare to controls
Hi FreeSurfer, What would be the best way to compare the patient group before and after treatment with a control group? Should one use the tp1 and tp2 registered to the template from longitudinal analysis and compare those with the control group? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Fwd: treatment effect compare to controls
Hi FreeSurfer, I want to study the treatment effect on group pf 20 patients in 2 time points ( 6 month to 2 years) , I have also 2 time points from controls ( 2 to 3 years) . I ran longitudinal pile line and looked at the rate using qdec and the results shows positive significance from zero , does this mean increase? Would you please advise the best strategy for analysis ? Does Linear Mixed Model can help to investigate more? or improve the analysis? What would be the best way to compare the patient group before and after treatment with a control group? Should one use the tp1 and tp2 registered to the template from longitudinal analysis and compare those with the control group? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Apply a label to longitudinal measures and extract stats
Dear experts, I have created a label from Qdec and used mri_label2label to apply it to all subjects. Now I need to extract the pc1 measure from longitudinal analysis in my label. Would you please advise how to do this since kris_anatomical_stats doesn't work here? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Cortical Segmentation reliability in Mid-Line structures
Dear Bruce, I meant cingulate cortex, the cuneus and precuneus ! Best regards, Amirhossein Manzouri On Mon, Aug 11, 2014 at 12:53 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Amirhossein which structures do you mean? Like the ventricles? We usually mask those regions out using the ?h.cortex.label. The surfaces should be frozen in those regions in any case, meaning that the white and pial are in the same location (and the thickness is 0) cheers Bruce On Mon, 11 Aug 2014, amirhossein manzouri wrote: Dear All, I wonder if you have experienced or there is any report on cortical segmentation reliability in the mid-line structures of the brain, so one should take them into consideration in running group differences with Qdec? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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@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] Cortical Segmentation reliability in Mid-Line structures
Dear All, I wonder if you have experienced or there is any report on cortical segmentation reliability in the mid-line structures of the brain, so one should take them into consideration in running group differences with Qdec? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] effect of demeaning the age
http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/12505825.html 2) Do I have to include age covariate in that model even if I clearly matched the age distribution? Technically, you do not, but it should be a good idea to do so. You can try one of these things: (a) use DOSS (fits the same slope to both groups), or (b) stay with DODS and demean the ages. This is the same as what you are doing already, but it tests for the difference at the mean of your group instead of at 0. Best regards, Amirhossein Manzouri On Tue, Aug 5, 2014 at 12:53 AM, Sarah Whittle swhit...@unimelb.edu.au wrote: Hi, I have a follow-up question about demeaning, specifically applied to running linear mixed effects models. For example, we have a design matrix X with the following columns: intercept (all ones) age gender age*age pubertal status If we want to look at the effect of age*age, controlling for pubertal status and gender [0 0 0 1 0 ], should age be demeaned prior to calculating the interaction term? I presume so, because if not, age*age will be highly correlated with age. I also presume that the covariate pubertal status should be demeaned? Thanks, Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Tuesday, 5 August 2014 2:09 AM To: amirhossein manzouri; free surfer Subject: Re: [Freesurfer] effect of demeaning the age check out this web page http://mumford.fmripower.org/mean_centering/ On 08/04/2014 12:01 PM, amirhossein manzouri wrote: Hi, I am looking at group differences between patients(20) and controls(n=20). I get significant results when I use Age, while I get no significance using Demeaned age both with DODS, also the pattern of significance is different. Would you please explain why? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] effect of demeaning the age
Hi, I am looking at group differences between patients(20) and controls(n=20). I get significant results when I use Age, while I get no significance using Demeaned age both with DODS, also the pattern of significance is different. Would you please explain why? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Thanks Doug, I used the first link and works perfectly now! Best regards, Amirhossein Manzouri On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I just ran it, and it works fine. It may be that I need to give you more libraries. Start with this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.py Copy it into $FREESURFER_HOME/bin (after making a backup of the original one) If that still does not work, then copy this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.pyc doug On 05/20/2014 04:36 AM, amirhossein manzouri wrote: Dear Doug, Kindly find attached a sample of my lh.aparc.stats file! Best regards, Amirhossein Manzouri On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send me your lh.aparc.stats file? doug On 05/14/2014 01:41 PM, amirhossein manzouri wrote: Yes! On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Is the mean thickness in the ?h.aparc.stats file? Something like # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm On 05/13/2014 05:18 PM, amirhossein manzouri wrote: Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html ) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http
Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Dear Doug, Kindly find attached a sample of my lh.aparc.stats file! Best regards, Amirhossein Manzouri On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you send me your lh.aparc.stats file? doug On 05/14/2014 01:41 PM, amirhossein manzouri wrote: Yes! On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.edu wrote: Is the mean thickness in the ?h.aparc.stats file? Something like # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm On 05/13/2014 05:18 PM, amirhossein manzouri wrote: Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post(https://www.mail-archive. com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ lh.aparc.stats Description: Binary data ___ Freesurfer mailing list Freesurfer
Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Yes! On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is the mean thickness in the ?h.aparc.stats file? Something like # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm On 05/13/2014 05:18 PM, amirhossein manzouri wrote: Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post(https://www.mail-archive.com/freesurfer@nmr.mgh. harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 gr...@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@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.
Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post(https://www.mail-archive.com/freesurfer@nmr.mgh. harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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@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.
Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Dear Doug, I have read this post( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Mean Thickness for each hemisphere from ?.aparc.stats
Dear Doug, I have read this post( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html) regarding extracting Mean Cth of each hemisphere and I just get insula as the last and totally 34 numbers, I use aparcstats2table --hemi lh --subjects bert -m thickness --tablefile lh.Cth.bert.txt Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Restrict QDEC analysis to a region
Tanks doug, Is it ok like this: mri_glmfit-sim --glmdir qdec/Untitled --cache 1.3 neg ? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 8:25 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: you will have to run the correction for multiple comparisons with mri_glmfit-sim (ie, you can't do it in qdec). doug On 03/17/2014 02:03 PM, amirhossein manzouri wrote: Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] Which Volume is the one in Qdec measures?
Thanks. Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 5:55 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Yes, GM volume. doug On 03/12/2014 09:58 AM, amirhossein manzouri wrote: Hi All, Would please let me know about the origin of volume in the measures menu of Qdec, so I can interpret the results from group comparisons. Is it Gray Matter volume? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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@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.
Re: [Freesurfer] Restrict QDEC analysis to a region
Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ 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@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.
Re: [Freesurfer] Restrict QDEC analysis to a region
Yes. Basically I want to see the effect of restricting the brain area on the group comparison clusters from Monte Carlo Simulation (threshold 1.3). As you mentioned before from mdi_glmfit I just get a masked version of whole brain analysis. How can I do the correction for multiple comparison with Monte Carlo (threshold 1.3) command based? Best regards, Amirhossein Manzouri On Mon, Mar 17, 2014 at 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: I don't know what you mean. Can you elaborate? doug On 03/17/2014 01:19 PM, amirhossein manzouri wrote: Can I also use mri_surfcluster as it is in qdec since I want to compare the whole brain and masked brain results? Best regards, Amirhossein Manzouri On Fri, Mar 14, 2014 at 4:49 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you are doing it the right way. There is no difference in the uncorrected analysis. There will be a difference when you correct for multiple comparisons doug On 03/14/2014 11:15 AM, amirhossein manzouri wrote: Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 gr...@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@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] Restrict QDEC analysis to a region
Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Which Volume is the one in Qdec measures?
Hi All, Would please let me know about the origin of volume in the measures menu of Qdec, so I can interpret the results from group comparisons. Is it Gray Matter volume? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Wrong pail surfaces in few slices
Hi all, There is incorrect pial surface lines (red and yellow) in the right hemisphere of some of my subjects. The white matter and grey matter are very close regarding intensity and this can be seen in just a few slices and then it gets correct. I tried control points but regarding the low intensity they can be effective. I wonder if there is a way to correct this, or if they may affect the qdec analysis between group afterwards a lot.(since they are present in one or few slices and create thick GM in those slices!) Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Wrong pail surfaces in few slices
Thanks Bruce for the prompt reply. Would you please explain how can I control mris_make_surfaces parameters, is this a part of recon-all process? Best regards, Amirhossein Manzouri On Mon, Feb 17, 2014 at 3:35 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Amirhossein it's hard to tell without looking at the data, but you could try using the expert options to change the allowable intensity ranges for the different surfaces (e.g. if the white is too far out, don't allow mris_make_surfaces to put the gray/white border at intensities that are that dark) cheers Bruce On Mon, 17 Feb 2014, amirhossein manzouri wrote: Hi all, There is incorrect pial surface lines (red and yellow) in the right hemisphere of some of my subjects. The white matter and grey matter are very close regarding intensity and this can be seen in just a few slices and then it gets correct. I tried control points but regarding the low intensity they can be effective. I wonder if there is a way to correct this, or if they may affect the qdec analysis between group afterwards a lot.(since they are present in one or few slices and create thick GM in those slices!) Best regards, Amirhossein Manzouri 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@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.
Re: [Freesurfer] Wrong pail surfaces in few slices
Thanks a lot. Best regards, Amirhossein Manzouri On Mon, Feb 17, 2014 at 4:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: they are automatically detected, but sometimes they can be too permissive (or restrictive) in some regions in some acquisitions. If you look through the recon-all.log file in your subject's scripts dir you can see what they are set to (search for mris_make_surfaces), then look at where the surfaces are wrong and see if you think changing some of the thresholds would help. It will say something like: computing class statistics... border white:238722 voxels (1.42%) border gray 265205 voxels (1.58%) WM (101.0): 100.4 +- 7.9 [70.0 -- 110.0] GM (76.0) : 75.1 +- 10.0 [30.0 -- 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.0 (was 70) setting MAX_BORDER_WHITE to 113.9 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 50.9 (was 40) setting MAX_GRAY to 98.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.9 (was 40) and you can change any of them with expert options (look in the recon-all --help). cheers Bruce On Mon, 17 Feb 2014, amirhossein manzouri wrote: Thanks Bruce for the prompt reply. Would you please explain how can I control mris_make_surfaces parameters, is this a part of recon-all process? Best regards, Amirhossein Manzouri On Mon, Feb 17, 2014 at 3:35 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Amirhossein it's hard to tell without looking at the data, but you could try using the expert options to change the allowable intensity ranges for the different surfaces (e.g. if the white is too far out, don't allow mris_make_surfaces to put the gray/white border at intensities that are that dark) cheers Bruce On Mon, 17 Feb 2014, amirhossein manzouri wrote: Hi all, There is incorrect pial surface lines (red and yellow) in the right hemisphere of some of my subjects. The white matter and grey matter are very close regarding intensity and this can be seen in just a few slices and then it gets correct. I tried control points but regarding the low intensity they can be effective. I wonder if there is a way to correct this, or if they may affect the qdec analysis between group afterwards a lot.(since they are present in one or few slices and create thick GM in those slices!) Best regards, Amirhossein Manzouri 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@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.
Re: [Freesurfer] Longitudinal analysis within one group
Dear Doug and Martin, Thanks a lot. I just have one group including 20 subjects. The scans have been done in a range of 0.9 to 1.5 years difference (tp2-tp1). Is ooh if I use the instructions from Paired Analysis : https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ? Regards, Best regards, Amirhossein Manzouri On Thu, Jan 30, 2014 at 10:31 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi, with one group you want to check if atrophy is significantly different from zero? That is probably the case for any group (e.g. aging), so it won't tell you anything really. Also, if you don't find atrophy in a region it doesn't mean it's not there (only your group size is too small to detect it). So the only real use I can think of, would be a test-retest study, where the assumption is that there is no change? Sadly Qdec cannot do 'one sample group mean', otherwise you could do that in qdec. If only you had a second 'control' group, then it could be done. You can use long_mris_slopes to compute rate or percent change maps (one for each subjects) and then you can use qdec to analyze those rate maps across groups. If you don't have a control group, you could still use long_mris_slopes (it can also map and stack the rate maps on fsaverage) and then simply run the one sample group mean in mri_glmfit. some info is also here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial_freeview and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel Best, Martin On 01/30/2014 09:18 AM, amirhossein manzouri wrote: Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with two time points in Qdec. And if it is not possible in Qdec how I suppose to do it? Best regards, Amirhossein Manzouri ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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@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] Longitudinal analysis within one group
Hi, Would you please advise if it is possible to do longitudinal statistical analysis within a group with two time points in Qdec. And if it is not possible in Qdec how I suppose to do it? Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] DOSS or DODS (Don't use DOSS with QDEC)
Dear Doug, I need also to correct for Age and Years of Education by using them as nuisance covariate. Would you please explain: Why the covariates should be demeaned? Is subtracting the mean from each individual the only way of demeaning? How Qdec regress out the effect of the covariates , linear or …? Thanks in advance, Best regards, Amirhossein Manzouri On Mon, Jan 13, 2014 at 5:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: If there is no interaction, then either DODS or DOSS is appropriate. DOSS will be more powerful and a little more interpretable. If there is an interaction then DODS must be used, and the interpretation of the difference between groups becomes more problematic. Eg, if age is the covariate, and there is an interaction, it means that there will be some age where the two best fit lines cross. At this point, there will be no difference between the groups. Far away from this point, there will be a difference. doug On 01/13/2014 03:49 AM, yaya ya wrote: Hey All, I am sorry to jump into this discussion. I know how to check the slope difference between groups. I want to ask help from you to confirm that if difference in thickness in some brain areas arising from (0 0 1 -1) happens, it means that there is a group * age interaction, right? Then, the only option is DODS rather than DOSS. If no difference in thickness is found for this contrast, it means that there is no interaction. Then DOSS is more appropriate. Am I right? Lickey On Mon, Jan 13, 2014 at 12:03 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If you have two groups and a single covariate, when you run it with mri_glmfit create a contrast with [0 0 1 -1]. In QDEC, it will be one of the default contrasts (something like do the two groups differ in slope?) doug On 1/12/14 5:31 AM, amirhossein manzouri wrote: Thanks Doug and how can check if the slopes are different? On Jan 12, 2014 12:33 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Use DODS to test whether the slopes differ between the three groups. If they do not, then use DOSS. doug On 1/11/14 5:03 PM, amirhossein manzouri wrote: Thanks Doug for the prompt reply. I just want to if DODS is ok to be used in my case or I should use DOSS? On Jan 11, 2014 10:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: HiAmirhossein, don't use the DOSS feature in QDEC because there is a bug such that it does not always do the right thing. Sorry, I sent out an email about 8mo ago on this, but it is not easy to let people know about a bug once the bug is out there. If you want to use DOSS, use mri_glmfit directly. If you still have a question, then repost to the list. doug On 1/11/14 1:22 PM, amirhossein manzouri wrote: Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri 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@nmr.mgh.harvard.edu mailto: Freesurfer@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
Re: [Freesurfer] DOSS or DODS (Don't use DOSS with QDEC)
Thanks Doug and how can check if the slopes are different? On Jan 12, 2014 12:33 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Use DODS to test whether the slopes differ between the three groups. If they do not, then use DOSS. doug On 1/11/14 5:03 PM, amirhossein manzouri wrote: Thanks Doug for the prompt reply. I just want to if DODS is ok to be used in my case or I should use DOSS? On Jan 11, 2014 10:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Amirhossein, don't use the DOSS feature in QDEC because there is a bug such that it does not always do the right thing. Sorry, I sent out an email about 8mo ago on this, but it is not easy to let people know about a bug once the bug is out there. If you want to use DOSS, use mri_glmfit directly. If you still have a question, then repost to the list. doug On 1/11/14 1:22 PM, amirhossein manzouri wrote: Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri 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@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] DOSS or DODS
Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] DOSS or DODS (Don't use DOSS with QDEC)
Thanks Doug for the prompt reply. I just want to if DODS is ok to be used in my case or I should use DOSS? On Jan 11, 2014 10:56 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Amirhossein, don't use the DOSS feature in QDEC because there is a bug such that it does not always do the right thing. Sorry, I sent out an email about 8mo ago on this, but it is not easy to let people know about a bug once the bug is out there. If you want to use DOSS, use mri_glmfit directly. If you still have a question, then repost to the list. doug On 1/11/14 1:22 PM, amirhossein manzouri wrote: Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri 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@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.
Re: [Freesurfer] Power analysis for Qdec
Thanks Doug, Would you please provide me the MATLAB code and instruction! BR On Tue, Oct 29, 2013 at 3:25 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Power analysis for Qdec
Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] DOSS FS 5.3
Thanks for the reply. Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values, are they generated by q-dec? Thanks in advance, On Wed, Oct 16, 2013 at 5:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: From the command line you will need to run mri_glmfit. The mri_glmfit.log file in the QDEC output folder will have a sample mri_glmfit command line. You will need to modify this by adding doss after the FSGD file. You will also need to create new contrast matrices to match the DOSS model. Search for fsgd on our wiki to get examples doug On 10/16/2013 03:19 AM, amirhossein manzouri wrote: Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. -- Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Extract Cortical Thickness from my data based on ROIs from Qdec
DEar FS experts, I need to extract the CTh from my whole data (90 subjects) based on generated ROI from Qdec(mc-z.neg.th13.sig.ocn.mgh). Would you please advise if I can do it in the same way you have mentioned in this post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22973.html -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] DOSS FS 5.3
Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] DOSS in FS 5.3 QDEC
Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] CORTICAL Thicknesses
Thanks a lot! On Mon, Sep 23, 2013 at 3:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Amirhossein as long as the surfaces are correct (yellow and red lines), then you don't need to worry about the segmentation, as it is the surfaces that define the thickness cheers Bruce On Mon, 23 Sep 2013, amirhossein manzouri wrote: Hi, In the attached Slice image of a processed brain, there is a yellow line which defines the WM and red line for the cortex but in segmentation some WM have been segmented as cortex and some part of cortex have not been segmented ! Would you please let me know how to handle the situation while I am reporting cortical thicknesses of my data? -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] bvecs error from Tracula
Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are encountering a memory error? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__**scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: Hi, The content is : freesurfer-Darwin-snowleopard-**__i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.** harvard.edu zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__har**vard.edu http://harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@nmr.mgh.harvard.edu wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory? -Zeke On 07/22/2013 04:23 PM, amirhossein manzouri wrote: Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard._**___edu/pipermail//freesurfer/_** ___2011-July/019392.html https://mail.nmr.mgh.harvard.**__edu/pipermail//freesurfer/__** 2011-July/019392.html https://mail.nmr.mgh.harvard.**edu/pipermail//freesurfer/** 2011-July/019392.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__ha**r__vard.eduhttp://har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com**__ mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__ha**r__vard.eduhttp://har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend
Re: [Freesurfer] bvecs error from Tracula
Hi, The content is : freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory? -Zeke On 07/22/2013 04:23 PM, amirhossein manzouri wrote: Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.**edu/pipermail//freesurfer/** 2011-July/019392.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.**__edu/fswiki/FsTutorial/**Tracula http://surfer.nmr.mgh.**harvard.edu/fswiki/FsTutorial/**Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri
Re: [Freesurfer] bvecs error from Tracula
Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.** edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] bvecs error from Tracula
Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.**gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] bvecs error from Tracula
Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] bvecs error from Tracula
Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.** edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Non-grey matter classified as grey matter
Dear Bruce, Thanks again for the response. I have FLAIR images for each subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR images in the analyses of cortical thickness to be able to edit (subtract) only the part of the brain which is missegmented (segmented as gray matter where the structure is tentorium of the cerebellum) and improve segmentation? On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Thanks a lot! On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Amir I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such. cheers Bruce On Fri, 12 Jul 2013, amirhossein manzouri wrote: Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote: Dear Bruce and Doug, Thank you very much! PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon! Ye On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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/ ftp
[Freesurfer] bvecs error from Tracula
Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri bvals Description: Binary data bvecs Description: Binary data dwi_orig.mghdti.bvals Description: Binary data dwi_orig.mghdti.bvecs Description: Binary data ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Xhemi results
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres! On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean by overlaying the results on L R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error
Re: [Freesurfer] Non-grey matter classified as grey matter
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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Non-grey matter classified as grey matter
Thanks a lot! On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Amir I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such. cheers Bruce On Fri, 12 Jul 2013, amirhossein manzouri wrote: Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye...@gmail.com wrote: Dear Bruce and Doug, Thank you very much! PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon! Ye On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: Dear Freesurfers, Do you think I should delete the extra dura-like structure in the attached case? Thank you very much! Sincerely, Ye __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e
Re: [Freesurfer] Xhemi results
Thanks a lot! On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It is the difference but it is on the tesselation of the left hemisphere. If you want it on the right hemisphere, then you need to perform the analysis on the right hemisphere. doug On 07/12/2013 02:37 AM, amirhossein manzouri wrote: Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres! On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: I don't know what you mean by overlaying the results on L R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH
Re: [Freesurfer] Xhemi results
Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 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@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. -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Xhemi results
As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: I don't know what you mean by overlaying the results on L R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? Yes. 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. 4) Is there any way to look at the results through the brain per slice and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 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@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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Xhemi results
Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain? -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] Fwd: problem downloading Xhemi files
Dear Doug, I just installed 5.3 version and now I have the Xhemi. I need to study asymmetry of the brains -processed with FS 5.1- comparing right and left hemispheres for each subject individually and between male and female groups including 40 subjects each. Would you please let me know the procedure with Xhemi. BR-Amir On Wed, Jun 19, 2013 at 9:18 AM, amirhossein manzouri a.h.manzo...@gmail.com wrote: I use curl to download in MAC with the links you mentioned and it is not there! amir% curl -O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- 0:00:01 --:--:-- 0 curl: (78) RETR response: 550 On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: I have version 5.1 so please recreate the links! BR On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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@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.
Re: [Freesurfer] problem downloading Xhemi files
I use curl to download in MAC with the links you mentioned and it is not there! amir% curl -O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 0 00 00 0 0 0 --:--:-- 0:00:01 --:--:-- 0 curl: (78) RETR response: 550 On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: I have version 5.1 so please recreate the links! BR On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If not, I'll have to recreate the links. let me know doug On 6/17/13 6:52 AM, amirhossein manzouri wrote: Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list Freesurfer@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] problem downloading Xhemi files
Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir ___ Freesurfer mailing list Freesurfer@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.
