[Freesurfer] Standalone Freeview?
Hi! I'm wondering if the latest version of Freeview is available in standalone version. I'm currently using FreeSurfer v5.1's tktools for correcting the recon-all outputs, but would like to switch to Freeview. However the version that I have doesn't seem to have the Recon tools, and if I install the latest FS, I will have to rerun the preprocessing... So is it possible to install the latest Freeview separately? Thanks. Jeni Chen ___ 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] Subcortical segmentation for PAG
Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni ___ 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] unit in 'search area' in the glmfit log
Hello, When running the Clusterwise Correction for Multiple Comparisons, I used a label as a mask to restrict search area. I want to find out the size of that label, so I guess I can pull that information out from the "mri_glmfit.log", specifically under 'searchspace'? Also I only see a numerical value there, I assume it is in mm2? Thanks. Jeni ___ 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] unit in 'search area' in the glmfit log
Thank you Doug. I was actually referring to the following values (example of my log output below): $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/pathname cmdline mri_glmfit --y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C ./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C ./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask ./pathname/mask.mgh --sim mc-z 5000 1.3 ./pathname/csd/mc-z.abs.1.3.j001 --sim-sign abs --fwhm 13.034857 --fsgd ./pathname/y.fsgd dods --label /Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white sysname Darwin hostname computer.local machine x86_64 user jeni FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.034857 niters125.00 OneSampleGroupMean 0 y/Volumes/pathname/lh.Group_abcd.thickness.10.mgh logyflag 0 usedti 0 FSGD ./pathname/y.fsgd labelmask /Volumes/pathname/lh_abcd_mask.label maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 14.1782 Matrix condition is 289425 Found 9260 points in label. Found 7440 voxels in mask Reshaping mriglm->mask... search space = 3795.353314 DOF = 37 thresh = 1.3, threshadj = 0.99897 I do see that it gives information on the number of voxels in the mask (which is 7440 in the above example). What I was referring to is the next number "search space = 3795.35..." Is that the search area? Also in your reply, I see the need to specify the mask.mgh. How do I specify it if my mask is a label file and not in mgh format? Thanks again. Jeni > On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote: > That number is in voxels or vertices. If you want surface area, then use > mri_segstats something like >> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh >> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat >> >> doug >> >> On 10/29/15 5:10 PM, Jeni Chen wrote: >> > Hello, >> > >> > When running the Clusterwise Correction for Multiple Comparisons, I used a >> > label as a mask to restrict search area. I want to find out the size of >> > that >> > label, so I guess I can pull that information out from the >> > "mri_glmfit.log", >> > specifically under 'searchspace'? Also I only see a numerical value there, >> > I >> > assume it is in mm2? >> > >> > Thanks. >> > >> > Jeni ___ 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] cwpvalthresh not specified
Hello, Just a quick question, if the 'cwpvalthresh' flag wasn't specified when running mri_glmfit-sim, the script will use the default .05 value, correct? Thanks for clairfying. Jeni Chen ___ 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] cwpvalthresh not specified
Phew! Thanks! jeni ___ 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] mri_glmfit --no-sim error: cannot find any csd files
Hello,I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered:mri_glmfit-sim \--glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \--cwpvalthresh .999 \--no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI copied and pasted the csd file from its own folder to the top directory, but it gave the same error. I've attached the error log in case you want to have a look. Thanks for your help!Jeni mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd.mri_glmfit-sim.log 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] mri_glmfit --no-sim error: cannot find any csd files
Thansk Doug. I tried it but still doesn't work. Any other thoughts? jeni ___ 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] mri_glmfit --no-sim error: cannot find any csd files
Hi Doug,Sorry; didn't realize it wasn't included.So to state the original problem, I tried running mri_glmfit-sim with the following options (previous message included below):mri_glmfit-sim \--glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \--cwpvalthresh .999 \--no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI get an error message saying "cannot find any csd files". You suggested putting just the csd base (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I did, but still gave the same error message. I've attached the error log if you want to have a look.Thanks.Jeni 1GroupAvg-Cor-thickness-Mod-VAS.mri_glmfit-sim.log Description: Binary data Hi Jeni, what is your command line and terminal output? In general, just saying that something does not work is not enough information to track down the problem. Also, please include previous correspondence. We answer a lot of emails here, and the easier you make it on us, the faster we can solve your problem. thanks! doug On 04/25/2013 04:41 PM, Jeni Chen wrote: > Thansk Doug. I tried it but still doesn't work. Any other thoughts? > > jeni > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >Hi Jeni, done pass that path to the csd, just the csd base. In your case I think it would be 1GroupAvg-Cor-thickness-Mod-VASdoug On 4/24/13 8:47 PM, Jeni Chen wrote: Hello, I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I specified the --no-sim option to avoid re-running the entire simulation again. I entered my DSC file but in the end I get the error message: "cannot find any csd files". Here is what I entered:mri_glmfit-sim \ --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ --cwpvalthresh .999 \ --no-sim GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI copied and pasted the csd file from its own folder to the top directory, but it gave the same error. I've attached the error log in case you want to have a look.Thanks for your help! Jeni___ 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] mri_glmfit --no-sim error: cannot find any csd files
The original command line: > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd To which you suggested > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim 1GroupAvg-Cor-thickness-Mod-VAS And it did not work either. Thanks. jeni Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 > what was your orignal mri_glmfit-sim command line? On 04/25/2013 05:17 PM, Jeni Chen wrote: > Hi Doug, > > Sorry; didn't realize it wasn't included. > > So to state the original problem, I tried running mri_glmfit-sim with > the following options (previous message included below): > > mri_glmfit-sim \ > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > --cwpvalthresh .999 \ > --no-sim > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd > > I get an error message saying "cannot find any csd files". You > suggested putting just the csd base > (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I > did, but still gave the same error message. I've attached the error > log if you want to have a look. > > Thanks. > > Jeni > > > > >> Hi Jeni, what is your command line and terminal output? In general, >> just saying that something does not work is not enough information to >> track down the problem. Also, please include previous correspondence. >> We answer a lot of emails here, and the easier you make it on us, the >> faster we can solve your problem. thanks! doug > On 04/25/2013 04:41 PM, Jeni Chen wrote: > > Thansk Doug. I tried it but still doesn't work. Any other thoughts? > > > > jeni > > > > > > ___ > > Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> Hi Jeni, done pass that path to the csd, just the csd base. In your >> case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS >> doug >>> On 4/24/13 8:47 PM, Jeni Chen wrote: >> >> Hello, >> >> I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I >> specified the --no-sim option to avoid re-running the entire >> simulation again. I entered my DSC file but in the end I get the >> error message: "cannot find any csd files". Here is what I entered: >> >> mri_glmfit-sim \ >> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> --cwpvalthresh .999 \ >> >> --no-sim >> >> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI >> copied and pasted the csd file from its own folder to the top >> directory, but it gave the same error. I've attached the error >> log in case you want to have a look. >> >> Thanks for your help! >> >> Jeni >> > > > > ___ > 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.
Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files
Hi Doug, The very first command line was: mri_glmfit-sim \ --glmdir /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ --sim mc-z 5000 3 mc-z.abs.3 \ --cwpvalthresh .05 \ --sim-sign abs \ --overwrite I was wondering, since the purpose of running mri_glmfit-sim at --cwpvalthresh .999 is to see all clusters, would it be the same if I were simply to look at sig.mgh? Thanks. Jeni > Sorry, I mean the first time that you ran it to create the csd files in > the first place > doug On 2013-04-25, at 5:30 PM, Jeni Chen wrote: > The original command line: > > mri_glmfit-sim \ > > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > > --cwpvalthresh .999 \ > > --no-sim > > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd > > To which you suggested > > > mri_glmfit-sim \ > > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > > --cwpvalthresh .999 \ > > --no-sim 1GroupAvg-Cor-thickness-Mod-VAS > > And it did not work either. > > Thanks. > > jeni > > > > Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 > > what was your orignal mri_glmfit-sim command line? > > On 04/25/2013 05:17 PM, Jeni Chen wrote: > > Hi Doug, > > > > Sorry; didn't realize it wasn't included. > > > > So to state the original problem, I tried running mri_glmfit-sim with > > the following options (previous message included below): > > > > mri_glmfit-sim \ > > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > > --cwpvalthresh .999 \ > > --no-sim > > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd > > > > I get an error message saying "cannot find any csd files". You > > suggested putting just the csd base > > (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I > > did, but still gave the same error message. I've attached the error > > log if you want to have a look. > > > > Thanks. > > > > Jeni > > > > > > > > > >> Hi Jeni, what is your command line and terminal output? In general, > >> just saying that something does not work is not enough information to > >> track down the problem. Also, please include previous correspondence. > >> We answer a lot of emails here, and the easier you make it on us, the > >> faster we can solve your problem. thanks! doug > > On 04/25/2013 04:41 PM, Jeni Chen wrote: > > > Thansk Doug. I tried it but still doesn't work. Any other thoughts? > > > > > > jeni > > > > > > > > > ___ > > > Freesurfer mailing list > > >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >> Hi Jeni, done pass that path to the csd, just the csd base. In your > >> case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS > >> doug > >>> On 4/24/13 8:47 PM, Jeni Chen wrote: > >> > >> Hello, > >> > >> I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I > >> specified the --no-sim option to avoid re-running the entire > >> simulation again. I entered my DSC file but in the end I get the > >> error message: "cannot find any csd files". Here is what I entered: > >> > >> mri_glmfit-sim \ > >> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ > >> --cwpvalthresh .999 \ > >> > >> --no-sim > >> > >> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csdI > >> copied and pasted the csd file from its own folder to the top > >> directory, but it gave the same error. I've attached the error > >> log in case you want to have a look. > >> > >> Thanks for your help! > >> > >> Jeni > >> > > > > > > > > ___ > > 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.
Re: [Freesurfer] mri_glmfit --no-sim error: cannot find any csd files
aha! That did the trick. Thanks! My other question is, since the purpose of running mri_glmfit-sim at --cwpvalthresh .999 is to see all the clusters, wouldn't it be the same if I were simply to look at sig.mgh? Jeni > The csdbase is mc-z.abs.3 > Try using that > doug > > On 2013-04-25, at 5:55 PM, Jeni Chen wrote: > Hi Doug, > > The very first command line was: > > mri_glmfit-sim \ > --glmdir > /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS > \ > --sim mc-z 5000 3 mc-z.abs.3 \ > --cwpvalthresh .05 \ > --sim-sign abs \ > --overwrite > > I was wondering, since the purpose of running mri_glmfit-sim at > --cwpvalthresh .999 is to see all clusters, would it be the same if I were > simply to look at sig.mgh? > > Thanks. > > Jeni > >> Sorry, I mean the first time that you ran it to create the csd files in >> the first place >> doug > > On 2013-04-25, at 5:30 PM, Jeni Chen wrote: > >> The original command line: >> > mri_glmfit-sim \ >> > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> > --cwpvalthresh .999 \ >> > --no-sim >> > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd >> >> To which you suggested >> >> > mri_glmfit-sim \ >> > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> > --cwpvalthresh .999 \ >> > --no-sim 1GroupAvg-Cor-thickness-Mod-VAS >> >> And it did not work either. >> >> Thanks. >> >> jeni >> >> >> >> Douglas N Greve Thu, 25 Apr 2013 14:08:32 -0700 >> > what was your orignal mri_glmfit-sim command line? >> >> On 04/25/2013 05:17 PM, Jeni Chen wrote: >> > Hi Doug, >> > >> > Sorry; didn't realize it wasn't included. >> > >> > So to state the original problem, I tried running mri_glmfit-sim with >> > the following options (previous message included below): >> > >> > mri_glmfit-sim \ >> > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> > --cwpvalthresh .999 \ >> > --no-sim >> > GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd >> > >> > I get an error message saying "cannot find any csd files". You >> > suggested putting just the csd base >> > (i.e. 1GroupAvg-Cor-thickness-Mod-VAS) for the --no-sim flag, which I >> > did, but still gave the same error message. I've attached the error >> > log if you want to have a look. >> > >> > Thanks. >> > >> > Jeni >> > >> > >> > >> > >> >> Hi Jeni, what is your command line and terminal output? In general, >> >> just saying that something does not work is not enough information to >> >> track down the problem. Also, please include previous correspondence. >> >> We answer a lot of emails here, and the easier you make it on us, the >> >> faster we can solve your problem. thanks! doug >> > On 04/25/2013 04:41 PM, Jeni Chen wrote: >> > > Thansk Doug. I tried it but still doesn't work. Any other thoughts? >> > > >> > > jeni >> > > >> > > >> > > ___ >> > > Freesurfer mailing list >> > >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> >> Hi Jeni, done pass that path to the csd, just the csd base. In your >> >> case I think it would be 1GroupAvg-Cor-thickness-Mod-VAS >> >> doug >> >>> On 4/24/13 8:47 PM, Jeni Chen wrote: >> >> >> >> Hello, >> >> >> >> I was trying to run mri_glmfit-sim at a lower cwpvalthresh so I >> >> specified the --no-sim option to avoid re-running the entire >> >> simulation again. I entered my DSC file but in the end I get the >> >> error message: "cannot find any csd files". Here is what I entered: >> >> >> >> mri_glmfit-sim \ >> >> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \ >> >> --cwpvalthresh .999 \ >> >> >> >> --no-sim >> >> >> >> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-t
[Freesurfer] Directed search for group analysis
Hello Freesurfer experts, I've been trying to figure out a way to run a directed search in a group analysis. I read the tutorial on ROI analysis and some of the posts here, but we can only do it with individual subject. Simply pout, I want to restrict my search areas to 4 ROIs (determined from the fsaverage or common template) when I run the group analysis (thus lowering the corrected stats threshold based on search criteria). What's the best way of doing it? Also, some posts suggests using the --mask option when running the glmfit command, but it seems some people also used the --label option. What is the difference? Thank you for your help. Jeni ___ 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] Smoothing in -qcache and the -fwhm option in mri_glmfit
Hello Freesurfer experts, Just a question about smoothing. I did recon-all -qcache to get pre-smoothed fsaverage surface at 0, 5, 10, 15, 20 and 25mm FWHM, so for mris_preproc I used the "--cache-in" option (eg. for the *10mm.fsaverage file). When I run mri_glmfit, I see the option "--fwhm". Is this option for those who did not pre-smooth their data so that they can do the smoothing there? If I'm using a *.thickness.10.mgh file (10mm FWHM) obtained from the previously described steps as my input file (--y), then by specifing again a value in --fwhm does it mean I'm 'double' smoothing my data? Jeni --- Jeni Chen, M.Sc. Agente de recherche Laboratoire de recherche en neuropsychologie de la douleur Pav. Paul-G. Desmarais, Université de Montréal CP 6128, Succ. A, Montréal, QC H3C 3J7 Tel: 514-343-6111 x4359 ___ 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] Smoothing in -qcache and the -fwhm option in mri_glmfit
So essentially the -fwhm option in mri_glmfit does the same thing as mri_surf2surf --fwhm ? Just want to make sure... Thanks again! Jeni ___ 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] Thickness and variable plot in glmfit
Hello again, In Qdec we get a plot of the data for a particular vertex showing the variable and the thickness in the x, y axis respectively. Is there a way to get the same plot when using glmfit? Where do I find the data for the plot? Thank you! Jeni Chen ___ 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] Freeview bus error
Hi, I was recently at the FreeSurfer workshop in Boston and learned about the "Freeview" tool in Freesurfer. However, when I tried to run it from my own laptop (Mac book pro), it crashes and gives the error message: "Bus error". I didn't get a chance to have this problem solved while I was there, and after coming back from Boston, I tried running the program on the Mac Pro in my lab, and I got the same error message. Does Freeview have known issue on Mac? Here are some info about the Mac in my lab: Mac Pro Mac OS X version 10.6.8 2x2.4GHz quad core 8GB memory FreeSurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd really appreciate it if someone could help me figure it out. Thank you in advance! Jeni ___ 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] Assigning multiple cores to virtual machine
Hello Everyone, I'm wondering if someone could post how to assign multiple cores to the virtual machine in the VirtualBox Ubuntu version of FS. I saw an earlier post that mentioned it but did not say how they did it. Basically we have an Intel i7 with 4 cores and 12GB of RAM. When I installed the Virtualbox, the only setting that it asked me to assign was the virtual memory, to which I gave 6GB. I'd like to have the same setting mentioned in that earlier post (i.e. assigning 3 cores to the virtual machine) so that I can rum multiple instances of FS all at the same time. Your help is much appreciated! Thank you in advance. Jeni No virus found in this message. Checked by AVG - www.avg.com Version: 10.0.1375 / Virus Database: 1509/3657 - Release Date: 05/24/11 ___ 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] Export table of cluster stats from Qdec
Hi, I have 2 questions regarding Qdec: 1. We would like to save the results of 'cluster stats' (the printout on the terminal after pressing the "Find clusters and go to max" button) to a text file. Is there a way to do that? Or is it automatically saved in somewhere and where would that location be? 2. Also, would it be possible to save the plot information at cluster's max in a particular region and later on read them in a text or excel file? Thank you for your help. Jeni ___ 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.
