Re: [Freesurfer] error in mri_glmfit-sim using a per-vertex regressor
that is just a warning, it is not a problem. the results should be fine On 11/30/15 6:28 AM, Carme Uribe Codesal wrote: Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* * * * * *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme ___ 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] error in mri_glmfit-sim using a per-vertex regressor
Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme ___ 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] Error from mri_glmfit-sim - Input volume voxel dimensions do not match
Hello, We're running into a bit of a hiccup in trying to do an analysis of subcortical volume differences between groups using mri_glmfit instead of the tables generated by asegstats2table. The error occurs at the end of our pipeline when running mri_glmfit-sim: ERROR: Input volume voxel dimensions do not match those in the registration file.” The full processing script is currently doing these steps: 1. mri_vol2vol --mov somesubj/mri/aseg.mgz —targ $FREESURFER_HOME/average/mni305.cor.mgz —xfm somesubj/mri/transforms/talairach.xfm —o somesubj/mri/aseg-in-mni305.mgz 2. mri_concat to concatenate all participants data together and output GroupAnalysis-in-MNI305.mgz 3. mri_glmfit --y GroupAnalysis-in-MNI305.mgz --fsgd Study1.fsgd dods --C group_diff.mtx --C group-x-age.mtx --C g1g2.intercept.mtx --C g1g2.age.mtx --glmdir study1.glmdir 4. Visualization works: tkmedit fsaverage orig.mgz -aseg -overlay study1.glmdir/group_diff/sig.mgh -fminmax 0.1 5 5. Correction (mri_glmfit-sim) breaks. mri_glmfit-sim --glmdir study1.glmdir --grf 1.3 neg --cwpvalthresh .05 Full error below, any help would be appreciated! Freesurfer 5.3 running on Mac OS X 10.9.x Peter J. Molfese, Ph.D. Research Scientist Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 pmolf...@haskins.yale.edu cd /zappa/kstudy /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir study1.glmdir --grf 1.3 neg --cwpvalthresh 0.05 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Dec 17 15:37:22 EST 2014 Darwin cab.haskins.lab 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 pmolfese setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y GroupAnalysis-in-MNI305.mgz --fsgd study1.fsgd --C DATA/group_diff.mtx --C DATA/group-x-age.mtx --C DATA/g1g2.intercept.mtx --C DATA/g1g2.age.mtx --glmdir study1.glmdir DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 2.396839 mri_volcluster --in study1.glmdir/g1g2.age/sig.mgh --mask study1.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig study1.glmdir/g1g2.age/grf.th1.3.neg.sig.cluster.mgh --sum study1.glmdir/g1g2.age/grf.th1.3.neg.sig.cluster.summary --ocn study1.glmdir/g1g2.age/grf.th1.3.neg.sig.ocn.mgh --cwpvalthresh 0.05 --seg fsaverage aparc+aseg.mgz --fwhmdat study1.glmdir/fwhm.dat --sign neg --thmin 1.3 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: study1.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 795592 Found 795592 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file.___ 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] error in mri_glmfit-sim when using --bg and doss
sorry, you are right, the csd files are in the csd folder. The csf file will have a name with the contrast name in it. Copy it to a file with a name where you substitute the old contrast name for another contrast name. doug On 02/21/2014 09:18 PM, charujing123 wrote: Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFile, I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22 charujing123 *发件人：*Douglas Greve gr...@nmr.mgh.harvard.edu *发送时间：*2014-02-21 23:49 *主题：*Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu *抄送：* When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 ___ 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 -- 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] error in mri_glmfit-sim when using --bg and doss
When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 ___ 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] error in mri_glmfit-sim when using --bg and doss
Hi doug and others, Thanks doug. According this information https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ViewCSDFile, I try to find the csd files in the csd folder(I am not sure this is what you just told me). But there are the csd files as I run simulation with --bg option. Also I try to find the csd files in the first contrast directory, but I think, maybe I am wrong, none of these is csd files that you suggest. Doug, would you please describe it more detailly, as I am a new user for FS? Thanks doug and others. All the best. Rujing Zha 2014-02-22 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-02-21 23:49 主题：Re: [Freesurfer] error in mri_glmfit-sim when using --bg and doss 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： When you actually run the simulation, it only runs it for the first contrast. The simulation is the same for all contrasts, so you can just copy the csd files from the first contrast to the others, then run mri_glmfit-sim with the --no-sim option doug On 2/21/14 5:47 AM, charujing123 wrote: Hi FS experts, I ran the mri_glmfit with DOSS, followed by the mri_glmfit-sim(running with --bg option). I have 4 contrasts, but only the first one has some files of corrected results(i.e. mc-z.neg.3.sig.cluster.summary). I donot know why. So I upload the log file in the attachment. However, previously I ran mri_glmfit by DODS, and mri_glmfit-sim with --bg option.All the contrasts have corrected results. Thanks. All the best. Rujing Zha 2014-02-21 charujing123 ___ 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] Error with mri_glmfit-sim -- sim perm
Dear all, I was running the simulation: mri_glmfit-sim \ --glmdir GroupAnalysis_abs.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign abs \ --cwpvalthresh .05 and unfortunately I got the following error: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz Seems that the simulation was completed saying that mri_glmfit simulation done but I did not get any clusters or any file permcsd.sig.cluster.summary. Also I am not sure if I need to use the while running the mri_volcluster the fsaverage or I should use the cvs_avg35 since my FA data was registered over the CVS space. Can I just do something further to catch my corrected clusters? I attached my log file. Thank you very much. Antonella permcsd.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.
[Freesurfer] ERROR with mri_glmfit-sim
Hi, I was trying to run for my FA group study the following: mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim neg perm 1 3 permcsd\ --cwpvalthresh .05 but I got an error: Flag permcsd unrecognized and then is asking me agout --sim sign. Can you please help? THANK YOU! Antonella ___ 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] Error with mri_glmfit-sim \
Is this volume data? If so, then use --grf with mri_glmfit-sim instead of --cache. doug Antonella Kis wrote: Dear Doug, Can you please advise me how I can do a multiple comparison for my DTI group analysis? I tried and I ran: mri_glmfit --y group-fa-tal.nii --fsgd DTI_group_analysis.fsgd dods --cwpvalthresh .99 \ --C contrast.mtx --glmdir group_analysis-0.99.glmdir but I got: ERROR: Option --cwpvalthresh unknown so I really don't know how I can do the multiple comparison in this case: the DTI data. Also, I tried to run the: mri_glmfit-sim \ --glmdir group_analysis.glmdir \ --cache 2 neg \ --cwpvalthresh .99 \ --overwrite but I got another ERROE: ERROR: cannot find /usr/local/freesurfer//average/mult-comp-cor///cortex/fwhm04/neg/th20/mc-z.csd Thank you very much! Antonella -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Error with mri_glmfit-sim
Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK ___ 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] Error with mri_glmfit-sim
What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Error with mri_glmfit-sim
Good afternoon, I tried running the -sim on my QDEC output (as recommended last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK___ 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] Error with mri_glmfit-sim
again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 . 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error with mri_glmfit-sim
No, unfortunately not. doug jm wrote: Doug: I have processed 20 subjects. By mistake, five of them with LAS orientation and 15 RAS orientation.RAS that's right in my case. I could change name of files in '/surf' folder from left to right in the first ones? or I need do it over? for instance: I could change name of file rh.thickness.fwhm25.fsaverage to lh.thickness.fwhm25.fsaverage? or that have others implications to statistical analysis outcomes thanks On Wed, 2011-09-28 at 13:33 -0400, Douglas N Greve wrote: again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with --cache 2 sign where sign is pos, neg, or abs doug Antonella Kis wrote: Hi Doug, Thanks again for helping. I am trying to use QDEC but there are no clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that I cannot run the -sim if there is no FDR data (stats) so I cannot cache the clusters formed only by thresh 2 in QDEC. Is theer a way to do it? Many thanks, AK *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim What does FDR have to do with it? FDR should not come into play in this. doug Antonella Kis wrote: Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 . 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error in mri_glmfit-sim
Dear all, I am running a surface-based group analysis. When I try to run mri_glmfit-sim, I always get the following error: ERROR: you must supply --fwhm with --sim, even if it is 0 I get this error (which does not make any sense, since there is not fwhm info in the simulation) using both qdec-generated script and using command-line tools. The script that qdec generates is the following : /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/eider/subjects/qdec/Untitled --sim perm 5000 2 perm.abs.2 --sim-sign abs --overwrite Does anyone know what could be happening?? Thanks - Roser - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error in mri_glmfit-sim
True, I am using version 4.3.1. Can I update only mri_glmfit-sim script?? Thanks 2009/11/9 Douglas N Greve gr...@nmr.mgh.harvard.edu What version are you using? I think this was a problem with 4.3. doug Roser Sala wrote: Dear all, I am running a surface-based group analysis. When I try to run mri_glmfit-sim, I always get the following error: ERROR: you must supply --fwhm with --sim, even if it is 0 I get this error (which does not make any sense, since there is not fwhm info in the simulation) using both qdec-generated script and using command-line tools. The script that qdec generates is the following : /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/eider/subjects/qdec/Untitled --sim perm 5000 2 perm.abs.2 --sim-sign abs --overwrite Does anyone know what could be happening?? Thanks - Roser - ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- - Roser - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
