[Freesurfer] rmanova contrast file error
Dear Experts, I am running a rmanova using FSGD file and mri_glmfit. I have done the mris_preproc step, and am currently trying to do the mri_glmfit step. I keep getting an error that appears to be related to the contrast files and matricies (highlighted in yellow below) I have also attched the FSGD file and a contrast file. Everything is in ASCII. The output from the command terminal is below: mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh gdfReadHeader: reading rmanova.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 tp1_vs_tp2 0 0.840168 1 tp2_vs_tp3 0 0.766965 Class Means of each Continuous Variable 1 ECT_001 0. 0. 2 ECT_002 0. 0. 3 ECT_003 0. 0. 4 ECT_004 0. 0. 5 ECT_005 0. 0. 6 ECT_006 0. 0. 7 ECT_007 0. 0. 8 ECT_008 0. 0. 9 ECT_009 0. 0. 10 ECT_010 0. 0. 11 ECT_011 0. 0. 12 ECT_012 0. 0. 13 ECT_013 0. 0. 14 ECT_014 0. 0. 15 ECT_015 0. 0. 16 ECT_016 0. 0. 17 ECT_017 0. 0. 18 ECT_018 0. 0. 19 ECT_019 0. 0. 20 ECT_020 0. 0. 21 ECT_021 0. 0. 22 ECT_022 0. 0. 23 ECT_023 0. 0. 24 ECT_024 0. 0. INFO: gd2mtx_method is doss Reading source surface /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1 cmdline mri_glmfit --glmdir lh.rmanova --y lh.thickness.mgh --fsgd rmanova.fsgd doss --C tp1_vs_tp2.mtx --C tp1_vs_tp3.mtx --C tp2_vs_tp3.mtx --C tp_effect.mtx --C mean.mtx --surface fsaverage lh sysname Linux hostname fs-OptiPlex-755 machine i686 user fs FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.rmanova Loading y from /media/My_Book/MyDATA/ECT_Structure_For_Harry/FreeSurfer_Analysis/priorEDIT/T1/lh.thickness.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.rmanova/Xg.dat Normalized matrix condition is 2.67942 Matrix condition is 32.198 Found 149955 points in label. Pruning voxels by thr: 0.00 Found 148274 voxels in mask Saving mask to lh.rmanova/mask.mgh Reshaping mriglm->mask... search space = 73670.427324 MatrixReadTxT: could not scan value [2][1] ERROR: loading C tp1_vs_tp2.mtx Any help would be greatly appreciated. Thanks, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5...@uni.sydney.edu.au | W www.rng.org.au rmanova.fsgd Description: rmanova.fsgd tp1_vs_tp2.mtx Description: tp1_vs_tp2.mtx ___ 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] FW: long.qdec.table.dat
Addtionally what is the difference between using: qdec.table.dat from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview and cross.qdec.table.dat from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial_freeview?action=fullsearch&context=180&value=fsid&titlesearch=Titles#AdditionalNotesonQDEC if ultimately im just trying run a simple analysis to see any differnces amongst 1 group of ppl at 2 timepoints. Thanks, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5...@uni.sydney.edu.au | W www.rng.org.au From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Harry Hallock [hhal5...@uni.sydney.edu.au] Sent: Tuesday, 15 April 2014 12:37 PM To: freesurfer Subject: [Freesurfer] long.qdec.table.dat Hi all, I am currently doing longitundal processing. I have gone through the turtoial but still cannot find the answer. When creating a long.qdec.table.dat, should the first column entitled "fsid" be long or cross data? Cheers, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5...@uni.sydney.edu.au | W www.rng.org.au ___ 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] long.qdec.table.dat
Hi all, I am currently doing longitundal processing. I have gone through the turtoial but still cannot find the answer. When creating a long.qdec.table.dat, should the first column entitled "fsid" be long or cross data? Cheers, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 F +61 9351 0930 E hhal5...@uni.sydney.edu.au | W www.rng.org.au ___ 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] Tksurfer abbreviations
Hi all, Apologies for this basic question, but im quite the newbie. I'mcurrently using tksurfer and got this result: surfer: filling (ctrl-c to cancel) done, 4646 vertices filled surfer: performing FDR on 1989 vertices MRISfdr2vwth(): np = 1989, nv = 163842, fdr = 0.05, vwth=2.24098 MRISfdr2vwth(rate=0.05, sign=0, 1, only_marked=1) = 2.240980 surfer: MRISfdr2vwth with rate 0.05 and sign 0 returned threshold 2.240980 I was wondering what np, nv and vwth actually stand for? Also does anyone know how to get the T or F statistic? Thanks, Harry Harry Hallock | MPhil Candidate Regenerative Neuroscience Group | Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY Room 408, Level 4, M02K | 94 Mallett St Camperdown | NSW | 2050 | Australia T +61 2 9114 4138 E hhal5...@uni.sydney.edu.au | W www.rng.org.au ___ 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] qdec - 3 timepoints
Hi, I'm currently doing a long analysis of a data set that contains two groups (training and control) and 3 timepoints (baseline -BL, follow up1- FU1 follow up2-FU2) I've put it through qdec. But for the analysis qdec only gives me one measure for long.thickness-avg, rate, pc1 and spc. How do i know which timepoints are being analyzed? i.e. is it simply FU2-BL? Or is it FU2-FU1 or FU1-BL? Is there a way i can test for each of these changes over time? Cheers, Harry ___ 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] Mixed-effects models for longitudinal data analysis in Freesurfer
Hi Martin, If you could make available that lme toolbox link, that would be great! Thanks for the help. Cheers, Harry From: jorge luis [jbernal0...@yahoo.es] Sent: Tuesday, 16 October 2012 8:16 AM To: Martin Reuter; Harry Hallock [hhal5...@uni.sydney.edu.au] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Mixed-effects models for longitudinal data analysis in Freesurfer Hi Harry As Martin said, longitudinal linear mixed-effects models (lme) are the recommended tool for analyzing longitudinal data obtained from the Freesurfer longitudinal image processing pipeline. The increase in power can be dramatic. Coming up there is a paper about this subject. We are working on making our lme tools available and easy to use but in the mean time, if you are interested, I can make available a link for you to download our Matlab-based lme toolbox. Best -Jorge De: Martin Reuter Para: Harry Hallock ; Douglas N Greve ; "freesurfer@nmr.mgh.harvard.edu" Enviado: Domingo 14 de octubre de 2012 21:06 Asunto: Re: [Freesurfer] 3 Factor glm group analysis Hi Harry. I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that . However, we recommend to run a linear mixed effects model (external software). We are working on making that available. Best Martin Harry Hallock wrote: Thanks Doug! If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction? Harry 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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug On 10/09/2012 12:45 AM, hhal5...@uni.sydney.edu.au wrote: Hello, We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC? Regards, Harry 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. ___ 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. ___ 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.
