Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

Re: [Freesurfer] Event-Related design and jitter in stimulus onset
by Douglas N Greve 09 Dec '11

09 Dec '11

By default, optseq uses an internal clock synchronize to the TR (so events can only start on the TR). This can be changed by setting dPSD (eg, to 1). This would allow the NULL events to be multiples of 1 instead of 2. The PSD is specified in seconds. doug SHAHIN NASR wrote: > optseq2 --ntp 132 --tr 2 --tsearch 0.5 --ev C1 6 4 --ev C2 6 4 --ev C3 > 6 4 --ev C4 6 4 --ev C5 6 4 --ev C6 6 4 --ev C7 6 4 --ev C8 6 4 --ev > C9 6 4 --ev C10 6 4 --nkeep 10 --psdwin 10 16 --o Opt_Par_2nd > > > On Fri, Dec 9, 2011 at 2:03 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > What is your command line? > > > SHAHIN NASR wrote: > > Thanks Doug. > In my experiment, each trial (event) consists of 1 sec > stimulus presentation and 5 sec blank interval (TR=2). I have > also added a condition with just blank presentation which will > be repeated as much as other events. > > I have used optseq2 commands to generate the trial > sequence. But I faced two problem/questions: > > 1) Using this command, I expected to see a Null event > (other than my blank condition) with variable length > (irrespective of TR) between other trials. But to my surprise, > length of the Null event was always a multiplication of TR. Is > that correct? > > > 2) Also, for "psdmin psdmax" I wasn't sure if they are > number of TRs or number of seconds and what is a safe window > length when my stimuli are very simple visual objects (and no > cognitive task). > > Once again, thanks for your help. > > > > On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Shahin, there are several ways to answer this question. > If you > are going to analyze assuming a shape to the HRF, then the > actual > delay between stimuli is technically not important (though > 4s will > be good to avoid attenuation in the following stimulus). If > you're > using an FIR model of the HRF (no assumed shape), then I > usually > advise that you have, in total, as much time spent on > fixation (or > whatever your null stimulus is) as you have for any other > stimulus. You can use optseq to compute the actual schedule. > doug > > > SHAHIN NASR wrote: > > Hi Surfers, > > It is my first experience with Event-related > paradigms. In > my experiment, trials take minimum 6s (TR=2s). I wonder > what > is the optimum variable delay between trials to be able to > analyze data without any confound. > > Regards > > -- Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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: > 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> > > > > > 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. > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_glmfit search space = 0
by Douglas N Greve 09 Dec '11

09 Dec '11

What are these asc files? Is this the input that you are having qdec load? If so, then there is at least one subject that has a 0 value at each vertex. The other 187 subjects may be non-zero. doug KYLE ROLLINS HANSEN wrote: > Doug- > Thank you for your response. The data set did not change between the two analyses. They both used the loading of the exact same .dat file. I think the error is in setting up and creating the new measures, and something went wrong in the process of creating the new measure entitled middle45.asc while it was done correctly for middle30.asc. That measurement is the only difference between the two analyses. Which file does mri_glmfit read in the case of creating a new measure? When I pull up the new measurement .asc files they look identical and don't have zero values for most of the values. Is there a different file the mri_glmfit command is running that would have those zeros in it? > Kyle Hansen > University of Utah > kyle.rollins.hansen(a)utah.edu > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, December 09, 2011 10:46 AM > To: KYLE ROLLINS HANSEN; freesurfer > Subject: Re: [Freesurfer] mri_glmfit search space = 0 > > Sorry, hit the send before I was ready. I was also going to point out > that mri_glmfit will zero-out a voxel unless it finds that all inputs > are non-zero (pruning). It looks like it could not find any voxels that > met this criterion. > doug > > Douglas N Greve wrote: > >> Did the data set change between the two analyses? The >> >> KingLab wrote: >> >> >>> Hello Doug- >>> In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! >>> Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. >>> middle30.asc >>> >>> lh-Avg-Intercept-middle30.asc ----------------------- >>> >>> Does the average middle30.asc differ from zero? >>> >>> 1.000 1.000; >>> >>> lh-Diff-Normal-AD-Intercept-middle30.asc ----------------------- >>> >>> Does the average middle30.asc differ between Normal and AD? >>> >>> 1.000 -1.000; >>> >>> ninputs = 188 >>> >>> Checking inputs >>> >>> nframestot = 188 >>> >>> Allocing output >>> >>> nframes = 188 >>> >>> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.648438 >>> >>> AvgVtxArea 0.399267 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> >>> $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >>> >>> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >>> >>> cmdline mri_glmfit --y >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >>> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >>> fsaverage lh --label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat >>> >>> >>> sysname Darwin >>> >>> hostname b417w74-106.med.utah.edu >>> >>> machine i386 >>> >>> user kinglab >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> labelmask >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> maskinv 0 >>> >>> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> IllCondOK 0 >>> >>> DoFFx 0 >>> >>> Creating output directory >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >>> >>> Matrix condition is 1 >>> >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> Found 149955 points in label. >>> >>> Pruning voxels by thr: 0.000000 >>> >>> Found 149953 voxels in mask >>> >>> Saving mask to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >>> >>> search space = 75250.1 >>> >>> DOF = 186 >>> >>> Starting fit and test >>> >>> Fit completed in 0.0740167 minutes >>> >>> Computing spatial AR1 on surface >>> >>> INFO: fwhmFromAR1: Fixing group surface area >>> >>> Residual: ar1mn=0.998860, ar1std=0.000986, gstd=11.981826, fwhm=28.215043 >>> >>> Writing results >>> >>> lh-Avg-Intercept-middle30.asc >>> >>> maxvox sig=1e+10 F=86188.1 at index 0 0 0 seed=1324082303 >>> >>> lh-Diff-Normal-AD-Intercept-middle30.asc >>> >>> maxvox sig=9.81891 F=46.013 at index 70329 0 0 seed=1324082303 >>> >>> mri_glmfit done >>> >>> ninputs = 2 >>> >>> Checking inputs >>> >>> nframestot = 2 >>> >>> Allocing output >>> >>> nframes = 2 >>> >>> Writing to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> reading group avg surface area 1041 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >>> >>> INFO: ignoring tag Creator >>> >>> INFO: ignoring tag SUBJECTS_DIR >>> >>> INFO: ignoring tag SynthSeed >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> >>> >>> ============================================================ >>> >>> Completed loading of analyzed data. >>> >>> >>> >>> Middle45.asc >>> >>> lh-Avg-Intercept-middle45.asc ----------------------- >>> >>> Does the average middle45.asc differ from zero? >>> >>> 1.000 1.000; >>> >>> lh-Diff-Normal-AD-Intercept-middle45.asc ----------------------- >>> >>> Does the average middle45.asc differ between Normal and AD? >>> >>> 1.000 -1.000; >>> >>> ninputs = 188 >>> >>> Checking inputs >>> >>> nframestot = 188 >>> >>> Allocing output >>> >>> nframes = 188 >>> >>> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> INFO: gd2mtx_method is dods >>> >>> Reading source surface >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> Number of vertices 163842 >>> >>> Number of faces 327680 >>> >>> Total area 65416.648438 >>> >>> AvgVtxArea 0.399267 >>> >>> AvgVtxDist 0.721953 >>> >>> StdVtxDist 0.195470 >>> >>> >>> >>> $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >>> >>> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >>> >>> cmdline mri_glmfit --y >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >>> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >>> fsaverage lh --label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle45.asc.mat >>> --C >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle45.asc.mat >>> >>> >>> sysname Darwin >>> >>> hostname b417w74-106.med.utah.edu >>> >>> machine i386 >>> >>> user kinglab >>> >>> FixVertexAreaFlag = 1 >>> >>> UseMaskWithSmoothing 1 >>> >>> OneSampleGroupMean 0 >>> >>> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> logyflag 0 >>> >>> usedti 0 >>> >>> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >>> >>> labelmask >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> maskinv 0 >>> >>> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> IllCondOK 0 >>> >>> DoFFx 0 >>> >>> Creating output directory >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >>> >>> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >>> >>> INFO: gd2mtx_method is dods >>> >>> Saving design matrix to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >>> >>> Matrix condition is 1 >>> >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >>> >>> Found 149955 points in label. >>> >>> Pruning voxels by thr: 0.000000 >>> >>> Found 0 voxels in mask >>> >>> Saving mask to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >>> >>> search space = 0 >>> >>> DOF = 186 >>> >>> Starting fit and test >>> >>> Fit completed in 0.0002 minutes >>> >>> Computing spatial AR1 on surface >>> >>> INFO: fwhmFromAR1: Fixing group surface area >>> >>> WARNING: ar1 = nan <= 0. Setting fwhm to 0. >>> >>> Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 >>> >>> Writing results >>> >>> lh-Avg-Intercept-middle45.asc >>> >>> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >>> >>> lh-Diff-Normal-AD-Intercept-middle45.asc >>> >>> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >>> >>> mri_glmfit done >>> >>> ninputs = 2 >>> >>> Checking inputs >>> >>> nframestot = 2 >>> >>> Allocing output >>> >>> nframes = 2 >>> >>> Writing to >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >>> >>> reading group avg surface area 1041 cm^2 from file >>> >>> Reading in average area >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >>> >>> reading group avg surface area 822 cm^2 from file >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> reading colortable from annotation file... >>> >>> colortable with 36 entries read (originally >>> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>> >>> gdfReadHeader: reading >>> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >>> >>> INFO: ignoring tag Creator >>> >>> INFO: ignoring tag SUBJECTS_DIR >>> >>> INFO: ignoring tag SynthSeed >>> >>> INFO: demeaning continous variables >>> >>> Continuous Variable Means (all subjects) >>> >>> Class Means of each Continuous Variable >>> >>> 1 Diagnosis2Normal >>> >>> 2 Diagnosis2AD >>> >>> >>> >>> ============================================================ >>> >>> Completed loading of analyzed data. >>> >>> Thank you! >>> >>> Kyle Hansen >>> >>> Research Assistant - AIAL >>> >>> University of Utah >>> >>> Hi Kevin, the problem is that once you threshold for >0, there are no >>> voxels that have non-zero values in all of the input subjects. Such >>> voxels are "pruned" because there is not a good model for them. The GLM >>> code does not do a different design at each voxels. In general, doing >>> such thresholding is bad statistically. If you really want to do it, run >>> it with --no-prune. >>> >>> doug >>> >>> kevin bickart wrote: >>> >>> >>>> Hi all, >>>> >>>> I am conducting a contrast of z (r) maps from 3 seed-based >>>> resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence >>>> of anticorrelations on the contrast results, I thresholded the z (r) >>>> maps at 0 before running mri_glmfit, thereby eliminating voxels with >>>> negative z (r) values. The command completed successfully but the >>>> resulting sig maps did not contain voxels with any values. I have >>>> attached the fsgd and contrast files and pasted the command and output >>>> below. Can anyone identify the problem here? >>>> Thanks, >>>> Kevin >>>> >>>> *Potentially problematic portion of output:* >>>> Pruning voxels by thr: 0.000000 >>>> Found 0 voxels in mask >>>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>>> search space = 0.000000 >>>> >>>> *Entire command and output: * >>>> [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] >>>> (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 >>>> _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd >>>> /autofs/homes/006/kbickart/AmySubNet_glm/pa >>>> ired3.fsgd doss --C >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir >>>> LR_Amy_lOFC2_glm2 >>>> gdfReadHeader: reading >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>>> Continuous Variable Means (all subjects) >>>> 0 roi1_vs_roi2_vs_roi3 0 0.707107 >>>> Class Means of each Continuous Variable >>>> 1 Class_081028_BC77WB 0.0000 >>>> 2 Class_081028_XE45TK 0.0000 >>>> 3 Class_081028_YY28TK 0.0000 >>>> .... >>>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >>>> cwd >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne >>>> r_YC >>>> cmdline mri_glmfit --y >>>> LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep >>>> --fsgd /autof >>>> s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C >>>> /autofs/homes/006/kbickart/AmySubNet_glm/paired >>>> .mat --glmdir LR_Amy_lOFC2_glm2 >>>> sysname Linux >>>> hostname kreature >>>> machine x86_64 >>>> user kbickart >>>> FixVertexAreaFlag = 1 >>>> UseMaskWithSmoothing 1 >>>> OneSampleGroupMean 0 >>>> y >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn >>>> er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>>> logyflag 0 >>>> usedti 0 >>>> FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>>> glmdir LR_Amy_lOFC2_glm2 >>>> IllCondOK 0 >>>> ReScaleX 1 >>>> DoFFx 0 >>>> Creating output directory LR_Amy_lOFC2_glm2 >>>> Loading y from >>>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am >>>> yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>>> llINFO: gd2mtx_method is doss >>>> Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat >>>> Normalized matrix condition is 1 >>>> Matrix condition is 44.5 >>>> Pruning voxels by thr: 0.000000 >>>> Found 0 voxels in mask >>>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>>> search space = 0.000000 >>>> DOF = 177 >>>> Starting fit and test >>>> Fit completed in 0.0148667 minutes >>>> Computing spatial AR1 in volume. >>>> fMRIspatialAR1(): hit 0 voxels >>>> WARNING: no voxels in AR1 computation >>>> Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan >>>> Writing results >>>> paired >>>> maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 >>>> mri_glmfit done >>>> >>>> >>>> >>>> -- >>>> Kevin Bickart >>>> MD-PhD Student >>>> Department of Anatomy and Neurobiology >>>> Boston University School of Medicine >>>> >>>> >>>> live UP to it >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...(a)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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 > greve(a)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 > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Event-Related design and jitter in stimulus onset
by SHAHIN NASR 09 Dec '11

09 Dec '11

Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...
by Gonzalo Rojas Costa 09 Dec '11

09 Dec '11

Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa

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downsampling white matter surface and converting to .tri
by John Griffiths 09 Dec '11

09 Dec '11

Dear FS peeps, I am trying to downsample a (white matter) surface with mri_surf2surf. I also want the output in .tri format. First problem is that mri_surf2surf doesn't let me output in .tri format mri_surf2surf --hemi lh --srcsubject subj1 --sval-xyz white --trgsubject subj1 --trgicoorder 4 --trgsurfval subj1_white_downsampled.tri --tfmt tri gives me ERROR: could not determine type of temp_surf_white.tri (that happens with the 'tfmt' flag or not) The command does work when the output is a .gii or .mgh file, but when I then try to convert those files to .tri format with mris_convert I get the error ERROR: MRISread: cannot read surface data from file subj1_white_downsampled.gii! ...which is also the error I get when trying to load the file into freeview as a surface. Any idea what I'm doing wrong here? If there is a better way to convert lh.white into a downsampled .tri file please do tell. Thanks very much, john (p.s. thanks to Dan, Doug, and Bruce for getting me to this point...)

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Re: [Freesurfer] Contrasts in GLM
by Douglas N Greve 09 Dec '11

09 Dec '11

Linda Zhang wrote: > Hi Doug, > > Thanks for the clarification. If I were to add another two class > variables (patient and subject, for example) and I wanted to see if > they affected thickness, assuming they come after gender in the fsgd > file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory? > From the powerpoint slides, there's an example where two contrast > matrices are used (age, gender), what kind of output would that produce? It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast. > > /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh > doesn't exist, I'm not sure why... Your mris_preproc failed or you are not in the directory that has this file. doug > > Cheers, > Linda > > > > On 3 December 2011 01:26, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does > /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh > exist? > doug > > Linda Zhang wrote: > > Dear all, > > I think I figured out the contrasts (I'm using [0 0 0 0 0.5 > 0.5 0 0]...is that correct?) but I've come across an error > when trying to do the next step in the tutorial. > > I didn't cache the data during recon-all, so I ran the following: > > mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh > --meas thickness --out lh.MMSE-AD.thickness.00.mgh > > It seemed to run smoothly (I've attached the log below) so I > ran the next step: > > mri_surf2surf --hemi lh --s fsaverage --sval > lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval > lh.MMSE-AD.thickness.10.mgh > > I got the following error: > > Reading source surface reg > /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg > Loading source data > mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh, > -1): could not open file > ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 > > Can anyone tell me where the problem is? Thanks! > > Cheers, > Linda > > The log for mris_preproc (truncated to the last subject and > last line): > > --------------------------------------------------- > #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -------------- > ----------------------- > mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg > sphere.reg --tval ./tmp.mris_preproc.18275/avo1249.12.mgh > --sval > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness > --sfmt curv --noreshape --no-cortex > Source registration surface changed to sphere.reg > Target registration surface changed to sphere.reg > srcsubject = avo1249 > srcval = > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness > srctype = curv > trgsubject = fsaverage > trgval = ./tmp.mris_preproc.18275/avo1249.12.mgh > trgtype = > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > OKToRevFaceOrder = 1 > Reading source surface reg > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.sphere.reg > Loading source data > Reading curvature file > /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness > Reading target surface reg > /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg > Done > Mapping Source Volume onto Source Subject Surface > surf2surf_nnfr: building source hash (res=16). > Surf2Surf: Forward Loop (163842) > > surf2surf_nnfr: building target hash (res=16). > Surf2Surf: Reverse Loop (121128) > Reverse Loop had 15750 hits > Surf2Surf: Dividing by number of hits (163842) > INFO: nSrcLost = 0 > nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506 > nSrc121 = 78171, nSrcLost = 0, nSrcMulti = 42957, > MnSrcMultiHits = 2.36099 > Saving target data > Saving to ./tmp.mris_preproc.18275/avo1249.12.mgh > > > > ----------------------- > mri_concat ./tmp.mris_preproc.18275/avo0015.1.mgh > ./tmp.mris_preproc.18275/avo0260.2.mgh > ./tmp.mris_preproc.18275/avo0403.3.mgh > ./tmp.mris_preproc.18275/avo0441.4.mgh > ./tmp.mris_preproc.18275/avo0493.5.mgh > ./tmp.mris_preproc.18275/avo0622.6.mgh > ./tmp.mris_preproc.18275/avo0677.7.mgh > ./tmp.mris_preproc.18275/avo0920.8.mgh > ./tmp.mris_preproc.18275/avo1086.9.mgh > ./tmp.mris_preproc.18275/avo1206.10.mgh > ./tmp.mris_preproc.18275/avo1241.11.mgh > ./tmp.mris_preproc.18275/avo1249.12.mgh --o > lh.MMSE-AD.thickness.00.mgh > > > > On 2 December 2011 11:42, Linda Zhang <lzhang87(a)gmail.com > <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com > <mailto:lzhang87@gmail.com>>> wrote: > > Dear all, > > I have a bit of an amateur question. I've read the slides and > tutorial for group analysis, but I'm still confused about the > contrasts. I made my fsgd file, which contains two groups: > M and > F. I also have three continuous variables: Age, MMSE, > Education. I would like to test whether thickness is > correlated with MMSE > scores, after controlling for gender, age, and education. What > should my contrast file be in this case? > Thanks for the help! > > Cheers, > Linda > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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> > > > > 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 greve(a)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

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Re: [Freesurfer] mri_glmfit search space = 0
by Douglas N Greve 09 Dec '11

09 Dec '11

Did the data set change between the two analyses? The KingLab wrote: > Hello Doug- > In going through the threads for freesurfer, I found the following which also describes the issue I am having. However, the error arises for me while running a collection of brains through qdec, so I have not been running the script directly in order to simply add the --no-prune tag. I am running the qdec analysis on new measurements created specifically for analysis in our lab. Someone prior to me set up everything for the qdec analysis to work fine with another database, and was halfway through another brain database when I picked up. For this database, the prior person completed the measurement entitled middle30.asc, which works fine. When using the same .dat file for the database, and the only difference is using the measure of middle45.asc, no data is mapped to the brains. In looking through the code, the same error appeared to happen in the mri_glmfit command in the same place. -qcache has been run for all of the brains for the new measurement, and the middle30.asc files appear similar in structure to the middle45.asc files, as would be expected. Why would it be pruning the one measurement and not the other? Where can I look to solve the issue to run the data in qdec to compare the measurements? If I just run mri_glmfit with --no-prune, will qdec read it in without overwriting it automatically? I have a feeling I missed something in preparing the new region that the person I took over for has done for the other measurements, but I'm not sure what it is or where to look for it. Any help would be appreciated. Thanks! > Below I have included the output for both measurements. The codes appear identical up until after the pruning command comes about which provides 0 voxels. > middle30.asc > > lh-Avg-Intercept-middle30.asc ----------------------- > > Does the average middle30.asc differ from zero? > > 1.000 1.000; > > lh-Diff-Normal-AD-Intercept-middle30.asc ----------------------- > > Does the average middle30.asc differ between Normal and AD? > > 1.000 -1.000; > > ninputs = 188 > > Checking inputs > > nframestot = 188 > > Allocing output > > nframes = 188 > > Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > gdfReadHeader: reading > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 Diagnosis2Normal > > 2 Diagnosis2AD > > INFO: gd2mtx_method is dods > > Reading source surface > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65416.648438 > > AvgVtxArea 0.399267 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > > > $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ > > cwd /Volumes/MacintoshHD2/ADNI-PreProcessed > > cmdline mri_glmfit --y > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods > --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf > fsaverage lh --label > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > --C > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat > --C > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat > > > sysname Darwin > > hostname b417w74-106.med.utah.edu > > machine i386 > > user kinglab > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd > > labelmask > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > > maskinv 0 > > glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled > > IllCondOK 0 > > DoFFx 0 > > Creating output directory > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled > > Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat > > Matrix condition is 1 > > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > > Found 149955 points in label. > > Pruning voxels by thr: 0.000000 > > Found 149953 voxels in mask > > Saving mask to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh > > search space = 75250.1 > > DOF = 186 > > Starting fit and test > > Fit completed in 0.0740167 minutes > > Computing spatial AR1 on surface > > INFO: fwhmFromAR1: Fixing group surface area > > Residual: ar1mn=0.998860, ar1std=0.000986, gstd=11.981826, fwhm=28.215043 > > Writing results > > lh-Avg-Intercept-middle30.asc > > maxvox sig=1e+10 F=86188.1 at index 0 0 0 seed=1324082303 > > lh-Diff-Normal-AD-Intercept-middle30.asc > > maxvox sig=9.81891 F=46.013 at index 70329 0 0 seed=1324082303 > > mri_glmfit done > > ninputs = 2 > > Checking inputs > > nframestot = 2 > > Allocing output > > nframes = 2 > > Writing to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh > > reading group avg surface area 1041 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh > > reading group avg surface area 822 cm^2 from file > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) > > gdfReadHeader: reading > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 Diagnosis2Normal > > 2 Diagnosis2AD > > > > ============================================================ > > Completed loading of analyzed data. > > > > Middle45.asc > > lh-Avg-Intercept-middle45.asc ----------------------- > > Does the average middle45.asc differ from zero? > > 1.000 1.000; > > lh-Diff-Normal-AD-Intercept-middle45.asc ----------------------- > > Does the average middle45.asc differ between Normal and AD? > > 1.000 -1.000; > > ninputs = 188 > > Checking inputs > > nframestot = 188 > > Allocing output > > nframes = 188 > > Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > gdfReadHeader: reading > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 Diagnosis2Normal > > 2 Diagnosis2AD > > INFO: gd2mtx_method is dods > > Reading source surface > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65416.648438 > > AvgVtxArea 0.399267 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > > > $Id: mri_glmfit.c,v 1.138.2.12 2009/06/03 00:06:45 greve Exp $ > > cwd /Volumes/MacintoshHD2/ADNI-PreProcessed > > cmdline mri_glmfit --y > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods > --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf > fsaverage lh --label > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > --C > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle45.asc.mat > --C > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle45.asc.mat > > > sysname Darwin > > hostname b417w74-106.med.utah.edu > > machine i386 > > user kinglab > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd > > labelmask > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > > maskinv 0 > > glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled > > IllCondOK 0 > > DoFFx 0 > > Creating output directory > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled > > Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat > > Matrix condition is 1 > > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label > > Found 149955 points in label. > > Pruning voxels by thr: 0.000000 > > Found 0 voxels in mask > > Saving mask to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh > > search space = 0 > > DOF = 186 > > Starting fit and test > > Fit completed in 0.0002 minutes > > Computing spatial AR1 on surface > > INFO: fwhmFromAR1: Fixing group surface area > > WARNING: ar1 = nan <= 0. Setting fwhm to 0. > > Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 > > Writing results > > lh-Avg-Intercept-middle45.asc > > maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 > > lh-Diff-Normal-AD-Intercept-middle45.asc > > maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 > > mri_glmfit done > > ninputs = 2 > > Checking inputs > > nframestot = 2 > > Allocing output > > nframes = 2 > > Writing to > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh > > reading group avg surface area 1041 cm^2 from file > > Reading in average area > /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh > > reading group avg surface area 822 cm^2 from file > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) > > gdfReadHeader: reading > /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 Diagnosis2Normal > > 2 Diagnosis2AD > > > > ============================================================ > > Completed loading of analyzed data. > > Thank you! > > Kyle Hansen > > Research Assistant - AIAL > > University of Utah > > Hi Kevin, the problem is that once you threshold for >0, there are no > voxels that have non-zero values in all of the input subjects. Such > voxels are "pruned" because there is not a good model for them. The GLM > code does not do a different design at each voxels. In general, doing > such thresholding is bad statistically. If you really want to do it, run > it with --no-prune. > > doug > > kevin bickart wrote: > > Hi all, > > > > I am conducting a contrast of z (r) maps from 3 seed-based > > resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence > > of anticorrelations on the contrast results, I thresholded the z (r) > > maps at 0 before running mri_glmfit, thereby eliminating voxels with > > negative z (r) values. The command completed successfully but the > > resulting sig maps did not contain voxels with any values. I have > > attached the fsgd and contrast files and pasted the command and output > > below. Can anyone identify the problem here? > > Thanks, > > Kevin > > > > *Potentially problematic portion of output:* > > Pruning voxels by thr: 0.000000 > > Found 0 voxels in mask > > Saving mask to LR_Amy_lOFC2_glm2/mask.mgh > > search space = 0.000000 > > > > *Entire command and output: * > > [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] > > (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 > > _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd > > /autofs/homes/006/kbickart/AmySubNet_glm/pa > > ired3.fsgd doss --C > > /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir > > LR_Amy_lOFC2_glm2 > > gdfReadHeader: reading > > /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 roi1_vs_roi2_vs_roi3 0 0.707107 > > Class Means of each Continuous Variable > > 1 Class_081028_BC77WB 0.0000 > > 2 Class_081028_XE45TK 0.0000 > > 3 Class_081028_YY28TK 0.0000 > > .... > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ > > cwd > > /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne > > r_YC > > cmdline mri_glmfit --y > > LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep > > --fsgd /autof > > s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C > > /autofs/homes/006/kbickart/AmySubNet_glm/paired > > .mat --glmdir LR_Amy_lOFC2_glm2 > > sysname Linux > > hostname kreature > > machine x86_64 > > user kbickart > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y > > /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn > > er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz > > logyflag 0 > > usedti 0 > > FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd > > glmdir LR_Amy_lOFC2_glm2 > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory LR_Amy_lOFC2_glm2 > > Loading y from > > /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am > > yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz > > llINFO: gd2mtx_method is doss > > Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat > > Normalized matrix condition is 1 > > Matrix condition is 44.5 > > Pruning voxels by thr: 0.000000 > > Found 0 voxels in mask > > Saving mask to LR_Amy_lOFC2_glm2/mask.mgh > > search space = 0.000000 > > DOF = 177 > > Starting fit and test > > Fit completed in 0.0148667 minutes > > Computing spatial AR1 in volume. > > fMRIspatialAR1(): hit 0 voxels > > WARNING: no voxels in AR1 computation > > Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan > > Writing results > > paired > > maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 > > mri_glmfit done > > > > > > > > -- > > Kevin Bickart > > MD-PhD Student > > Department of Anatomy and Neurobiology > > Boston University School of Medicine > > > > > > live UP to it > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 greve(a)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

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Probabilistic V1 labels to volume
by Ian Charest 09 Dec '11

09 Dec '11

Hi There was a post recently on the mailing list about exporting Probabilistic V1 labels to a volume. I have applied the probabilistic mapping of an individual subject and now have the "lh.v1.prob.label" I would like to convert this label as a volume, and the function mri_label2vol is a little bit confusing. One important thing here is that I don't want the created volume to be binary. but rather to keep the probabilities of a voxel being on V1. I have tried mri_label2vol --label lh.v1.prob.label --subject $SUBJECT --o lh.v1.prob.label I don't understand why I one should need a register.dat file here or even a template file, as I want to generate a volume in RAS space, from a label which I would think is also in RAS space. As for the template file, should it be orig.mgz? Any suggestions here would be appreciated! Regards Ian Charest

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Re: [Freesurfer] mri_glmfit-sim error with v5.0
by Yuko Yotsumoto 09 Dec '11

09 Dec '11

Thank you Doug, > Hi Yuko, I think you must have an older version of glmfit-sim some how. > I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd In stead of making csdCache = /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd it did csdCache = /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd It looks like I failed to tell freesurfer that $subject=fsaverage and $hemi=lh. I changed this line to: set csdCache = $CacheDir/fsaverage/lh/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd and this worked. But I still don't understand why I got the error with mri_glmfit-sim. [ERROR 2] In line 93, anattype is set to volume, but I'm doing surface analysis. set anattype = volume; Changing this to set anattype = surface; worked, but does this mean mri_glmfit-sim is specialized for volume analysis only? Is there a way to change this in the command line not in the original code? Best, Yuko > Hi Yuko, I think you must have an older version of glmfit-sim some how. > I've put a newer version here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-si… > copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the > name; and make a backup copy). > doug On Nov 23, 2011, at 2:07 PM, yukoyy wrote: > Hello > > I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. > > Whan I ran: > mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 > > I got: > ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd > > I have > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd > in my directory. > > It looks like I need to somehow tell freesurfer "/fsaverage/lh/", but how? > > Before mri_glmfit-sim, I did the followings: > isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup > mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz > > > % ------------------------------------------------------------------------- > Also, when I did: > mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite > > I got several warnings and errors (full error message pasted at the end of this email): >> cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz >> WARNING: unrecognized mri_glmfit cmd option --surface >> WARNING: unrecognized mri_glmfit cmd option fsaverage >> WARNING: unrecognized mri_glmfit cmd option lh >> WARNING: unrecognized mri_glmfit cmd option --nii.gz > .... >> mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C >> MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd >> /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer >> /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii >> Bus error > > I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste "mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz" in the command line, it works without any error. > > Thanks in advance! > Yuko Yotsumoto > > > % full error message regarding the second question ------------------------------------------- > cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz > WARNING: unrecognized mri_glmfit cmd option --surface > WARNING: unrecognized mri_glmfit cmd option fsaverage > WARNING: unrecognized mri_glmfit cmd option lh > WARNING: unrecognized mri_glmfit cmd option --nii.gz > log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log > cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 > /Applications/freesurfer/bin/mri_glmfit-sim > --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite > > $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ > Wed Nov 23 13:55:01 JST 2011 > Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 > kawabata > setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects > FREESURFER_HOME /Applications/freesurfer > DoSim = 1 > UseCache = 0 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = 15.248189 > nSimPerJob = 100 > 1/1 Wed Nov 23 13:55:01 JST 2011 > mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii > Bus error ----------------------------------- Yuko Yotsumoto, Ph. D. Associate Professor (research) The Global Centers of Excellence Program, Keio University TEL:011-81-3-5427-1156 x 23851 e-mail: yukoyy(a)a7.keio.jp HP : http://web.keio.jp/~yukoyy/ ------------------------------------

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Problem with .stats files for aparcstats2table
by tenny＠nmr.mgh.harvard.edu 09 Dec '11

09 Dec '11

Hi All, I apologize if this is a simple fix, I am very very new to freesurfer. I am trying to combine the ?h.aparc.stats of a number of subjects into a table file that I can load into excel. I have run the following: "aparcstats2table --hemi lh --subjects 01_bay6 02_bay6 --meas thickness --tablefile aparc_stats.txt" and am receiving the following message: "ERROR: The stats file ../subjects/01_bay6/stats/lh.aparc.stats is not found or is too small to be a valid statsfile" I have checked the content of the file in question and it appears to have the same format as the aparc.stats files displayed in the wiki. Is there a way to go around this problem or perhaps some easy solution that I am unaware of? I couldn't find anything in the wiki. Thanks! Rob

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Freesurfer December 2011