[Freesurfer] Qdec question when examining group differences with continuous covariate and nuisance factor
Hi there, I am running an analysis to examine differences in cortical thickness between two groups (clinical vs control) and have entered ICV as a nuisance variable and age as a covariate. The analysis results in qdec do not appear to give a result that answers the question: does the average cortical thickness differ between clinical and control with both the nuisance factor and the covariate accounted for. The only result comparing average thickness between the groups lists ICV as a nuisance factor, and does not include age as a covariate. Other results are examining correlation between age and thickness accounting for group, or whether the thickness-age correlation differs between groups accounting for ICV. A second question: when i just include ICV as a nuisance factor and do not enter age as a covariate (groups mean age is almost identical), there are some areas of cortical thickening in the clinical group, which become much larger after correction for multiple comparisons using Monte Carlo Null-Z simulation (threshold 0.05). This seems counterintuitave to me as I would expect a reduction in significant clusters after correction. One of the main clusters traverses the cingulate gyrus, however, when I extract cortical thickness values for each individual subject and compare group means for subregions of the cingulate in SPSS, there are no significant differences on any of the subregions. In fact, they are almost identical. Could adding ICV as a nuisance variable account for this? Mean ICV values are almost identitical between groups. Or is there some additive affect at the cluster level? Many thanks for any clarity you can provide. Kind regards, James ___ 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] qdec question
If you are asking whether you can mix versions of FS, the answer is no. You should analyze all your data using a single version. On 12/30/17 3:27 AM, Giovanni de Marco wrote: Hello, I’ve got a question concerning qdec running with freesurfer. I just downloaded the latest version of freesurfer. Before to run qdec, I read than I have to run "recon-all -s ID -all" (about 7 hours) and then recon-all -s ID -qcache (about 5'). So I tried it with one subject and everything is fine. Indeed, I got the files like *.fwhm5.fsaverage.mgh, *.fwhm10.fsaverage.mgh, *.fwhm20.fsaverage.mgh, etc... in the surf folder absolutely necessary for qdec. My question is very simple : I have already treated all my subjects (n = 45) two years ago. Today, I would like to use qdec. Do I need to restart _for each subject_ all my preprocessing with recon-all -s ID -allfollowed by recon-all -s ID -qcache ? or Is there a routine faster to get the smoothed surfaces for each subject ? Many thank for any advice. Best wishes and happy new year. Giovanni ___ 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] qdec question
Hello, I’ve got a question concerning qdec running with freesurfer. I just downloaded the latest version of freesurfer. Before to run qdec, I read than I have to run "recon-all -s ID -all" (about 7 hours) and then recon-all -s ID -qcache (about 5'). So I tried it with one subject and everything is fine. Indeed, I got the files like *.fwhm5.fsaverage.mgh, *.fwhm10.fsaverage.mgh, *.fwhm20.fsaverage.mgh, etc... in the surf folder absolutely necessary for qdec. My question is very simple : I have already treated all my subjects (n = 45) two years ago. Today, I would like to use qdec. Do I need to restart *for each subject* all my preprocessing with recon-all -s ID -all followed by recon-all -s ID -qcache ? or Is there a routine faster to get the smoothed surfaces for each subject ? Many thank for any advice. Best wishes and happy new year. Giovanni ___ 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 question
Dear Freesurfer experts, I would like to use "Qdec" tool to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists and not the BA stat list. I am wondering if we could do that with "Qdec"? Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.ba...@uliege.be ___ 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] qdec question
Try using the data in the csdbase.y.ocn.dat file rather than
transferring the clusters back into the individual space. What are you
using to do the ROI-based analysis? You have to make sure that the
design matrix and contrasts are exactly the same. You can do this in
matlab with FS commmands, eg,
X = load('Xg.dat'); % Xg.dat created by qdec
[beta rvar] = fast_glmfit(y,X); % y is the vector of average areas, one
row for each subject, one column for each cluster
C = load('contrastfolder/C.dat'); % Created by qdec
[F p] = fast_fratio(beta,X,rvar,C);
p will be a vector of p-values
On 11/24/2016 04:43 AM, Yaakub, Siti Nurbaya wrote:
> Dear Experts,
>
> I'm looking at differences in area between two groups of subjects in
> FreeSurfer using qdec.
> I've delineated an ROI based on a cluster that showed significant
> differences in surface area between the two groups (taking gender into
> account, and with age and ICV as nuisance covariates).
> As a sanity check, I extracted the total surface area values for that
> ROI for each subject in native space (using mri_label2label and
> mris_anatomical_stats)
> When I plot these values (and do an ANCOVA with the same covariates,
> or even just a simple t-test) there is almost no difference between
> the groups. Did I do something wrong? How do I get the average surface
> area values for each subject (in that ROI that shows a difference) so
> I can see the spread of values in each group?
>
> Thanks,
> Siti
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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dispose of the e-mail.
[Freesurfer] qdec question
Dear Experts, I'm looking at differences in area between two groups of subjects in FreeSurfer using qdec. I've delineated an ROI based on a cluster that showed significant differences in surface area between the two groups (taking gender into account, and with age and ICV as nuisance covariates). As a sanity check, I extracted the total surface area values for that ROI for each subject in native space (using mri_label2label and mris_anatomical_stats) When I plot these values (and do an ANCOVA with the same covariates, or even just a simple t-test) there is almost no difference between the groups. Did I do something wrong? How do I get the average surface area values for each subject (in that ROI that shows a difference) so I can see the spread of values in each group? Thanks, Siti ___ 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 question
Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks___ 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] QDEC question
Hello Dr Greve, Many thanks for replying to me. We are not including eTIV as a covariate. Since we did not find any correlation with the thickness. Kind regards, Sampada ___ 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] QDEC question
Dear freesurfer experts, I was able to figure out the problem! I was not supposed to write the eTIV values in my .dat.table which I did and for that reasons my continuous factors were being read as 4 instead of 3. Thanks and regards, Sampada AIIMS, Delhi ___ 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] QDEC question
Dear Freesurfer experts, Thanks for your valuable input. Since, comparison with global thickness does not provide any valuable information we have decided to forego the average thickness and lh-thickness comparison and now added eTIV as another covariate with age and lh/rh thickess ( please see the attached .table.dat and the created fsgd file with this mail). I was facing an error while trying to run the qdec with eTIV as a covariate so I searched the forum and followed the same instructions ( http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19987.html) t hat Dr Schmansky said over the same issue. But still, I am getting the same error of *MatrixMultiply: m1 is null!* *No such file or directory*. My error log on my the terminal says the following: *1 Gender discrete 21 Male2 Female2 Age continuous 03 lh-thickness continuous 04 eTIV continuous 05 EstimatedTotalIntraCranialVol continuous 0Continuous Factors: Mean: StdDev: --- - ---Age33.320 10.566 lh-thickness 2.201 0.306 eTIV 1229696.542246342.246 EstimatedTotalIntraCranialVol 1229696.542246342.246Number of subjects: 25Number of factors:5 (1 discrete, 4 continuous)Number of classes:2Number of regressors: 10lh-Avg-Intercept-thickness ---Does the average thickness differ from zero? 1.000 1.000 0.000 0.000;lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor ---Does the correlation between thickness and EstimatedTotalIntraCranialVol, accounting for Gender, differ from zero? 0.000 0.000 1.000 1.000;lh-Diff-Male-Female-Intercept-thickness ---Does the average thickness differ between Male and Female? 1.000 -1.000 0.000 0.000;lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol ---Does the thickness--EstimatedTotalIntraCranialVol correlation differ between Male and Female? 0.000 0.000 1.000 -1.000;ninputs = 25Checking inputsnframestot = 25Allocing outputDone allocingnframes = 25Writing to /home/anup/Desktop/QDEC/qdec/Untitled/y.mghgdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 EstimatedTotalIntraCranialVol 1.2297e+06 241365Class Means of each Continuous Variable1 GenderMale 1307770.0139 2 GenderFemale 1028936.1875 INFO: gd2mtx_method is dodsReading source surface /home/anup/Desktop/QDEC/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 0.195470$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd /home/anup/Desktop/QDECcmdline mri_glmfit --y /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh --fsgd /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd dods --glmdir /home/anup/Desktop/QDEC/qdec/Untitled --surf fsaverage lh --label /home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.label --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol.mat sysname Linuxhostname localhost.localdomainmachine x86_64user anupFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 0y /home/anup/Desktop/QDEC/qdec/Untitled/y.mghlogyflag 0usedti 0FSGD /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgdlabelmask /home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.labelmaskinv 0glmdir /home/anup/Desktop/QDEC/qdec/UntitledIllCondOK 0ReScaleX 1DoFFx 0Creating output directory /home/anup/Desktop/QDEC/qdec/UntitledLoading y from /home/anup/Desktop/QDEC/qdec/Untitled/y.mghINFO: gd2mtx_method is dodsSaving design matrix to /home/anup/Desktop/QDEC/qdec/Untitled/Xg.datNormalized matrix condition is 147.732Matrix condition is 1e+08Found 148151 points in label.Pruning voxels by thr: 0.00Found 148025 voxels in maskSaving mask to /home/anup/Desktop/QDEC/qdec/Untitled/mask.mghReshaping mriglm-mask...search space = 73649.347769DOF = 21Starting fit and testFit completed in 0.0211 minutesComputing spatial AR1 on surfaceResidual: ar1mn=0.998310, ar1std=0.001122, gstd=9.841412, fwhm=23.174754Writing results lh-Avg-Intercept-thicknessmaxvox sig=10.1323 F=143.803 at index 23648 0 0seed=1438013578 lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cormaxvox sig=-3.89264 F=21.9015 at index 54769 0 0
Re: [Freesurfer] QDEC question
I don't know what is going on with that, but one thing you should do is to normalize the eTIV (ie, remove it's mean and divide by the std dev). Also, why are you including eTIV in the first place? Thickness does not change with head size, only volume and surface area. doug On 7/24/15 2:34 AM, Dr Sampada Sinha wrote: Dear Freesurfer experts, Thanks for your valuable input. Since, comparison with global thickness does not provide any valuable information we have decided to forego the average thickness and lh-thickness comparison and now added eTIV as another covariate with age and lh/rh thickess ( please see the attached .table.dat and the created fsgd file with this mail). I was facing an error while trying to run the qdec with eTIV as a covariate so I searched the forum and followed the same instructions (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19987.html) t hat Dr Schmansky said over the same issue. But still, I am getting the same error of /MatrixMultiply: m1 is null!/ /No such file or directory/. My error log on my the terminal says the following: / 1 Gender discrete 2 1 Male 2 Female 2 Age continuous 0 3 lh-thickness continuous 0 4 eTIV continuous 0 5 EstimatedTotalIntraCranialVol continuous 0 Continuous Factors: Mean: StdDev: --- - --- Age33.320 10.566 lh-thickness 2.201 0.306 eTIV 1229696.542 246342.246 EstimatedTotalIntraCranialVol 1229696.542 246342.246 Number of subjects: 25 Number of factors:5 (1 discrete, 4 continuous) Number of classes:2 Number of regressors: 10 lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor --- Does the correlation between thickness and EstimatedTotalIntraCranialVol, accounting for Gender, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-Male-Female-Intercept-thickness --- Does the average thickness differ between Male and Female? 1.000 -1.000 0.000 0.000; lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol --- Does the thickness--EstimatedTotalIntraCranialVol correlation differ between Male and Female? 0.000 0.000 1.000 -1.000; ninputs = 25 Checking inputs nframestot = 25 Allocing output Done allocing nframes = 25 Writing to /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh gdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 EstimatedTotalIntraCranialVol 1.2297e+06 241365 Class Means of each Continuous Variable 1 GenderMale 1307770.0139 2 GenderFemale 1028936.1875 INFO: gd2mtx_method is dods Reading source surface /home/anup/Desktop/QDEC/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 /home/anup/Desktop/QDEC cmdline mri_glmfit --y /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh --fsgd /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd dods --glmdir /home/anup/Desktop/QDEC/qdec/Untitled --surf fsaverage lh --label /home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.label --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Avg-thickness-EstimatedTotalIntraCranialVol-Cor.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /home/anup/Desktop/QDEC/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-EstimatedTotalIntraCranialVol.mat sysname Linux hostname localhost.localdomain machine x86_64 user anup FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/home/anup/Desktop/QDEC/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/anup/Desktop/QDEC/qdec/Untitled/qdec.fsgd labelmask /home/anup/Desktop/QDEC/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/anup/Desktop/QDEC/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/anup/Desktop/QDEC/qdec/Untitled Loading y from /home/anup/Desktop/QDEC/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/anup/Desktop/QDEC/qdec/Untitled/Xg.dat Normalized matrix condition is 147.732 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.00 Found 148025 voxels in mask Saving mask to /home/anup/Desktop/QDEC/qdec/Untitled/mask.mgh Reshaping mriglm-mask... search space = 73649.347769 DOF = 21 Starting fit and test Fit
Re: [Freesurfer] QDEC question
The statements are automatically generated based on the names of the variables you provide. In this case, you've included (global?) lh thickness as a covariate. This will have a slope when plotted against thickness at a given vertex, and this slope my differ between genders. The average thickness in this case is difficult to interpret because you have included the global thickness as a covariate. In this case, the average thickness actually represents the deviation from the global thickness. I'm not sure how to interpret this, but if you can come up with a convincing story then you can include it in a manuscript. doug On 7/22/15 9:37 AM, Dr Sampada Sinha wrote: Dear Freesurfer experts, Thanks for replying me. I was able to sort out the problem. I have one question to ask though...In my SCA1 category patients I am trying to correlate cortical thickness between male and female patients. When I am choosing age as a continous factor out of two covariates (age and lh-thickness) and Gender as a Discrete factor to compare the lh thickness , I am not getting any significant result. but when i choose lh-thickness as a covariate and Gender as a discrete factor with age as nuisance, I am getting few clusters. But I don't understand the fourth description, which says thickness-lhthickness correlation differ between male and female.? Which thickness and why is trying to find a relationship between thickness and lh-thickness is it talking about? I am attaching the fsgd file created by the Qdec and few snapshots with gender and lh thickness as analysis result. Also, can I use the picture which says that the average thickness differ from zero, for my paper? Will be grateful if i can have any response. Thanks much for your time and patience! Sampada AIIMS, India */ /* ___ 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] QDEC question
Does /home/anup/Desktop/QDEC/fsaverage/surf/lh.white exist? If not, cd /home/anup/Desktop/QDEC/ ln -s $FREESURFER_HOME/subjects fsaverage It looks like you will have a second problem in that the subject class GenderFemale-DiagnosisSCA1 does not have any members doug On 07/17/2015 08:17 AM, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do cortical thickness-age correlation in Spinocerebellar ataxia patients (SCA1 and SCA2). ## I successfully ran qcache command on these 10 subjects of SCA1 and SCA2. ##Since my discrete factors are *Gender *(Male and Female) and*Diagnosis* (SCA1 and SCA2), I created Gender.levels and Diagnosis.levels files as a superuser. ##My subject directory is /home/anup/Desktop/QDEC and the qdec.table.dat has this format: ID Gender Age Diagnosis l h-thickness AMARJEET Male 23 SCA1 2.45563 ANIL Male 25 SCA1 2.21909 ANNU Female 20 SCA2 2.36158 ASHOKSINGH Male 23 SCA2 2.41038 GANPAT Male 18 SCA2 2.30408 GOVIND Male 27 SCA1 2.32102 GULSAN Male 24 SCA2 2.36911 IMRAN Male 22 SCA2 2.31279 JASBIR Male 18 SCA2 2.3191 KAILASH Male 24 SCA1 2.36319 ##I copied the link of fsverage using the command on one of the thread of qdec for bash: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi /So far, these all steps I have followed from freesurfer Qdec wiki.../ ##My subject directory which is /home/anup/Desktop/Qdec has all the 10 subjects, two .levels files, a qdec,table.dat file and link of fsaverage. After setting up the freesurfer and exporting the subject directory to I am able to load the qdec.table.dat file, which shows the following: Loading data table /home/anup/Desktop/QDEC/mydata.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 10 Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Gender.levels Male Female done. Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Diagnosis.levels SCA1 SCA2 done. ## I am also able to get the aparc and asegs data but when I click on the design tab which I named it as lh10 I get the following error: SUBJECTS_DIR : /home/anup/Desktop/QDEC Parsing the .stats files Building the table.. Writing the table to /home/anup/Desktop/QDEC/qdec/stats_tables//rh.aparc.a2009s.meancurv.stats.dat Completed creation of aseg and aparc stats data tables. lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000; lh-Avg-thickness-lh-thickness-Cor --- Does the correlation between thickness and lh-thickness, accounting for Gender and Diagnosis, differ from zero? 0.000 0.000 0.000 0.000 1.000 1.000 1.000 1.000; lh-Diff-Male-Female-Intercept-thickness --- Does the average thickness, accounting for Diagnosis, differ between Male and Female? 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-Male-Female-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Diagnosis, differ between Male and Female? 0.000 0.000 0.000 0.000 1.000 -1.000 1.000 -1.000; lh-Diff-SCA1-SCA2-Intercept-thickness --- Does the average thickness, accounting for Gender, differ between SCA1 and SCA2? 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-SCA1-SCA2-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Gender, differ between SCA1 and SCA2? 0.000 0.000 0.000 0.000 1.000 1.000 -1.000 -1.000; lh-X-Gender-Diagnosis-Intercept-thickness --- Is there a Gender--Diagnosis interaction in the mean thickness? 1.000 -1.000 -1.000 1.000 0.000 0.000 0.000 0.000; lh-X-Gender-Diagnosis-Cor-thickness-lh-thickness --- Is there a Gender--Diagnosis interaction in the thickness--lh-thickness correlation? 0.000 0.000 0.000 0.000 1.000 -1.000 -1.000 1.000; ninputs = 10 Checking inputs nframestot = 10 Allocing output Done allocing nframes = 10 Writing to /home/anup/Desktop/QDEC/qdec/lh-10/y.mgh gdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/lh-10/qdec.fsgd WARNING: gdfReadV1: class GenderFemale-DiagnosisSCA1 is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 lh-thickness 2.3436 0.0612307 Class Means of each Continuous
[Freesurfer] QDEC question
Dear freesurfer experts, I am trying to do cortical thickness-age correlation in Spinocerebellar ataxia patients (SCA1 and SCA2). ## I successfully ran qcache command on these 10 subjects of SCA1 and SCA2. ##Since my discrete factors are *Gender *(Male and Female) and* Diagnosis* (SCA1 and SCA2), I created Gender.levels and Diagnosis.levels files as a superuser. ##My subject directory is /home/anup/Desktop/QDEC and the qdec.table.dat has this format: ID Gender Age Diagnosis l h-thickness AMARJEET Male 23 SCA1 2.45563 ANIL Male 25 SCA1 2.21909 ANNU Female 20 SCA2 2.36158 ASHOKSINGH Male 23 SCA2 2.41038 GANPAT Male 18 SCA2 2.30408 GOVIND Male 27 SCA1 2.32102 GULSAN Male 24 SCA2 2.36911 IMRAN Male 22 SCA2 2.31279 JASBIR Male 18 SCA2 2.3191 KAILASH Male 24 SCA1 2.36319 ##I copied the link of fsverage using the command on one of the thread of qdec for bash: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi *So far, these all steps I have followed from freesurfer Qdec wiki...* ##My subject directory which is /home/anup/Desktop/Qdec has all the 10 subjects, two .levels files, a qdec,table.dat file and link of fsaverage. After setting up the freesurfer and exporting the subject directory to I am able to load the qdec.table.dat file, which shows the following: Loading data table /home/anup/Desktop/QDEC/mydata.table.dat... Number of columns: 5 fsid column:1 Number of factors: 4 Number of subjects: 10 Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Gender.levels Male Female done. Reading discrete factor levels from config file /home/anup/Desktop/QDEC/Diagnosis.levels SCA1 SCA2 done. ## I am also able to get the aparc and asegs data but when I click on the design tab which I named it as lh10 I get the following error: SUBJECTS_DIR : /home/anup/Desktop/QDEC Parsing the .stats files Building the table.. Writing the table to /home/anup/Desktop/QDEC/qdec/stats_tables//rh.aparc.a2009s.meancurv.stats.dat Completed creation of aseg and aparc stats data tables. lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000; lh-Avg-thickness-lh-thickness-Cor --- Does the correlation between thickness and lh-thickness, accounting for Gender and Diagnosis, differ from zero? 0.000 0.000 0.000 0.000 1.000 1.000 1.000 1.000; lh-Diff-Male-Female-Intercept-thickness --- Does the average thickness, accounting for Diagnosis, differ between Male and Female? 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-Male-Female-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Diagnosis, differ between Male and Female? 0.000 0.000 0.000 0.000 1.000 -1.000 1.000 -1.000; lh-Diff-SCA1-SCA2-Intercept-thickness --- Does the average thickness, accounting for Gender, differ between SCA1 and SCA2? 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000; lh-Diff-SCA1-SCA2-Cor-thickness-lh-thickness --- Does the thickness--lh-thickness correlation, accounting for Gender, differ between SCA1 and SCA2? 0.000 0.000 0.000 0.000 1.000 1.000 -1.000 -1.000; lh-X-Gender-Diagnosis-Intercept-thickness --- Is there a Gender--Diagnosis interaction in the mean thickness? 1.000 -1.000 -1.000 1.000 0.000 0.000 0.000 0.000; lh-X-Gender-Diagnosis-Cor-thickness-lh-thickness --- Is there a Gender--Diagnosis interaction in the thickness--lh-thickness correlation? 0.000 0.000 0.000 0.000 1.000 -1.000 -1.000 1.000; ninputs = 10 Checking inputs nframestot = 10 Allocing output Done allocing nframes = 10 Writing to /home/anup/Desktop/QDEC/qdec/lh-10/y.mgh gdfReadHeader: reading /home/anup/Desktop/QDEC/qdec/lh-10/qdec.fsgd WARNING: gdfReadV1: class GenderFemale-DiagnosisSCA1 is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 lh-thickness 2.3436 0.0612307 Class Means of each Continuous Variable 1 GenderMale-DiagnosisSCA1 2.3397 2 GenderFemale-DiagnosisSCA1 -nan 3 GenderMale-DiagnosisSCA2 2.3431 4 GenderFemale-DiagnosisSCA2 2.3616 INFO: gd2mtx_method is dods Reading source surface /home/anup/Desktop/QDEC/fsaverage/surf/lh.white MRISread(/home/anup/Desktop/QDEC/fsaverage/surf/lh.white): could not open file Permission denied mri_glmfit: could not read surface /home/anup/Desktop/QDEC/fsaverage/surf/lh.white
Re: [Freesurfer] Qdec question
If you know the vertex you want to extract, then you can run something like mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf out.dat where y.mgh is the stack created by qdec and out.dat is the data file you want doug On 8/28/14 8:37 AM, Abrishamchi, Aurash David wrote: Hello, I still cannot solve this issue. All help will be appreciated. I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the find clusters and go to max button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 aabrisham...@mgh.harvard.edu ___ 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] Qdec question
Hello, I still cannot solve this issue. All help will be appreciated. I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the find clusters and go to max button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 aabrisham...@mgh.harvard.edu ___ 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] qdec question
thank you. I have another question; I am getting several significant clusters for group, when correcting for multiple comparisons and total brain size and age, but when I enter sex in, msot of these disappear, but i do not understand whether this is a power issue (as qdec automatically incorporates the interaction effect) or whether this is actually a gender effect? Because the group*gender interaction is non-significant, and the main effect of gender does not have a significant effect of any of the cortical measures either? Please, any help would be greatly appreciated. Kind Wishes, Anna On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: DOSS is not working in QDEC. It should be disabled in 5.3 doug On 05/05/2014 09:39 AM, Anna Jonsson wrote: Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec question
If you don't see an effect of gender, then it is ok to leave it out of the model. I could be affecting the power as you suspect. doug On 5/6/14 3:55 AM, Anna Jonsson wrote: thank you. I have another question; I am getting several significant clusters for group, when correcting for multiple comparisons and total brain size and age, but when I enter sex in, msot of these disappear, but i do not understand whether this is a power issue (as qdec automatically incorporates the interaction effect) or whether this is actually a gender effect? Because the group*gender interaction is non-significant, and the main effect of gender does not have a significant effect of any of the cortical measures either? Please, any help would be greatly appreciated. Kind Wishes, Anna On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: DOSS is not working in QDEC. It should be disabled in 5.3 doug On 05/05/2014 09:39 AM, Anna Jonsson wrote: Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ Freesurfer mailing list Freesurfer@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...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 ___ 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 question
Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ 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] qdec question
DOSS is not working in QDEC. It should be disabled in 5.3 doug On 05/05/2014 09:39 AM, Anna Jonsson wrote: Dear group, when using the qdec gui interface, I was wondering where the button or the likes is to change the estimation from its standard doss to dods (different osnet, different slope). I believe I can do this somewhere on the qdec gui without changing to mri_glmfit? ___ 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] Qdec question: opening previously ran group analysis
You can do it in QDEC by going running QDEC, then loading the surface, curvature, and overlay files (they are in the output folder (default Untitled)). Load the sig.mgh file for the overlay. This can also be done in tksurfer. doug On 01/24/2014 11:11 AM, Estephan Moana wrote: Dear Freesurfer experts, I ran some surface-based group analysis using Qdec. I would like to re-open those analysis and threshold them using FDR, for example. I read through the Qdec tutorial and it points out how to do so for new analysis, however there is no mention on how to open previously ran analysis. My questions are: 1. Is there a way to open previously ran group analysis in Qdec, or do I have to re-run it every time?; 2. What other program might allow me to open previously ran group analysis (and use multiple comparisons correction) if Qdec cannot do it: freeview, tksurfer? Thank you. Estephan Moana-Filho, D.D.S., M.S. Ph.D. Candidate Clinical Fellow, Oral Maxillofacial Pain Program Regional Center for Neurosensory Disorders UNC School of Dentistry mo...@unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec question: discrepancy in sig. clusters
Hello, I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit Find clusters and goto Max. For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit Find clusters and goto Max, I only see the Frontalpole. Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. Can you please help me reconcile the 2 types of output? Thanks! *** terminal output: # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxs Annot 14.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.0 0.00020 1292 medialorbitofrontal 23.968 135840466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 33.954 115431497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 43.242 133890439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral Simulation complete. ___ 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] qdec question: discrepancy in sig. clusters
Hi Maria, can you tar up the qdec output folder and send it to our file drop? I'm traveling now, so it might be the 1st week of august before I can take a look. You can also go into the qdec output folder and run tksurfer to show you the results. doug On 7/26/13 1:37 PM, Maria Kharitonova wrote: Hello, I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit Find clusters and goto Max. For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit Find clusters and goto Max, I only see the Frontalpole. Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. Can you please help me reconcile the 2 types of output? Thanks! *** terminal output: # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 4.75828 at vertex 134555 # Overall min -2.56762 at vertex 93241 # NClusters 4 # Total Cortical Surface Area 65020.8 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxs Annot 14.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.0 0.00020 1292 medialorbitofrontal 23.968 135840466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal 33.954 115431497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal 43.242 133890439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral Simulation complete. ___ 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] qdec question
I think the right way to do it is to use the symmetric template (fsaverage_sym) as the target (instead of fsaverage). You will need to run the symmetric registration. See http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi (if you have 5.2, you do not need to download anything). You can map either the left hemi or right hemi to the template, depending upon the subject. I'm not sure you can use QDEC at that point, depending upon what you want to do. doug On 3/12/13 3:22 AM, Kristina Nalbandian wrote: Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian ___ 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] qdec question
Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian ___ 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 question
Hello! I am running qdec group analysis on my patient data and have one very important question. I am studying the differences between two Epilepsy subtypes. Each one of my patients has a hemisphere of onset, either Left or Right, that I would like to use in looking for differences between ipsilateral and contralateral hemispheres. However, ipsilateral patients need to be grouped together, but qdec only allows me to visualize left or right hemispheres separately. Is there a way to combine left hemispheres with right hemispheres in an attempt to study grey matter thickness in hemispheres ipsilateral to seizure onset? [Because the ipsilateral hemisphere is the right hemisphere for some patients and left hemisphere for others]. For example, is it possible to somehow flip the right hemisphere such that ipsilateral hemispheres align together? Thank you in advance for your help, Kristina Nalbandian ___ 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] qdec question
Maria, In qdec there is not a built-in mechanism to restrict analysis to a particular region. By design it runs a whole-cortex analysis, masking just the medial (non-cortical) region, and then i suppose if your lucky (if your ROI is significant compared to everything else) your region will appear as a cluster which hopefully would survive a subsequent multiple-comparisons analysis. There might be a way to mask the glm analysis using the command line tools, but I dont think its recommended. Others might comment differently. Nick Dear Freesurfer users, I have a question regarding qdec and I would like your help. When conducting qdec analyses, is it possible to restrict the analyses to specific brain regions? I would like to limit my qdec analyses to brain regions typically associated with social cognition and have chosen these regions based on the existing literature. If so, could you tell me how this is done? Thank you so much for your help! Best, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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] qdec question
Hi Maria, you can do it with the commandline tools (mri_glmfit) by specifying --mask or --label. This is a common thing to do, but you will need to run simulations for multiple comparisons correction. doug On 01/04/2013 06:35 AM, Nick Schmansky wrote: Maria, In qdec there is not a built-in mechanism to restrict analysis to a particular region. By design it runs a whole-cortex analysis, masking just the medial (non-cortical) region, and then i suppose if your lucky (if your ROI is significant compared to everything else) your region will appear as a cluster which hopefully would survive a subsequent multiple-comparisons analysis. There might be a way to mask the glm analysis using the command line tools, but I dont think its recommended. Others might comment differently. Nick Dear Freesurfer users, I have a question regarding qdec and I would like your help. When conducting qdec analyses, is it possible to restrict the analyses to specific brain regions? I would like to limit my qdec analyses to brain regions typically associated with social cognition and have chosen these regions based on the existing literature. If so, could you tell me how this is done? Thank you so much for your help! Best, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec question
Dear Freesurfer users, I have a question regarding qdec and I would like your help. When conducting qdec analyses, is it possible to restrict the analyses to specific brain regions? I would like to limit my qdec analyses to brain regions typically associated with social cognition and have chosen these regions based on the existing literature. If so, could you tell me how this is done? Thank you so much for your help! Best, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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 question
Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani ___ 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] QDEC question
Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks, Manish On 2/2/12 2:47 PM, Manish Dalwani manish.dalw...@ucdenver.edu wrote: Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani ___ 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] QDEC question
Nevermind, I figured out both my questions! I just have to read the instructions carefully :) Manish On 2/2/12 3:02 PM, Manish Dalwani manish.dalw...@ucdenver.edu wrote: Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks, Manish On 2/2/12 2:47 PM, Manish Dalwani manish.dalw...@ucdenver.edu wrote: Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani ___ 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 question about covariates
Dear FreeSurfer experts, Hello, I started to use FreeSurfer recently. I want to do group analysis with QDEC in order to compare 2 groups (control group and patient group), regressing out age and gender. When I include 2 discrete factors (diagnosis and gender) and 1 continuous factor (age), and run QDEC, there appear a question of Does the average thickness, accounting for Gender, differ between Controls and Patients?, but there NOT appear a question of Does the average thickness, accounting for Gender *AND AGE*, differ between Controls and Patients?. So, it seems that age cannot be regressed out in this way. However, when I include 1 discrete factor (gender only) and 2 continuous factors (age and also diagnosis *dummy parameterized: Controls = 1, Patients = 0*), and run QDEC, there appear a question of Does the correlation between thickness and Diagnois, accounting for Age and Gender, differ from zero?, and the result seems OK. My question is; 1) Is it right to do the (above-mentioned) latter way to compare difference of thickness between the 2 groups, regressing out age and gender? 2) Why couldn't age regressed out in the former way? 3) In this way, generally is it OK if I enter simple discrete factor as a continuous factor in QDEC (for example, gender:male=1, female=0)? This time I want to ask, since I couldn't find an answer in the past archives. Thanks a lot, Manabu Kubota kubot...@kuhp.kyoto-u.ac.jp Graduate School of Medicine, Kyoto University ___ 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] qdec question
Prapti, To save results in another directory: setenv QDEC_WORKING_DIR some/pathname then run qdec. Nick On Thu, 2009-07-23 at 12:19 -0400, Douglas N Greve wrote: Prapti Gautam wrote: Dear freesurfers, I have a few additional questions regarding qdec. 1. Is it possible to specify in qdec so that the results of the analyses run are saved in a separate destination than the SUBJECTS_DIR? I'll leave this for Nick. 2. I have read in the qdec tutorial that it is possible to select up to 4 variables to regress in analyses, but I can only select 1 discrete and 2 continuous variables in my version. I am running Freesurfer v4.3.0. Does this mean I have an older version of qdec that only allows selection of 2 continuous variables and I need to update to a newer version of freesurfer?? The 4 variables are 2 discrete and 2 continuous. This is all it does right now. If you need more, you'll have to run mri_glmfit manually. doug Thank you for your help, Prapti -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Friday, 10 July 2009 4:15 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec question The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
Prapti Gautam wrote: Dear freesurfers, I have a few additional questions regarding qdec. 1. Is it possible to specify in qdec so that the results of the analyses run are saved in a separate destination than the SUBJECTS_DIR? I'll leave this for Nick. 2. I have read in the qdec tutorial that it is possible to select up to 4 variables to regress in analyses, but I can only select 1 discrete and 2 continuous variables in my version. I am running Freesurfer v4.3.0. Does this mean I have an older version of qdec that only allows selection of 2 continuous variables and I need to update to a newer version of freesurfer?? The 4 variables are 2 discrete and 2 continuous. This is all it does right now. If you need more, you'll have to run mri_glmfit manually. doug Thank you for your help, Prapti -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Friday, 10 July 2009 4:15 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec question The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
Dear freesurfers, I have a few additional questions regarding qdec. 1. Is it possible to specify in qdec so that the results of the analyses run are saved in a separate destination than the SUBJECTS_DIR? 2. I have read in the qdec tutorial that it is possible to select up to 4 variables to regress in analyses, but I can only select 1 discrete and 2 continuous variables in my version. I am running Freesurfer v4.3.0. Does this mean I have an older version of qdec that only allows selection of 2 continuous variables and I need to update to a newer version of freesurfer?? Thank you for your help, Prapti -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Friday, 10 July 2009 4:15 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec question The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison -- On Thu, 9 Jul 2009, Prapti Gautam wrote: Dear Freesurfers, I just have some quick questions regarding qdec: 1.How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2.Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison -- On Thu, 9 Jul 2009, Prapti Gautam wrote: Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qdec question
Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec question
Hi, I am using qdec for analysis and noticed that in addition to thickness measures I can select others such as area and volume. I have been trying to figure out what exactly the area measure refers to (surface area, etc.). I did not find it on the website. Can someone clarify that for me? If this is a repeat question, I apologize and ask that you point me to the archived post. Thank you, Dev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec question
Hi, I have been running into an error while using Qdec. *Error in Analyze: Couldn't open file $SUBJECT_DIR/SUBJECT_FOLDER/surf/lh.thickness.fwhm10.fsaverage.mgh* I checked and the file is there in that folder. I know this file is created when recon-all is run with -qcache option. I have run that twice and it still gives me the same error. What could be going wrong here and how can I fix it? Thanks, Dev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec question
hi Dev, You might have wrong SUBJECTS_DIR, check it using echo $SUBJECTS_DIR Hi, I have been running into an error while using Qdec. *Error in Analyze: Couldn't open file $SUBJECT_DIR/SUBJECT_FOLDER/surf/lh.thickness.fwhm10.fsaverage.mgh* I checked and the file is there in that folder. I know this file is created when recon-all is run with -qcache option. I have run that twice and it still gives me the same error. What could be going wrong here and how can I fix it? Thanks, Dev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec question
Hi all, I am using Qdec to examine the anatomical differences between two groups of subjects. The surface-based measures I can select are thickness, area, area.pial, sulc, curv, and jacobian_white. Could anybody tell me what anatomical features the later three (sulc, curv, and jacobian_white) actually measure? Thanks in advance, Xiangchuan Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec question
sulc = average convexity from our 1999 reconII paper. Essentially measures the depth/height of each point above the average surface. curv = smoothed mean curvature. jacobian_white = the jacobian of the spherical transform. Measures the amount of distortion needed to warp a subject into register with the atlas. On Mon, 5 Nov 2007, Xiangchuan Chen wrote: Hi all, I am using Qdec to examine the anatomical differences between two groups of subjects. The surface-based measures I can select are thickness, area, area.pial, sulc, curv, and jacobian_white. Could anybody tell me what anatomical features the later three (sulc, curv, and jacobian_white) actually measure? Thanks in advance, Xiangchuan Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec question
Xiangchuan Chen, You might want to look at the slides downloadable from the top of this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial which contain pictures showing the meaning of 'curv' and 'sulc'. Nick sulc = average convexity from our 1999 reconII paper. Essentially measures the depth/height of each point above the average surface. curv = smoothed mean curvature. jacobian_white = the jacobian of the spherical transform. Measures the amount of distortion needed to warp a subject into register with the atlas. On Mon, 5 Nov 2007, Xiangchuan Chen wrote: Hi all, I am using Qdec to examine the anatomical differences between two groups of subjects. The surface-based measures I can select are thickness, area, area.pial, sulc, curv, and jacobian_white. Could anybody tell me what anatomical features the later three (sulc, curv, and jacobian_white) actually measure? Thanks in advance, Xiangchuan Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC question
Dear all, I have 2 questions regarding doing analyses using QDEC: 1) can I use QDEC to analyse results on data for which I ran recon-all using the last (ie: older, not most recent) version of Freesurfer, or should I rerun recon-all on all the data using the new version of Freesurfer? (I hope not the latter!) 2) I have run the preprocessing required for using QDEC (ie, recon-all -s subjid -qcache) on one subject for whom I had run recon-all using the previous version of Freesurfer, and I get the following error messages: WARNING: File rh.volume does not exist skipping creation of smoothed data for rh.volume WARNING: File rh.white.K does not exist skipping creation of smoothed data for rh.white.K WARNING: File rh.white.H does not exist skipping creation of smoothed data for rh.white.H WARNING: File rh.jacobian_white does not exist skipping creation of smoothed data for rh.jacobian_white what might this mean? thanks in advance, best, Narly. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] QDEC question
Narly, You can use qdec on data processed with the v3.0 processing stream, as long as you create the 'qcached' files that qdec needs, which is done using v4.0 recon-all, as you have done. You can ignore those warning message. They are informative (I will change it to say INFO). The ?h.volume files are not yet created by recon-all, and the qcache option is just looking for them for future compatibility. Nick On Fri, 2007-09-14 at 14:34 +0100, Narly A Golestani wrote: Dear all, I have 2 questions regarding doing analyses using QDEC: 1) can I use QDEC to analyse results on data for which I ran recon-all using the last (ie: older, not most recent) version of Freesurfer, or should I rerun recon-all on all the data using the new version of Freesurfer? (I hope not the latter!) 2) I have run the preprocessing required for using QDEC (ie, recon-all -s subjid -qcache) on one subject for whom I had run recon-all using the previous version of Freesurfer, and I get the following error messages: WARNING: File rh.volume does not exist skipping creation of smoothed data for rh.volume WARNING: File rh.white.K does not exist skipping creation of smoothed data for rh.white.K WARNING: File rh.white.H does not exist skipping creation of smoothed data for rh.white.H WARNING: File rh.jacobian_white does not exist skipping creation of smoothed data for rh.jacobian_white what might this mean? thanks in advance, best, Narly. ___ 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
