Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Qdec Design
by dolphinede＠aol.com 26 Jan '12

26 Jan '12

Dear freesurfer experts, i am really a newbie in freesurfer. I want to compare the thickness between different ages. Is it correct to use gender as fixed factor, to look for its influence on thickness ? If i find no effects of gender on thickness i can put the factor gender out of the model ? Otherwise if there will be effects of gender on thickness it remains in the model. So that the effect of age on thickness can be questioned like this: Does the correlation between thickness and age, accounting for gender, differ from zero? Best regards Daniel

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Re: [Freesurfer] cwp threshold
by Douglas N Greve 26 Jan '12

26 Jan '12

The FA values are used to compute a p-value at each voxel. The p-value map is thresholded using the threshold you supply (3 in this case). Clusters are formed based on the number neighboring/contiguous voxels above threshold. The p-value for the cluster is determined based on the number of voxels in the cluster, the threshold you used, the amount of smoothing, and the number of voxels in the brain mask (ie, the search space). doug Antonella Kis wrote: > I understand that but how this value is related to my FA values? Is p > accounting for the FA's intensity within a cluster? > > THANKS! > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, January 26, 2012 11:30 AM > *Subject:* Re: [Freesurfer] cwp threshold > > This is the maximum p-value for a cluster that will be reported. You can > also raise the p-value to report more clusters, but you probably cannot > get anything published with p>.05 > > > Antonella Kis wrote: > > Dear all, > > > > I would like to know if while doing a group analysis for my FA data > > and I do the correction by multiple comparisons for the clusters: > > > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --grf 3 neg \ > > --cwpvalthresh .05 \ > > --overwrite > > > > what exactly is defined the cwpvalthresh. I mean I know that this is a > > cluster-wise p-value threshold but is this calculated from or based on > > the FA intensity values? > > > > > > Thank you very much for your clarification. > > Antonella > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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> > > _______________________________________________ > 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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Re: [Freesurfer] mri_glm with grf over CVS space
by Douglas N Greve 26 Jan '12

26 Jan '12

It will create another table called something like permcsd.sig.cluster.summary Antonella Kis wrote: > Hi Doug, > > Thank s so much for the valuable support. If I run the command below > how I can catch the clusters? When using the grf I was getting as > output my clusters in a table. > > Thanks so much! > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, January 26, 2012 11:28 AM > *Subject:* Re: [Freesurfer] mri_glm with grf over CVS space > > You can run the command below (it might take several hours). This will > get a p-value based on permutation. This will probably be larger (more > conservative) than the one you get from GRF. See the Nichols tutorial in > HBM 2001 for more info on permutation. > > doug > > mri_glmfit-sim \ > --glmdir Group_Analysis.glmdir \ > --sim perm 10000 3 permcsd\ > --cwpvalthresh .05 > > Antonella Kis wrote: > > Hi Doug, > > > > Many thanks for your help. I have one more questions please. You were > > telling me that: > > > > "Given that FA is very non-gaussian, a lot of people prefer to use > > permutation". What this means? Do I need to run something different > than: > > > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --grf 3 neg \ > > --cwpvalthresh .05 \ > > --overwrite > > > > > > Thank you. > > Antonella > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Monday, January 23, 2012 4:50 PM > > *Subject:* Re: [Freesurfer] mri_glm with grf over CVS space > > > > > > > > Antonella Kis wrote: > > > Hi, > > > > > > I would like to do a Group Analysis for my FA data. > > > > > > For all my subjects (controls + patients) I have all the > > fa-masked.ANAT+CVS-to-avg35.mgz (the resampled registered image to CVS > > space). > > > > > > I am not sure if my steps for the Group Analysis are the right one: > > These look correct > > > > > > 1) Concatenate FA from individuals into one file > > > > > > mri_concat */fa-masked.ANAT+CVS-to-avg35.mgz --o > > GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz > > > > > > 2) Make sure the order agrees with the fsgd: > > > > > > ls -l */fa-masked.ANAT+CVS-to-avg35.mgz > > > > > > 3) Create average of the input images for visualization: > > > mri_average */fa-masked.ANAT+CVS-to-avg35.mgz > > GroupAnalysis.Average-fa-masked.ANAT+CVS-to-avg35.mgz > > > > > > 4) mri_glmfit --y GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz \ > > > --fsgd Group_Analysis.fsgd dods --C contrast.mtx --glmdir > > Group_Analysis.glmdir > > > > > > To view uncorrected results: > > > > > > tkmedit fsaverage orig.mgz -aparc+aseg -overlay > > > /media/1Tra/Antonella_2011/DTI_FS/dtrecon/Group_Analysis.glmdir/contrast/sig.mgh > > > -fminmax 2 3 > > > > > > where -fminmax 2 3 : Voxel-wise threshold of 2 (p<.01), color > > saturation at 3 (p<.001) > > > > > > > > > To correct for multiple comparisons run: > > > > > > > > > 5) mri_glmfit-sim \ > > > --glmdir Group_Analysis.glmdir \ > > > --grf 3 neg \ > > > --cwpvalthresh .0166 \ > > > --overwrite > > > > > > > > > Is 3 (p<.001) neg as well as .0166 (.05/3) the best voxel-wise as > > well as cluster wise values to be tried? > > There is no answer to the voxel-wise threshold (a criticism of the > > method). For the CWP, you can use .05 instead of .0166 (that value is > > for the case where you are doing separate surface and subcortical > > analyses). Given that FA is very non-gaussian, a lot of people prefer > > to use permutation (which requires you to run a simulation -- also see > > my note from last week about a bug in the permutation code (not a > > problem if you only have one contrast)) > > > > > > > > > To view corrected results: > > > tkmedit fsaverage orig.mgz \ > > > -ov > > > /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh > > > \ > > > -seg > > > /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.anat.mgh > > > \ > > > > > > /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.lut > > > \ > > > -fminmax 1.3 5 > > > > > > with only positive values > > > > > > * p-values are p-values for cluster > > > * > > > Set threshold to 1.3 (p<.05) > > > > > > > > > Are this steps right? > > > > > > When I run the registration over the cvs space which file is the > > equivalent file of the fa-tal.nii.reg from the TAL space? > > I don't think there is one file that exists. > > doug > > > > > > > > > MANY THANKS! > > > > > > Antonella > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > 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 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: 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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(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 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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qdec: vertex thickness values
by Cat Chong 26 Jan '12

26 Jan '12

Dear Freesurfers: I am comparing two groups in qdec. I am looking at the scatter plot function for a specific vertex for thickness to age correlation. If I "click" on a dot on the scatter plot, it will provide me the thickness values for that vertex for a specific person in the scatter plot function as well as in the terminal. Is there a way to get ALL the thickness values (for that vertex) for everybody at once, rather than selecting each one by hand in the scatter plot function? thank you very much for your help, cheers, cat

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Re: [Freesurfer] group wrfx error: MRInormWeights: value less than or eq to 0.
by Douglas N Greve 26 Jan '12

26 Jan '12

Try the version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concat doug Sid Kundu wrote: > Hi Doug, > > The --prune argument doesn't work with mri_concat in the version of > freesurfer I am using. Any other way to accomplish this? > _________________________________ > Sid Kundu > Biomedical Engineering > Boston University > > > > On Wed, Jan 25, 2012 at 3:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > I'm guessing that there is a voxel (or more) in cesvar that is 0 > for a subject (or more). Usually such voxels are masked out by > pruning the input ces. You can create your own mask with > > mri_concat tal.cs.nii tal.cesvar.nii --prune --o junk.mgh > mri_binarize --i junk.mgh --min .00000000000001 --o newmask.mgh > > Then pass this mask to mri_glmfit with the --mask option. > > doug > > Finnegan Calabro wrote: > > Hi Doug et al, > > We're running into a problem doing a wrfx group analysis using > FreeSurfer 4.5. Looks like the glmfit is having trouble with > the weights. We tried running it for different subsets of our > subjects, and get the same thing, so it's not one subject > contaminating the analysis. Any guess where we should look > for tracking this down? Presumably the cesvar files are > screwed up somehow, which would imply something went wrong in > the individual selxavg3's. But any ideas about what could > lead to this? The individual overlays all seem to look ok. > > > > [sidkundu@brodmann all-vs-null]$ mri_glmfit --y tal.ces.nii > --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii > --wls tal.cesvar.nii > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > cwd > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null > cmdline mri_glmfit --y tal.ces.nii --osgm --glmdir > tal.wrfx.osgm --nii --mask ../tal.mask.nii --wls > tal.cesvar.nii sysname Linux > hostname brodmann.bu.edu <http://brodmann.bu.edu> > <http://brodmann.bu.edu/> > > machine x86_64 > user sidkundu > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii > logyflag 0 > usedti 0 > mask ../tal.mask.nii > maskinv 0 > glmdir tal.wrfx.osgm > IllCondOK 0 > DoFFx 0 > wFile tal.cesvar.nii > weightinv 1 > weightsqrt 1 > Creating output directory tal.wrfx.osgm > Loading y from > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii > Saving design matrix to tal.wrfx.osgm/Xg.dat > Matrix condition is 1 > Pruning voxels by thr: 0.000000 > Found 260736 voxels in mask > Saving mask to tal.wrfx.osgm/mask.nii > search space = 2.08589e+06 > ERROR: MRInormWeights: value less than or eq to 0. > c=34, r=2, s=33, v=0 > > > -- > 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> > > > > 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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Error message for getting the stat file into table format
by Rashmi Singh 26 Jan '12

26 Jan '12

Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA483.T3 AA486.T0 AA492.T1 AA492.T3 AA495.T0 AA495.T1 AA495.T2 AA495.T3 AA499.T0 AA534.T0 AA539.T0 AA543.T2 AA543.T3 AA549.T1 AA549.T2 AA549.T3 AA550.T1 --hemi rh --meas thickness --tablefile rh.aparc.thick.txt The message came: SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I used the skip option only to find this message SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA474.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA476.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA479.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA486.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA499.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA534.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA539.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA550.T1/stats/rh.aparc.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/aparcstats2table", line 338, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range Please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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Per-run registration in monkey fmri
by SHAHIN NASR 26 Jan '12

26 Jan '12

Hi In monkey fmri, we usually have to do the functional-anatomical registration manually since bbregister doesn't work very well. It was easy in version 4.5 since we usually used just one run for registration. In version 5.1 we can use per-run option to improve registration but I am wondering how can we use it in monkey fmri? Should we register each run separately? Then how can we combine those individual registration files to generate the final registration file.

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vertex extraction
by Alexander Lebedev 26 Jan '12

26 Jan '12

Dear Freesurfer users and developers! I am trying to extract vertices by the script suggested by Pedro Paulo de M. Oliveira Jr. for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $FSAVERAGE_DIR/surf/lh.$i.mgh mris_convert -c $i.mgh $FSAVERAGE_DIR/surf/lh.inflated lh.$i.asc done It works fine, but I'm just wondering if there is an easy opportunity to combine the vertices from each subject into one big N-by-V matrix (N - subject № , V- vertex №). Thank you very much for your time! -- Regards, Alexander Lebedev Stavanger University Hospital, Norway

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qdec analysis
by Cat Chong 26 Jan '12

26 Jan '12

Hello Experts: In qdec, I would like to analyze if the thickness- entorhinal volume correlation differs between APOE positive and negative subjects accounting for age. I have chosen age as a nuisance variable and entorhinal volume as a covartiate. ( hope this is correct) Results show me several clusters of group differences following FDR correction. Here is my question: I would like to know what the mean value differences are between the groups for various clusters. And I would also like to know which group shows less of a correlation for certain clusters. Could you tell me where I would find those values? Best Regards, Catherine

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qdec and analysis results
by Cat Chong 26 Jan '12

26 Jan '12

Hello Experts, I am analyzing cortical thickness of two groups (APOE 4carries vs. noncarriers) in freesurfer with age as a co-variate. I am uncertain about the statistical differences behind: 1)Does the correlation between thickness and age accounting for APOE, differ from 0? in contrast to: 2)Does the thickness-age correlation differ between 1 and 0? I get significant results after FDR correction for the first but not for the second analysis. thank you for your help, catherine

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