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30132 discussions

rewritten: updating the tables and volumes associated with aseg.mgz
by silver47＠gmx.com 18 Sep '13

18 Sep '13

Dear Freesurfer Experts, I'm sorry if I have not been clear with my question so far. I have completed the cortical analysis on a number of subjects using 5.3, with all requiring some editing and re-running. Now that I have the final surfaces, to update the aseg.mgz, I would like to run: recon-all -subjid subject -surfsegedit before examining the aseg.mgz more closely. Looking at one aseg.mgz (for example) I can see that edits could be made to label more of the cerebellar cortex as well as some relabelling of the brainstem. After performing edits such as these to aseg.mgz (and possibly to other subcortical structures) would I then run: recon-all -subjid subject -aparc2aseg -segstats -wmparc to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, and stats/wmparc.stats without changing the cortical stats files such as lh.aparc.stats? Using this approach, I'm hoping that I can begin the group analysis of the cortex using lh.aparc.stats (and the like) while the subcortical review is underway, without having to re-run this group analysis with subsequent updates of lh.aparc.stats that would occur by running -autorecon3 (or similar) to update aseg.stats, aparc+aseg.mgz, etc. Please let me know if this approach is valid, any suggestion would be appreciated. Thanks, P

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"Nuisance factors" in Qdec
by ye tian 17 Sep '13

17 Sep '13

Dear Freesurfers, I have a question concerning the "nuisance factors" in the qdec dialogue. Suppose I have two independent variables x1 (discrete) and x2 (continuous), and only one observable y. I choose "Discrete (Fixed factor) = x1", "Continuous (covariate) = x2". If I further chose "Nuisance factor = x2", does that imply that 1) my contrast matrix is (0 1) 2) null hypothesis: Y is independent of x2 Thank you very much! Sincerely, Ye

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Ventriculomegaly causing segmentation issues
by Victor Kovac 17 Sep '13

17 Sep '13

Dear FreeSurfer experts, There are a number of patients in my study with significant ventricular dilation, which is causing problems with segmentation of the ventricles and corpus callosum, in particular, after recon-all (image attached). I am using v5.3. I manually adjusted the talairach, but this did not fix the issue. Is there anything else I can try? It is very important that I get at least some volumetric data from these patients, as they are suffering from the worst neurologic disease. I appreciate any advice you can provide. Thanks, Victor

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volume of subcortical structure calculation
by Subhabrata Chaudhury 17 Sep '13

17 Sep '13

Hello Where can I get information on how freesurfer calculates volumes of subcortical structures ? Is there a paper which provides insights into this method ? Is it that for certain subcortical structures, it just counts the number of voxels and adds them up since the voxels are 1mm3 ? Thanks Subha

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Maximum significance
by Yang, Daniel 17 Sep '13

17 Sep '13

Hi all, I performed cluster analyses and obtained several clusters, which are indicated by the corresponding maximum significance levels. For example, cluster one -- 4.00, and cluster two -- 4.00. Then I did a conjunction analysis to see their overlap, and then did a mri_surfcluster to get the clusters from the overlap. Then I observed that I have TalX TalY TalZ for each cluster in the overlap -- my question is, how does mri_surfcluster determine those coordinates? Since the whole cluster might have the same significance level everywhere? Thanks, Daniel

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R: Re: Effect size
by stdp82＠virgilio.it 17 Sep '13

17 Sep '13

Thank you very much Doug! Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 17-set-2013 22.25 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Effect size what do you mean exactly by "effect size"? gamma.mgh is the contrast value (C*beta) doug On 9/17/13 8:01 PM, Chung, Yoonho wrote: > Hi all, > > Where can I find the effect size file(.mgh) after running mri_glmfit when doing group analysis (control vs patients adjusting for age and sex)? Somewhere in the wiki said gamma.mgh is the surface overlay for effect size. Is this true? If not, how would I compute one? > > Yoon > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Effect size
by Chung, Yoonho 17 Sep '13

17 Sep '13

Hi all, Where can I find the effect size file(.mgh) after running mri_glmfit when doing group analysis (control vs patients adjusting for age and sex)? Somewhere in the wiki said gamma.mgh is the surface overlay for effect size. Is this true? If not, how would I compute one? Yoon

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covariates in cortical thickness analysis
by stdp82＠virgilio.it 17 Sep '13

17 Sep '13

Hi list, I'm performing cortical thickness analysis on 3 groups. One of these is a control groups. Mean cortical thickness in right and left hemispheres do not show any significativity among groups. I'd like to not use mean cortical thickness as covariate becouse it worsens and make difficult to explain results. May I do it? Thank you very much. Stefano

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Mac OS X 10.8.5 breaks recon-all
by Peter J. Molfese 17 Sep '13

17 Sep '13

I updated my Mac OS X install to 10.8.5 late yesterday and now recon-all (FS 5.3) fails early in the processing pipeline (Talairach). I've attempted running the process with both my own data that works on Freesurfer 5.3 with 10.8.4 and receive the same error message. I have two identical computers, with only one updated to 10.8.5, which will make further testing straightforward. I attached the log below of the attempt to run the "bert" data with just one MRI. The error message is the same for other data. bugr output: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 12.5.0 x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name - bert (and any other subject) 2) the entire command-line executed - recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T 3) the error message generated - see below 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting =============== BEGIN ERROR REPORT =================== recon-all -s bert -i /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz -all -3T Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/MRIData/srtt/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/top) is setuid or setgid /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz \n mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Sep 17 12:49:59 EDT 2013 Found 1 runs /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Volumes/MRIData/srtt/freesurfer/bert/mri/orig/001.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz \n /Volumes/MRIData/srtt/freesurfer/bert \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform \n mri_convert /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/MRIData/srtt/freesurfer/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Volumes/MRIData/srtt/freesurfer/bert/mri/transforms/talairach.xfm /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz /Volumes/MRIData/srtt/freesurfer/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Sep 17 12:50:13 EDT 2013 /Volumes/MRIData/srtt/freesurfer/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin frankie.haskins.lab 12.5.0 Darwin Kernel Version 12.5.0: Mon Jul 29 16:33:49 PDT 2013; root:xnu-2050.48.11~1/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Tue Sep 17 12:50:20 EDT 2013 For more details, see the log file /Volumes/MRIData/srtt/freesurfer/bert/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] Significant clusters before and after Monte Carlo
by Anita van Loenhoud 17 Sep '13

17 Sep '13

Hi Doug, It is finally starting to make sense to me. It was indeed the case that before Monte Carlo, within a cluster there were different values for each vertex, and after Monte Carlo, each vertex had the same value. I had difficulty understanding the different functions of the color scale min/max threshold and the vertexwise threshold. Is the following correct: The min/max threshold is nothing more than a visualisation threshold; it does not change anything in subsequent analyses that are performed (such as Monte Carlo), it just decides which results are significant enough to be colored or opaque. The vertexwise threshold (the one that is next to Monte Carlo) is the one that decides which vertices should be considered in the simulation. So a vertexwise threshold of 2 only takes vertices into account that have a p value < 0.01. After Monte Carlo, the min/max (visualisation) threshold now decides which cluster wise p-values (cwp's) should be shown in color. So, compared to before Monte Carlo, it now has a slightly different function: it does not decide which individual vertices, but which clusters should be colored/opaque. One last question (if the above is correct): could one decide to set the vertex wise threshold at 1.3 for example, and the visualisation threshold at 2? Or do both threshold always have to be the same? Thanks a lot for your help, Anita

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