Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Re: [Freesurfer] conflicting Monte Carlo simulation results...
by Karl Liu 03 Mar '16

03 Mar '16

Dear Doug, Thank you for your clarification. It sounds the right way for correction is:mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces One last question: Is the resulting "cache.th40.neg.sig.cluster.summary" the right file to look for post-correction cluster information? The (old) manual said results should be stored in a files starting with "mc-z", but the "cache....summary" file is the only summary file FS produces after running the script above... thank you. Karl ******************************************************** In the first command you only used 5 samples in your simulation. If you read the "Notes" section below the command, you'll see that this should be something like 5000. Only 5 was used because it would take very long to run. In general, you don't need to run the simulation because it has already been run and the data tabulated (this is what is accessed in the 2nd command line).On 03/02/2016 10:03 PM, Karl Liu wrote: > > Dear Freesurfer experts: > > > I ran into a confusing problem when applying Monte Carlo simulation to > control for multiple comparisons. I am using the buckner data from > tutorial dataset. > > > I first tried the simulation based on Freesurfer;s 2012 manual: > > (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-…) > > > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 > mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite > > > This produced a "mc-z.negative.sig.cluster.summary". In this text, no > clusters survived correction. > > > Later on, I applied on a slightly different script, based on > Freesurfer tutorial > > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwi…) > > > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ > --cwp 0.05\ --2spaces > > > It produced a "cache.th40.neg.sig.cluster.summary" this time. But > according to this result, 22 clusters survived. > > > Now I am quite confused, because both corrections have the same > voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the > drastic discrepancies come from and which result is more reliable? > > > Many thinks in advance. > > Best, > > Karl > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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(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 erro

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error in mc-sess
by Ji Won Bang 03 Mar '16

03 Mar '16

Dear. freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried mc-sess onto runs that have different number of slices. However, due to this different number of slices in different runs, mc-sess gives an error. I expected that running mc-sess in freesurfer version 5.3.0 would handle this issue. If you can share your idea to fix this problem, that would be a great help. Thank you! Best, Ji Won

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AAL atlas question
by pfotiad＠nmr.mgh.harvard.edu 03 Mar '16

03 Mar '16

Hi FS community, I have recon-ed a set of subjects and I was interested in also obtaining structural info (cortical thickness, gray matter volume, surface area etc.) based on a different atlas than the ones FS is using, and in particular the AAL atlas. I was wondering whether my approach would be the correct one or whether there is another (better and more accurate) approach: 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI space into the native subjects' space, 2) Use mris_anatomical_stats to calculate the structural stats Sorry for the potentially trivial question, and thank you for your time! Best, Panos

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Qdec-statistical map
by John Anderson 03 Mar '16

03 Mar '16

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"wm" boundaries and stats
by Krieger, Donald N. 03 Mar '16

03 Mar '16

Freesurfer provides 34 ctx label volumes on each side of the brain with adjacent wm labels. The boundary between each ctx volume and the co-named adjacent wm volume is a third "white" label. I would like to extract a few pieces of information from the analogous boundary between each wm volume and those adjacent volumes to it which are not the co-named ctx volume. For instance many wm volumes share a boundary with the unsegmented white matter. Some share a boundary with sub-cortical structures. Here are some of the information I would like to extract. What do you think? What are the xyz coordinates of the complete boundary surrounding each wm volume and what is the name of the adjacent volume for each point on the boundary? I understand that for the boundary between the ctx volume and the adjacent wm volume, the white label provides this information. What is the percentage and area of the complete boundary surrounding a wm volume which is adjacent to the co-named ctx volume.? What are the names of the other volumes with which each wm volume shares a boundary and what is the percentage and area of the boundary shared with each? For each point within a wm volume, are the nearest points on the wm boundary adjacent to the co-named ctx volume or are some adjacent to unsegmented white matter or sub-cortical structures? More generally, is a particular few mm voxel surrounded by gray matter and so is likely primarily composed primarily of relatively short range fibers or is it adjacent to the deep white matter (unsegmented) and likely composed of a mix of relatively short range fibers and long range "en passage" fibers. It is this last question which most closely gets at the ideas I wish to explore. We are able to measure electric current in the white matter with mm resolution from the MEG. The mix of local and "en passage" fibers should effect the direction of the electric currents in the white matter and I can measure that. The distance scale is at the edge of that provided by DTI-derived tractography so we may be able to meld these measurements with those. Your thoughts would be welcome on what is already there in freesurfer that will help with this and what you think might be a good direction to proceed to develop what we need from what is there. Thanks - Don

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v5.3 fsaverage (accidentally) in v5.1 directory
by Adam Martersteck 03 Mar '16

03 Mar '16

Hi Freesurfer team, *Short question: *Will (accidentally) using the fsaverage v5.3 subject in our v5.1 directory influence our reconstructions? *Long question:* Our server has 2 different freesurfer environments. A recon was accidentally run on a single v5.1 subject in the v5.1 directory with freesurfer version 5.3. During the “balabels” stage of autorecon3, because FS 5.3 couldn’t find the perirhinal label – it deleted our 5.1 symlink and replaced it with the correct 5.3 symlink. We realized it had happened and correct the subject, but didn’t catch that the symlink had been changed. We have run multiple (hundreds) of brains through v5.1 since then – with the v5.3 fsaverage in the v5.1 directory. A cursory glance over the release notes from 5.1 to 5.3 makes me think nothing has fundamentally changed – only new files have been added to fsaverage 5.3 (e.g. cortical parcellation networks). No new GCA atlas or anything that would change how FS 5.1 reconstructs the brain? Thanks for any thoughts! Adam

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conflicting Monte Carlo simulation results...
by Karl Liu 03 Mar '16

03 Mar '16

Dear Freesurfer experts: I ran into a confusing problem when applying Monte Carlo simulation to control for multiple comparisons. I am using the buckner data from tutorial dataset. I first tried the simulation based on Freesurfer;s 2012 manual: (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-…) mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite This produced a "mc-z.negative.sig.cluster.summary". In this text, no clusters survived correction. Later on, I applied on a slightly different script, based on Freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwi…) mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces It produced a "cache.th40.neg.sig.cluster.summary" this time. But according to this result, 22 clusters survived. Now I am quite confused, because both corrections have the same voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the drastic discrepancies come from and which result is more reliable? Many thinks in advance. Best, Karl

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Extract LGI at MaxVertex and extract effect-sizes in table format
by Bittner, Nora 03 Mar '16

03 Mar '16

Dear FreeSurfer Experts, Sorry for reposting this massage again, but I still have two questions, which you can hopefully answer to: 1) I calculated several analyses with LGI as my dependent variable, resulting in several significant clusters. Now, I would like to extract the individual LGI value at the maximum vertex of each significant cluster to plot it against my experimental variables (instead of working with the mean LGI values of the clusters). What I tried so far is to use mri_segstats to extract the LGI at the maximum vertex: mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf vertexno84367.dat where y.mgh is my input file from the glm and vertexno 84367 is the maximum vertex of the cluster as reported in the cluster.summary-file. I found the command in the FS helpline documentation (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html) but regrettably<http://dict.leo.org/ende/index_en.html#/search=regrettably&searchLoc=0&resu…> I get the following error message: "ERROR: Option --crs unkown" In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the user description. Is there any other option or argument I can use in mri_segstats (or in any other command) to extract the LGI value per person at the given vertex? 2) I would like to calculate effect sizes of my results. Therefore I used fscalc: fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ glm/contrast/effectsize.mgh This worked fine and resulted in a surface overlay displaying the effect sizes. Now, I would like to extract these effect sizes in 'table' format. I tried to use mri-segstats: mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf effectsize.dat I am not sure, if this gives me the correct results. Is this the right command? I would really appreciate<http://dict.leo.org/ende/index_en.html#/search=appreciate&searchLoc=0&resul…> your help. Thank you in advance, Nora ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Reading values from overlays with PETcoreg
by Benjamin Spurny 03 Mar '16

03 Mar '16

Dear Freesurfer experts! I am currently working on PET analysis using FS I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file. In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis? Many thanks in advance! Benjamin

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[FreeSurfer] Repeated Measures ANOVA in FSFAST
by Afzal, Afsana 03 Mar '16

03 Mar '16

Hi, I'm analyzing a decision making task with a 3x3 condition matrix: pairings of low, medium, high levels of risk with low, medium, high levels of reward. I've set up the following FSGD file to do a repeated measures/within-subject ANOVA: GroupDescriptorFile 1 Class hc001 Class hc002 Class hc003 Class hc004 Class hc005 Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd Input hc001 hc001 1 1 1 1 1 1 1 1 1 Input hc002 hc002 1 1 1 1 1 1 1 1 1 Input hc003 hc003 1 1 1 1 1 1 1 1 1 Input hc004 hc004 1 1 1 1 1 1 1 1 1 Input hc005 hc005 1 1 1 1 1 1 1 1 1 I've also created the following contrast matrices: Con1: Does difference between highRisk and LowRisk differ from 0? 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1 Con2: Does difference between highRisk and MedRisk differ from 0? 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1 Is this an appropriate way of setting up the ANOVA? Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Freesurfer March 2016