Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

mri_glmfit-sim over PALM
by Martin Juneja 13 Sep '17

13 Sep '17

Hi experts, To calculate simulations on LGI measures, I ran: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 But it gives error: ERROR: design matrix is not orthogonal, cannot be used with permutation. I came across a post where its mentioned that: "Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs. https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim" - Douglas N. Greve So I was wondering if I can use this program for LGI measures and run the same command, lets say this new program is: mri_glmfit-sim_new, so can I run the following command (instead of doing PALM): mri_glmfit-sim_new --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 Thanks.

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Normalizing volumes
by Alexopoulos, Dimitrios 13 Sep '17

13 Sep '17

Hi, We running FS 5.3 analyses on 2 cohorts (control vs. malnourished adolescents) and I was wonderful what FS measure would be most accurate for normalizing the volumes. (i.e total GM, total WM, suparatentorial, etc). The eTIV measures are significantly different between the cohorts. Is eTIV the best way to normalize or perhaps BrainSegVol? What FS measure gives you total brain volume? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Cluster-Defining Threshold of p=0.025
by Jahn, Andrew 13 Sep '17

13 Sep '17

Hello, Is it possible to use cluster-defining thresholds such as p = 0.025 with mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.) My design doesn't allow the use of permutations for simulating cluster sizes, so I have to use the mczsim option; however, from what I can tell it doesn't allow using any non-cached options. Thanks, -Andy

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Results display tool
by Chris Adamson 12 Sep '17

12 Sep '17

Freesurfer users, I just wanted to advertise a set of display tools that I wrote for easy display, in MATLAB, of regional stats like p-values/effect sizes/arbitrary scalars with customisable masks for aparc, dkt, aparc.a2009s. https://chrisadamsonmcri.github.io/freesurfer_statsurf_display I hope people find it useful. Chris. ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Resampling Freesurfer - Human connectome workbench
by Xavier Guell Paradis 12 Sep '17

12 Sep '17

Dear freesurfer experts, I have an overlay freesurfer file (format is .w) which corresponds to a thresholded seed-based functional connectivity surface map (group result). The .w file was generated from an SPM analysis, following the instructions described here (http://spmsurfrend.sourceforge.net/Documentation/SPM_SurfRend_Tutorial_V0.2…) I have one .w file for each cerebral hemisphere. I would like to visualize these .w maps using workbench_view, and I have tried to follow the instructions the HCP team published here (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF…) As a first step I would need to convert the .w files into .func.gii files using mris_convert. Then I would use wb_command -metric-resample, as indicated in the instructions. This does not seem to work with my .w file: 1) mris_convert myfile.w myfile.func.gii This generates myfile.func.gii, but when I use wb_command -metric-resample I get the following error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 2) As an alternative approach, I opened myfile.w using Tksurfer and saved the overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then I do the following: mris_convert myfile.mgh myfile.func.gii This generates the myfile.func.gii file, but when I use wb_command -metric-resample with this file I get a different error: ERROR: All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 163842 rows. Array 2 contains 327680 rows. I have asked the HCP team, but they were not familiar with the .w files and suggested that I ask you instead. Thank you very much for your help, Xavier.

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glmfit: matrix error
by Wang, Xin 12 Sep '17

12 Sep '17

Hello, FreeSurfer group, When I ran glmfit I got the following error massage. I standardize ages but the problem remains. Any other suggestions? Alternatively, is there any way to by-pass this design checking step? Thank you very much. Xin -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh_group_currPTSD_AgeGenderSiteFACT_adult.fwhm10.fsaverage.mgh --fsgd group_currPTSD_AgeGenderSiteFACT_adult.fsgd dods --glmdir RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh --surf fsaverage/ lh --C group_currPTSD_AgeGenderSiteFACT_adult.mtx 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.330000 (col 38), Max=18.703472 (col 62) The scale is much different between columns 38 and 62, you may want to normalize by subtracting the mean and dividing by the standard deviation. ERROR: cannot find RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh/fwhm.dat

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Q re: cluster commands
by Omar Al-Louzi 12 Sep '17

12 Sep '17

Hi freesurfer team, I'm hoping to ask two questions: 1. We are using the mri_volcluster command to find manually delineated clusters in a volume. In the output file, the command outputs Talairach coordinates for each cluster (TalX, TalY, TalZ). What do these coordinates exactly correspond to in terms of voxels? (i.e. do they reference the central voxel of each cluster, the first voxel detected, or something else) 2. Are there any freesurfer command(s) that can measure the minimum distance between two clusters in the same volume, or measure the minimum distance between one cluster in one volume( let's call it reference cluster) and multiple clusters in a second volume, granted that both volumes are in the same space and registered to each other (in other words, generate minimum distance measurements between all the clusters in the second volume and the reference cluster in the first volume). My apologies if these questions are basic or have been asked before, but I haven't come across an answer on freesurfer forums or help files. Best, Omar _____ Omar Al-Louzi, MD PGY-3 Neurology resident Massachusetts General Hospital Brigham and Women's hospital

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(no subject)
by José Gómez-Feria Ferreiro 12 Sep '17

12 Sep '17

Dear Freesurfer, Is it possible to keep on the supporting list but without receiving emails from other people? My email account is getting stuck with so many emails. Thanks, Jose

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group analysis on thickness/mask
by Xianwei Che 12 Sep '17

12 Sep '17

Dear experts, I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html) I know I could extract the signal of the ROI but also interested in this way. Here are my questions: 1. mri_binarize should be working on the average data or the single data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants). 2. How the --match is used. I --helped the mri_binarize but did not get it. Is it for specifying the ROI by number, say the number of PFC? 3. If I could finish the mask creation and merge to label; do I have to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html) Thank you so much! *-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia

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PetSurfer GTM: gtmstats2table
by Elijah Mak 12 Sep '17

12 Sep '17

Hi Doug, Would it be possible to use the gtmstats2table command to extract GTM values from other parellations? Thanks! Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambridge, Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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Freesurfer September 2017