Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

recon-all error: mpr2mni305 failed
by Hickling, Alice 26 Jan '22

26 Jan '22

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to run recon-all on a high resolution (0.65mm iso) MP2RAGE however I am receiving the following error. talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log These are the options that I am using. recon-all -all -s Freesurfer -i denoised_MP2RAGE.nii -T2 mean_denoised_MP2RAGE_T2W.nii -T2pial -multistrip -hires Please let me know if you can help. * FreeSurfer version: 7.2.0 (freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b) * Platform: CentOS Linux release 7.9.2009 (Core), Rocks release 7.0 (Manzanita) * Uname -a: Linux compute-0-14.local 3.10.0-957.27.2.el7.x86_64 #1 SMP Mon Jul 29 17:46:05 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux * Recon-all.log: see attached * Talairach_avi.log: see attached Best wishes, Alice

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questions of tracula group analysis, freeview and pair analysis
by Zeng, Qi 26 Jan '22

26 Jan '22

External Email - Use Caution Hi, I got a couple of questions regarding group analysis of tracula with a longitudinal pipeline, freeview output heatmap key, and pair analysis's fsgd & correction analysis. 1). I followed FsTutorial/TraculaStatistics - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1AjTV10_qUpg01X4rpJJaZQufhlsihHV7tqqL_DCJ36KH6…> to conduct a GLM group analysis for tracula results. But for the first step, should I conduct a long_mris_slopes to get the rate of change just as surface-based analysis for a longitudinal pipeline? 2). I tried freeview my sig.mgh results both for positive and negative for my surface group analysis, is there a heatmap key I can put into the image or available to export? 3). I created the FSDG file for pair analysis as follows to indicate both the same and difference within the pair subject to hope to regress out the effect of age at baseline and time_diff between subjects, is that the correct way of formatting? and also how to create the subject name here if my previous FSDG is sub01_ses-1.long.sub01_base and sub01_ses-2.long.sub01_base for the subject name. > GroupDescriptorFile 1 > Class Main > Variables Age_bl Time_diff > Input sub01pair Main 30 7.1 > Input sub02pair Main 40 2.2 > Input sub03pair Main 50 3.7 > Input sub04pair Main 60 0.7 4). Even not indicated in the pair analysis page, a cluster correction "mri_glmfit-sim" is also necessary for the last step, right? Thank you so much! Best, Qi

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Problems with recon for manually fixed Talairach
by Goeckner, Bryna 26 Jan '22

26 Jan '22

External Email - Use Caution Hi, I am trying to decide how to proceed after manually updating a talairach since various ways I’ve tried the recon process give me different results. Our group used Freesurfer 7.2 for processing data with the T2 and 3T flags as follows: recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all After visual inspection, I made adjustments to the talairach using tkregister2 and then used the code below to rerun the recon: recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all When this was done, the talairach.xfm file was restored to the talairach from the original recon, while the talairach.xfm~ was still the fixed version. At no point in this entire process did the talairach (fixed or original) generate an error. To avoid the overwriting of the talairach.xfm file, I tried using (separately) the -notalairach and -notal-check flags. For both, the talairach.xfm file stayed as the fixed talairach, but I got different aseg and aparc results. I’d like to know more about how these to flags differ and if you have a recommendation on which process is best. The plan is to eventually use this data in TRACULA. Thanks for your help, Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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manual segmentation
by 刘卫 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides multiple comparison correction when surface based group analysis. Can I use the 6.0 version of free to analyze the results of the 7.2 version preprocessing?

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movement correction using 24 movement parameters or stick regressors to remove volumes
by stdp82＠virgilio.it 26 Jan '22

26 Jan '22

External Email - Use Caution Hi list, in functional connectivity assessment by FS-FAST, is possible to do movement correction using 24 movement parameters including derivatives or stick regressors to remove the volumes for which the FD value (framewise displacement) is superior to 0.5 mm (see Tapas procedures for physiological noise correction in Frassle et al., 2021 https://secure-web.cisco.com/19GvmE_VjebaugWB4X8sbjJje0pY5b_NU8J63aVJIrlpYM… Thanks Stefano

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Visualization of data
by Paul, Rahul 26 Jan '22

26 Jan '22

Hi FreeSurfer experts, I have a dataset of 60 patients. Is there a way to visualize the average cortical thickness/area for my dataset? Thank you in advance. Rahul

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dcmunpack multiple runs together
by Shi, Yuelin 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I am using dcmunpack to unpack a data session that is composed of many series/runs. It seems that I can only feed in unpacking rules for one of the runs at a time by the "-run run subdir format stemname" command. Also for each data session like this, it seems I'll need to manually type in the run number and its rule everytime. We actually just moved from a Siemens scanner to a GE scanner. With Siemens, the unpacksdcmdir function accept seqcfg file that only needs to be written once and will be able to apply to any sessions. I wonder with dcmunpack 1) if there is at least a command that allows unpacking all the runs together? 2) Moreover, is there a way to specify the whole set of rules as a seqcfg file that will be easily applied to all future sessions? Thank you very much! Best, Yuelin

2 1

statistical analysis of the volume of the hypothalamus_seg
by Xiaotong Zhang 26 Jan '22

26 Jan '22

External Email - Use Caution In the statistical analysis of the volume of the hypothalamus_seg, since the skull size of each person is different, it is necessary to exclude the influence of head size, that is, to regress the total intracranial volume, such as e TIV or sb TIV. I have a question: because the hypothalamus is the smaller subcutaneous nucleus, which indicator is more suitable for the analysis of the hypothalamus subregion? In addition, if the total volume of the hypothalamus as regression, is feasible? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev 2) Platform: CentOS 7.9 Sincerely, Zhang

2 1

Error in mri_glmfit
by Laura Willers de Souza 26 Jan '22

26 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ diagnosis (CU/CI) + plasma cortisol + diagnosis*plasma cortisol I am now performing a glm dods analysis to see if the diagnosis*plasma cortisol interaction is significant. I'm using this contrast: 0 0 1 -1 The fsgd file is attached. Cortisol values are converted to log. But when I run the mri_glmfit command it gives the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------- ERROR: READ THIS ----------------- 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 --y lh.CU_CI_plasma.thickness.10.mgh --fsgd CU_CI_plasma.fsgd dods --C group-x-cortisol_pl.mtx --surf fsaverage lh --cortex --glmdir lh.CU_CI_plasma.glmdir --eres-save 2. The terminal output of this program (ie, everything it prints to the screen) 3. The FSGD file (CU_CI_plasma.fsgd) - ATTACHED 4. The design matrix lh.CU_CI_plasma.glmdir/Xg.dat - ATTACHED Attempting to diagnose further SumSq: Min=0.000000 (col 3), Max=22.135944 (col 2) The scale is much different between columns 3 and 2, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 3, all values are 0 Column 4, all values are 0 Columns 3 and 4 are the same Could this error be because the n of the CU group is 54 and of the CI group is 490? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Re: [Freesurfer] Spatial distance between regions
by Julie Ottoy 26 Jan '22

26 Jan '22

External Email - Use Caution Hi Doug, Just checking in with the question below. Does Freesurfer have such an option? Thanks, Julie On Tue, 14 Dec 2021 at 18:38, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > Hello FreeSurfer team, > > I was wondering if there is a way to calculate a distance matrix between > atlas-based regions (e.g. between their centers of mass) in volumetric > space (MNI152) space? > > Thank you for the information! > Best regards > Julie >

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