Freesurfer May 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
125 discussions

Problem with talairach check in Freesurfer 7
by Gabor Perlaki 27 May '21

27 May '21

External Email - Use Caution Dear all, I tried to check the talairach transformation under Freesurfer 7 linux version (freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551). However, neither command works as expected. the command "freeview -v bert/mri/T1.mgz -v bert/mri/brainmask.mgz:reg=bert/mri/transforms/talairach.xfm" gives the following message in the terminal: "Not reading in xfm fileinfo". Both T1 and brainmask is loaded, but the transformation seems to be not applied. the command "tkregisterfv --s bert --fstal --surf orig" works only without the flag --surf. the command "tkregister2 --s bert --fstal" gives the following messages: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" The green border is not shown, only the target and movable images are visible. Any idea how to fix this? Best, Gabor

2 3

mris_anatomical_stats() for ODI maps inflated to surface
by Jensen, Alexandria 27 May '21

27 May '21

External Email - Use Caution Hello fellow Freesurfer users, I am attempting to reproduce the analysis conducted by Parker et al. in their 2018 paper, “Cortical microstructure in young onset Alzheimer's disease using neurite orientation dispersion and density imaging” (https://secure-web.cisco.com/1UgnQVFBMbbUsDXUzai5AvAOzqeQ34tRV2D60a4CwFPoV9…) Cortical reconstruction of the T1 structural image was done in Freesurfer and NODDI processing using the NODDI toolbox in Matlab. The final steps I am attempting to complete include (1) projecting the ODI/NDI maps to an inflated surface to create surface maps (2. Materials and Methods, 2.5 Diffusion-weighted MRI processing); and (2) calculating mean ODI/NDI values across both hemispheres for a selected number of ROIs from the Desikan parcellation (2. Materials and Methods, 2.6 Cortical ROIs). The Parker et al. paper has provided the Freesurfer functions used in each of these final steps, but I am getting stuck on step (2) and am now worried that I have made an error in step (1). Below is the code I have written so far to project an ODI map onto an inflated surface: bbregister \ --s freesurfer \ --mov odi.nii \ --init-fsl \ --reg register.dat \ --dti tkregister2 \ --s freesurfer \ --mov odi.nii \ --reg register.dat \ --surf mri_vol2surf \ --src odi.nii \ --out odi_in_cortex.nativespace.mgh \ --srcreg register.dat \ --hemi lh \ --projfrac 0.5 When I load lh.inflated, the lh.aparc.DKTatlas.annot annotation file, and the odi_in_cortex.nativespace.mgh overlay in Freeview, things seem to be correct. The issue I have is when I try to use mris_anatomical_stats(). I have tried different combinations of label and annotation files but am either getting errors or no errors but also no output. Any guidance would be much appreciated! I am new to Freesurfer and have been learning it as part of my graduate research assistantship. I am using Freesurfer version 7.1.1 on a macOS Catalina, version 10.15.7 operating system for reference. Cheers, Alexandria Jensen

3 9

mri_glm fit: gd2mtx method dods--C unrecoginzied
by Francisca Ferreira 27 May '21

27 May '21

External Email - Use Caution Dear Experts, I am new to FS. I'm trying to run mri_glm fit I've created FSGD with 2 classes -responders vs non-responders to a given intervention- and 3 variables to be regressed out-according age, gender, laterality. I've made my FSGD file is made in accordance with documented FS directions. I've created the contrast vector in accordance to Nregressors and it works out to be 1 -1 0 0 0 0 0 0 I add I'm using DODS to do this task. the constructed command I used is this mri_glmfit \--y lh_test.smoothed10FWHM.mgh \--fsgd newCH.fsgd dods\--C groupdiff.mtx \--surf fsaverage lh\--cortex \--glmdir lh.test.glmdir 1) The first problem encountered is INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done I have tried to demean my data adding the flag --demean, which I found in more than one forum, but i think this is an incorrect flag as it didnt work anyway. 2) I have constructed my contrast vector also in accordance with FS directions, in a text editor adding the extension .mtx I'm getting this error ERROR: gd2mtx method dods--C unrecoginzied. Legal values are dods, doss, and none. Help would be much appreciated. KR F. Ferreira

2 1

Question about mri_info
by Wei Shao 27 May '21

27 May '21

External Email - Use Caution Hello, Freesurfer exports My name is Wei Shao, I'm a beginner at Freesuefer and curious about the mri_info. I have searched the information through freesurfer online documents but there is not much I can find. I'm wondering are there any supplement documents that can explain each term of this information such as fov, dof, and frames and so on? [image: MRI_info.PNG] Best, Wei

2 1

dim of fmcpr.up.sm5.self.lh.nii.gz
by Mingyang Xia 27 May '21

27 May '21

External Email - Use Caution Dear freesurfer expert: I am sorry to disturb you. I have a question that when I use the command 'preproc-sess -s sess01 -fsd rest -stc up -surface self lhrh -mni305 -fwhm 0 -per-run -force', the dimension of output file of fmcpr.up.sm5.self.lh.nii.gz is 1*1*1*120. However, when I apply it to the fsaverage. It has correct dimensions. Could you tell me why it happens? Thank you Mingyang Xia

2 2

mask error in glm_fit
by Haley Park 27 May '21

27 May '21

External Email - Use Caution Hello, I am trying to run a correlational analysis with glm_fit on a masked area with the code: foreach hemi (lh) foreach smoothness (10) foreach meas (volume thickness) mri_glmfit \ --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \ --fsgd FSGD/{$study}.fsgd \ --C Contrasts/Scores_Slope.mtx \ --surf fsaverage {$hemi} \ --mask lhYeo2011_7NetworksConfidence_N1000.mgz \ --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir end end end I get the error message: ERROR: dimension mismatch 1 between y and mask I've also tried to run it with the .nii file found at https://secure-web.cisco.com/1sTopz8rXlJoh4VSQL7P0DYm1ff7H5Crs0Qg3iAG1M6HD6… Any help would be appreciated! Haley

2 3

Hippocampus ROI
by Hua, Jessica 27 May '21

27 May '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI? Best, Jessica

3 2

fspalm output
by Marina Fernández 27 May '21

27 May '21

External Email - Use Caution Dear experts, I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 10000 --cwp .05 --onetail Checking the palmcofig.txt file that is generated as output, I realized that even if the "–logp" flag wasn't specified in the function, this flag is always applied with fspalm, and therefore the p-values of the *dpv_tstat_uncp.mgz file are saved as -log10(p). Consequently, if I want to threshold with p, I must first convert these values to p-values using 10^(- p) and then use p<0.05. In contrast, when I load the files *dpv _tstat_fwep.mgz and *clustere_tstat_fwep.mgz, the results don't appear to be -log10(p), and then these files wouldn't need to be transformed with 10^(- p) to use a threshold of p<0.05. What is the use of this flag in fspalm and why does it only affect the uncorrected p values? Thank you in advance. Marina

2 1

Combined right and left analysis
by AJ 27 May '21

27 May '21

External Email - Use Caution Hi, I am trying to do long_stats_slopes on the aseg.stats file. Is there any way I could examine percent change as total thalamic or total corpus callosum instead of separately as right and left structures or various parts of CC? Thanks, AJ

2 1

How to Specify External Regressor Files for FSFAST
by Eli Bulger 27 May '21

27 May '21

External Email - Use Caution Hello, I am working with task-based functional data pre-processed with fMRIPrep that I am trying to run through the FSFAST pipeline. I would like to use some of the nuisance regressors / confounds outputted by fMRIPrep as external regressors. The documentation for "mkanalysis-sess" (shown below) lists this as an option, but I am not sure how to go about creating the .bfloat file(s). Is there any documentation / example / tool that can provide some guidance on how to do this? Any advice is much appreciated! "mk-analysis-sess" documentation referred to: -extreg [extregstem] external regressor Use external regressors when doing estimation. The external regressors should be stored in the bfloat "volume" with stem extregstem. There should actually be only one file there (extregstem_000.bfloat). It should have one row, and the number of columns should be equal to the number of external regressors. The number of frames must be equal to the number time points. There should be an external regressor file in each run directory. By default, all the regressors will be used, but this can be changed with -nextreg. See also -mcextreg.

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Freesurfer May 2021