Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

mri_surf2surf (and mri_preproc) clarification
by Daniel Leopold 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer experts, The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 7th order icosahedron. Does it place the lh.thickness curv into freesurfer space, or is it still in the subject's native space (i.e., pre-transformation to the fsaverage template)? I used a similar process to downsample subjects' thickness to fs5 resolution, which I then concatenated and used as input for PALM. What I'm now wondering is whether results may be due to misalignment between individual subjects because they were not transformed to the fsaverage template and space. Do the inputs below (-srcsurfval) need to be thickness.fsaverage.mgh (already mris_preproc'd in the recon-all pipeline) instead? mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type curv --cortex --trgsubject ico --trgicoorder 5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10 **Note: My apologies if this re-posts, but it doesn't seem like my initial submission went through** With gratitude, Dan

2 1

PETSurfer
by Boris Rauchmann 29 Nov '20

29 Nov '20

External Email - Use Caution Dear all, How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean intensity using PETSufer? Is there a command to use in mri_gtmpvc like --rescale X? I know that I can find the mean in global.gm.dat and I can use that value for scaling the atlas based results in gtm.stats.dat but how can I easily scale the image? Thanks, Boris

2 1

Time required to run permutations
by Basavaraju, Rakshathi 29 Nov '20

29 Nov '20

External Email - Use Caution Dear FS team, Does anyone have any idea how long does the permutation computation to handle multiple comparisons take on a surface based analysis? The command is given below: mri_glmfit-sim --glmdir rh.project.glmdir --perm 1000 3 abs --cwp 0.05 --2spaces --bg 1 Its seems like going on forever, saying Poll2 Job1...... Poll3 Job1..... I guessed it might stop at 1000 but its going on and on. Any help on this would be greatly appreciated. Thanks, Rakshathi Post-doc, Columbia.

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MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs
by Hengameh Marzbani 29 Nov '20

29 Nov '20

External Email - Use Caution Hello Freesurfer developers, For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps: Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir ~/myproject/processed/tmp Step 2: mri_surfcluster --in ~/myproject/processed/fsaverage/surf/lh.thickness --clabel lh.G_pariet_inf-Supramar.label --sum ~/myproject/processed/tmp/sum.lh_G_pariet_inf-supramar --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni Q1: All the ROIs appeared to have identical MNI coordinates. what should I do? Q2: For reporting the list of X Y Z coordinates in MNI space for all the labels in aseg.stats ROIs, What should I change? Thank you in advance, Best regards, Hengameh

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-openmp vs -threads, -parallel options in recon-all
by d m 29 Nov '20

29 Nov '20

External Email - Use Caution Hello, What is the difference between the -openmp and -threads option for recon-all? Do they reflect the same thing: Number of threads used concurrently? If we want to use 10 threads for the recon-all command, which option should we use? -openmp or -threads? How does this relate to the -parallel option? Does every part of recon-all use multi-threading or only does only a subset of parts within recon-all use multi-threading? Thanks in advance. d.m.

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Group Analysis
by Sara Lyn 29 Nov '20

29 Nov '20

External Email - Use Caution Hi Freesurfer experts, I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help. Best, Sara

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Re: [Freesurfer] extracting beta coefficients and p-values
by Batool Rizvi 29 Nov '20

29 Nov '20

External Email - Use Caution Hi, I had a couple additional questions related to this topic. 1. The beta-coefficients I derived from using the mri_segstats command with the input beta.mgh, are these values unstandardized? 2. Just wondering, is there a possible way to also derive 95% confidence intervals for my covariates that were included in the mri_glmfit analyses? Thanks so much for your help! Batool

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Mean thickness estimation
by Stephanie K 29 Nov '20

29 Nov '20

External Email - Use Caution Hi, I want to estimate the mean cortical thickness. For this I have summed the thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, I also have the average mean thickness of left and right hemispheres (direct output variables of Freesurfer). As there is no visual inspection of the imaging in the particular cohort, I remove measures that are 3 standard deviations above or below the mean. Hence, I may expect more outliers to be removed when I take the average across the regions. I am using these brain measures as outcomes in association analyses with the genetic score as the exposure. For the mean thickness (averaged across the left and right hemisphere thickness variables of freesurfer after removing outliers), the regression coefficients have a smaller standard deviation than with thickness averaged across the 34 regions. I’m not sure which one to use - which one is more accurate? When I look at the mean thickness (which I derived using 34 regions) and it’s standard deviation, it is similar to that of the average mean thickness across the two hemispheres as well as the standard deviation of that. Can you suggest what is most accurate please and what the difference is between the mean thickness across the two hemispheres obtained from freesurfer and those calculated across the regions? Why does one result in more precision than in the other? Thank you!

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PET image format
by Marina Fernández 29 Nov '20

29 Nov '20

External Email - Use Caution Dear experts! I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I would like to convert the images to nifti format to start processing the data. What function can I use to convert the images? How can I check that the left-right orientation doesn't flip? Thank you in advance! Marina.

2 1

eddy_correct with DTI {Disarmed}
by Wei Shao 29 Nov '20

29 Nov '20

External Email - Use Caution Hi, Freesurfer team, My name is Weishao, Here is a problem that bothers me a lot I try to run DTI. I have loaded the FSL module and use the most recent version of Freesurfer. it's appreciated if someone can help. Thanks. Here is the script. dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ Here is feedback -rw-r----- 1 weishao weishao 49041968 Sep 9 11:41 /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz INFO: SUBJECTS_DIR is /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects dt_recon logfile Tue Oct 27 16:19:28 EDT 2020 VERSION dt_recon 7.1.0 setenv SUBJECTS_DIR /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ gra95 weishao /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Oct 27 16:19:28 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz reading from /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999608, 0.017447, -0.021891) j_ras = (0.0104682, 0.958258, 0.285714) k_ras = (-0.0259621, -0.285373, 0.958065) writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... #@#------------------------------- Eddy/Motion Correct Tue Oct 27 16:19:44 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/ectmp eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct: line 95: /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob : *No such file or directory* Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value *ERROR: when running eddy_correct* Best, Wei

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