Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Effect size, Plotting and Heat maps
by Lyna Mariam El Haffaf 17 Nov '22

17 Nov '22

External Email - Use Caution Dear Freesurfer team, My colleagues and I performed a general linear model with FreeSurfer mri_glmfit for whole brain analysis in intergroup comparison (g2v1) with a Monte-Carlo correction. I'd like to get the effect size of the analysis and I was wondering how could I get the eta squared or R2? I I also saw that the gamma.mgh file was the contrast effect size. Could this be used as an effect size for this type of analysis? I was also wondering if it was possible to plot the results from the GLM and getting a linear regression with the ROI as the y axis and neuropsychiatric symptom severity on the x axis and displaying both groups (Alzheimer vs Mild cognitive impairment) in one plot? If it is possible, how can I do this? I found a plotting script (https://secure-web.cisco.com/1J2MTZ3C6wunLISy_F5rLCagiGKjtD_DqkJHs5AfuTnjbX…) but it was for FDR corrected, not Monte-Carlo. Finally, I was also wondering how could I display a heat map or gradient shading based on neuropsychiatric symptoms severity on the image from the significant regions I got from the GLM with freeview? Thank you in advance! Lyna El Haffaf Graduate student in neuropsychology University of Montreal

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Mapping the labels onto the aparc atlas
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Nov '22

17 Nov '22

External Email - Use Caution Hi Freesurfer devs, We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Recon-all output in MNI305, patient space, or other?
by Andrew M 17 Nov '22

17 Nov '22

External Email - Use Caution Greetings, I am running recon-all as per the iElvis pipeline with: recon-all -s <id> -i $SUBJECTS_DIR/.../T1.nii -all -localGI And followed by ct2mri My questions are: 1. What is the actual output "space" of the resulting T1.nii and postInPre.nii ? Does recon-all do keep everything in patient space, or does it register them to fsaverage space automatically? If so, how would I convert these MRIs and CTs to MNI305 space? Thank you very much. Andrew

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--pv flag in mri_segstats
by Julie Ottoy 17 Nov '22

17 Nov '22

External Email - Use Caution Hello FS team, If I want to calculate the average diffusion-weighted signal from a DWI image within WM regions using mri_segstats, would it be beneficial to use the --pv flag for "partial volume correction" , or would this only have an influence on the Volume calculation? mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${ whitematter_stats} --excludeid 0 or norm=${subject}/mri/norm.mgz mri_segstats --seg ${whitemattermask} --i ${DTI_image} --sum ${ whitematter_stats} --pv ${norm} --excludeid 0 Thanks, Julie

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Missing surface error when using tkregisterfv for checking Talairach Registration
by Peter J. Kohler 17 Nov '22

17 Nov '22

External Email - Use Caution Hello Freesurfer, I am trying to run recon-all on a dataset, and a subset of appear to have problems with the Talairach registration. I believe that I should be able to check the Talairach registration, using this command: tkregisterfv --s $sub_id --fstal Since I have not run autorecon2 yet, I leave out the --surf orig flag as instructed here: https://secure-web.cisco.com/1E3SjeefPDGlY-lL_zyf9V-NZPo_CP1Sa0NhDEJXmEjb3h… However, the command still throws an error because it cannot find "lh.white". How do I check Talairach registration before running autorecon2? Best, Peter J. Kohler

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Re: [Freesurfer] Resmoothing subjects that have already been standardised to fsaverage space
by Douglas N. Greve 17 Nov '22

17 Nov '22

sorry, you did not include the previous emails so I'm not sure what you are referring to. Also, please remember to post to the list. thanks! On 11/16/2022 6:12 PM, Akansha Mahesh Naraindas wrote: > External Email - Use Caution > > Thanks for your response, > > Yes the data is already in fsaverage space, however we had extracted it to perform combat harmonisation and entered it back to be smoothed on a different kernel and I was just wondering if that remapping might affect the data if it is already in fsaverage space?

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N4BiasFieldCorrection before recon-all
by Boa Sorte Silva, Narlon 17 Nov '22

17 Nov '22

External Email - Use Caution Hi there, Would it be problematic if N4BiasFieldCorrection were to be applied to the T1w before processing it in the standard recon-all pipeline? The reason is because we want and use the same T1w in other pipelines which require brain extraction and linear and nonlinear registrations, such as what would be for rsFMRI network analysis. Applying N4BiasFieldCorrection to the raw T1w would be quite useful in that regard. Something that would be similar to what is done for the HCP or UK Biobank pipelines. Thanks for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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Longitudinal FS: does ordering of time points matter in the command
by Julie Ottoy 17 Nov '22

17 Nov '22

External Email - Use Caution Hi FS team, I just wanted to double check if, for the longitudinal pipeline, it matters which time point is being read first? For example, in the command below, should -tp <tp1id> -tp <tp2id> in the order of the scans being acquired? recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all Thank you for the information. Best wishes Julie

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Recon-all in post stroke aphasic patients.
by Steve Petersen 17 Nov '22

17 Nov '22

External Email - Use Caution Dear FreeSurfer experts, I would like to run the recon-all command in MRI images of post-stroke aphasic patients. Should I use a particular flag in the recon-all command to avoid important errors during cortical reconstruction?. We are only interested in the right hemisphere (where there is no brain injury), can I conduct the recon-all only in the right hemisphere?. Any help would be appreciated. Thank you very much in advance. Best regards, Steve.

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Option -contrasurfreg in FreeSurfer 7.3.2
by Francois Tadel, Mr [Affiliate] 17 Nov '22

17 Nov '22

External Email - Use Caution Dear colleagues, The step "contrasurfreg" is still documented for recon-all: https://secure-web.cisco.com/1sNdAy_WhD93Ud31GJEbFbtzD8zuHWnO6zQotNCGvSLXYB… (btw, this page has typos, in some places it's spelled "contasurfreg", with a missing R) But when executing recon-all, it doesn't accept the flag "-contrasurfreg": ========================================= ftadel@dogberry:~$ recon-all -all -contrasurfreg -subjid ICBM152_2022 ERROR: Flag -contrasurfreg unrecognized. -contrasurfreg Linux dogberry.bic.mni.mcgill.ca 5.4.185-i686-64-smp #1 SMP Thu Mar 17 21:53:59 EDT 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Wed Nov 2 11:23:56 EDT 2022 For more details, see the log file To report a problem, see http://secure-web.cisco.com/1BjL8hP7NAz0x_d96RT5d6D0oOfiwH5zFjFw_sEeLHgXo3J… ========================================= Am I missing something here? Thanks Francois

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