Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

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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Cerebellum segmentation pipeline
by AJ 17 Nov '22

17 Nov '22

External Email - Use Caution Hi, Is there a specific pipeline for segmenting the cerebellum, cortical gray and deep nuclei? Like the one for hippocampus and thalamus? Best

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Global diffusion metrics
by Max Korbmacher 17 Nov '22

17 Nov '22

External Email - Use Caution Dear all, I have been trying a few things to compute global (not regional) average diffusion metrics. Is there a function available? Best, Max Max Korbmacher PhD student Western Norway University of Applied Sciences Bergen, Norway

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Forum Question
by Rubenstein, Samantha Leigh 17 Nov '22

17 Nov '22

External Email - Use Caution Hi, Our lab has previously used Freesurfer version 6, but we are interested in upgrading to 7.3.2. What are pros and cons for the different versions? I did not set the computer up or download the original version 6. We were previously using the CentOS version on Ubuntu 16 (unsure why CentOS vs Ubuntu), but upgraded to Ubuntu 20 for the 7.3.2 installation, using the Ubuntu version instead (not CentOS). From what I understand it’s not recommended to mix data between the versions so I’m just interested in anyone’s opinion on differences/advantages between 6.0 and 7.3.2 since I would have to redo ~60 subjects. Unsure if this is useful, but right now we do pial edits, CP edits, and our output is volumetric/segmentation/hippocampal subfields data (output in the aseg/aparc excel spreadsheet). Thanks, Samantha

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Glasser parcellation labelling
by Paulk, Angelique C.,PhD 17 Nov '22

17 Nov '22

Hello, I have yet another, likely obvious, question and I apologize if this is answered elsewhere. I ran the below series of functions to apply the HCP-MM1 (Glasser) atlas to the FreeSurfer output. I was able to produce an annotation file that had the labels in the right locations and mapping. Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain labels (which are inaccurate). Is there an additional step I need to convert the labels such as using a modified HCP-MMP1 LUT look up table (such as linked here<https://github.com/MRtrix3/mrtrix3/issues/1279>)? using the HCP-MMP1 annotation files: https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/349… And the use of mri_surf2volseg in the following sequence: https://github.com/ftadel/IntrAnat/issues/7#issuecomment-768996270 Thank you for any and all help, Angelique

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Freesurfer November 2022