Re: [Freesurfer] Updated Mac to Monterey, issues with Freesurfer

External Email - Use Caution Hello Lisa, Are you running the 7.2.0 release, e.g. as installed by the package installer,  https://secure-web.cisco.com/1WrA-NZx66e293R6KJNdyTGSNLLRCP3adzgCpi5RDIvdwv1re3mzN6jC303CfD51yVnbBD6LzPPxvrJi9loVDSmabuW99Dz5QguCq8EHdTYP-eMAk1wEu3cYsO1I80YUw5f

[Freesurfer] Updated Mac to Monterey, issues with Freesurfer

External Email - Use Caution Hi there, Not exactly sure if you'll be able to help but I am a bit stumped. I recently updated my MAC os to the new monterey update. I now get these error messages when trying to use Freesurfer, or even freeview: viewfreesurfer PATH/MRI/Freesurfer

[Freesurfer] Using -bigventricles for infant segmentation

External Email - Use Caution Dear FreeSurfer Developers, I am trying to use the InfantFS segmentation pipeline for segmenting images with Ventriculomegaly. I have looked up the archive and found out the -bigventricles. I have tried the following commands but it did not work. Can

[Freesurfer] Question glm analysis

External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki https://secure-web.cisco.com/1OE5gTnSPStX6C1rqwHBKIDpqIcnp_2ymvTKb8n7oDB8IxXRDqg

Re: [Freesurfer] Maps completely painted in freeview

External Email - Use Caution Sorry, I wrote it wrong! It was intercept contrast. Thanks so much for the explanation! Best, Laura. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

Re: [Freesurfer] mri_normalize error MP2RAGE

External Email - Use Caution > Can you send the recon-all.log file? Here you go, two examples. Thank you! Best Cornelius subject2_C.DWNR99A_MP2_recon-all.log Description: subject2_C.DWNR99A_MP2_recon-all.log subject1_C.AOVO99A_MP2_recon-all.log Description: subject1_C.AOVO9

Re: [Freesurfer] [External] Re: white matter measurements for labels/annotations

External Email - Use Caution Yes but instead of DKT regions, it would have brodmann area for example Get Outlook for iOS

Re: [Freesurfer] mri_concat error

External Email - Use Caution Hi Douglas! Thanks for the reply. Apparently, this error was due to a lack of license file in freesurfer folder. I downloaded a license, put it in the right place. When I try to process a subject, it works well, but when I try to analyze my data with q

Re: [Freesurfer] mri_concat error

Hard to say. This is one reason we are not supporting qdec anymore. Was there anything printed to the terminal? On 2/3/2022 8:27 AM, Mateus Aranha wrote: External Email - Use Caution Dear all, I'm constantly getting the following error and I have no idea where the problem is... im

Re: [Freesurfer] Recon-all reconstructed image coordinates

You can try registering them together like mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta Then mri_vol2vol --mov betmaskvol.nii.gz --targ orig.mgz --reg.lta --o betmask-in-fs.mgz --interp nearest The betmaskvol should be the intensity image (like orig.mgz) and not a binary m

Re: [Freesurfer] Maps completely painted in freeview

What do you mean by the interaction contrast? Or do you mean the intercept? It is not surprising that the intercept is completely yellow as that is just testing whether the mean thickness is different than 0, which it always will be. On 2/2/2022 2:47 PM, Laura Willers de Souza wrote:    

Re: [Freesurfer] Unsure About Longitudinal & GLM Tutorials

Yes, once you take the difference between two time points, then the steps are the same as cross-sectional analysis. But if you took the difference, you should have only one entry in the FSGD file for each subject (looks like you have 2). Also, it is probably a good idea to normalize the ages (o

Re: [Freesurfer] lGI value aberrantly high, again

The lGI is run from recon-all so it is still the lGI that is the problem On 2/1/2022 3:41 AM, Bernardoni, Fabio wrote: > External Email - Use Caution > > dear douglas > > thanks for your answer. I understand the developer is not maintaining the > program computing lGI. however, my questi

Re: [Freesurfer] white matter measurements for labels/annotations

Do you mean something like wmparc.mgz and wmparc.stats? On 2/1/2022 1:10 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi, is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the br

Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

Can you send all the terminal output?  Also, you only have 4 time points in time.dat. Is this accurate? It's going to be hard to do KM with 4 time points. On 1/31/2022 5:00 PM, Jennifer Bramen wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze

Re: [Freesurfer] impact of defacing on eICV calculations

It will impact it some as it changes the talairach reg. See https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 1/31/2022 2:59 PM, Ritobrato Datta wrote: External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through fr

Re: [Freesurfer] Display PCC in cluster

You can mask it out. First, create a mask of your cluster with something like mri_binarize --i ocn.mgh --match clusterno --o mask.clusterno.mgh Then mri_mask pcc.mgh mask.clusterno.mgh pcc.masked.mgh On 1/31/2022 9:26 AM, Andrei Bieger wrote: External Email - Use Caution Hi, Douglas,

Re: [Freesurfer] Co-Registration after recon-all

bbregister will compute the matrix, you don't have to give it a matrix. You can use mri_vol2vol to apply the matrix. There is also an option to apply the matrix in bbregister On 1/31/2022 7:24 AM, m-maiw...@web.de wrote: External Email - Use Caution Hi, I ran recon-all on a MPRAGE-fi

Re: [Freesurfer] mri_normalize error MP2RAGE

Can you send the recon-all.log file? On 1/31/2022 5:02 AM, Dr. Cornelius Kronlage wrote: > External Email - Use Caution > > Dear Falk, > > thanks for the hint! My understanding was that the "robust" MP2 actually > reintroduces some of the field inhomogeneity artefacts that MP2RAGE is >