Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution  We have no current reports about security issues with the FS release.   An address using the string fsbuild will email you directly so you can respond to only that address if you would like to report an issue.  Please check you spam folder.  PLEASE

[Freesurfer] Help: when will the next version of FreeSurfer become available?

External Email - Use Caution Hi, We have been pressured by our IT Security team to address some of the vulnerabilities (e.g., OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share with us when would the next version of FreeSurfer become available? Thanks,

Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

Hello Carina, There is a bug in the current implementation of the ConcatenateSubregionsResults.sh script. A patch is now available here and is in the dev branch of FS. The script was incorrectly sear

[Freesurfer] Does motion correction command mc-sess do censoring of high motion timepoints?

External Email - Use Caution Hi there, I'm using this version of Freesurfer: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 I'm using mc-sess to run motion correction on some functional task and resting state data. I would like to perform censoring on high motion timepo

[Freesurfer] PETSurfer: pvc'ed and scaled output nifti image

External Email - Use Caution Dear team, I am using mri_gtmpvc to obtain PVC'ed regional data which we will use as an input TAC to perform kinetic analysis. In addition, we are also doing static SUVR analysis (sum of frames from 60-90 mins) in which I am scaling input PET data w

[Freesurfer] cluster area from mri_surfcluster and read_curv are inconstant

External Email - Use Caution Dear Freesurfer experts, I got the area of a cluster by two methods, and found the results were inconstant. Method 1: During group level analysis, the individual surface was normalized to fsaverage. I exported the cluster area and label file by co

[Freesurfer] The Affective Neuroscience Project of the Midlife in the U.S. (MIDUS) study is recruiting a multimodal imaging scientist

External Email - Use Caution The Midlife in the U.S. (MIDUS; https://midus.wisc.edu/) Affective Neuroscience Project Team is excited to bring on an energetic and skilled Ph.D.-level scientist to join our dynamic team and ask questions within the national, longitudinal data to in

Re: [Freesurfer] Unequal size groups

We do not offer anything special for this. The difference in group size is not an issue in and of itself. The only problem that would arise is if the groups have different variances. On 5/18/2024 12:07 PM, std...@virgilio.it wrote: External Email - Use Caution Hi I’m using fs-fast t

Re: [Freesurfer] Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus

Mostly these: https://pubmed.ncbi.nlm.nih.gov/15501102/ https://doi.org/10.1016/S0896-6273(02)00569-X For a separate fornix seg, see https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic On 5/22/2024 1:34 PM, Ahsan Ali wrote: External Email - Use Caution Hello everyone, Could anyone

Re: [Freesurfer] Intensity affected after using -c flag in mri_convert

The -c means to "conform". In addition to changeing it to 1mm iso, it will change the data type to uchar. Uchar only has 8 bits, so it does an intensity rescaling to make sure all the intensities fit in this range On 5/22/2024 12:55 PM, ERNEST KISSI wrote: External Email - Use Caution

Re: [Freesurfer] Transformed geometry does not match

This usually means that there is a large difference in the geometry between time points eg, the voxel size has changed substantially. If you want  more help, make sure to include the recon-all.log file On 6/7/2024 7:45 AM, Yasmine Salman wrote: External Email - Use Caution Dear FreeS

Re: [Freesurfer] Issue with cortical data extraction for mkanalysis-sess

Sorry, I can't understand from you description what is going wrong. How do you know that something is off? Can you list your command lines? On 6/6/2024 8:22 PM, O'Dor, Sarah wrote: We are trying to run resting state connectivity analyses using amygdala ROI. The left hemisphere ran fine, but f

Re: [Freesurfer] negative values converting mgz files to nifty

That should have worked, but I would use the method on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 6/6/2024 4:07 PM, Nina Rouhani wrote: External Email - Use Caution hello! after freesurfer segmentation (through fmriprep v23), i converted the aparc+as

Re: [Freesurfer] Bug in mri_convert reslice-like with 4D images

Can you send us the terminal output? Can you point us to the data on the network so that we can recreate? @YH - can you take a look? On 6/6/2024 3:56 PM, Iglesias Gonzalez, Juan E. wrote: Dear FS experts, We get a segfault when I try to resample images with the command: mri_convert input.mgz

[Freesurfer] INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)

External Email - Use Caution [apologies for cross-posting] *INTERNATIONAL CONFERENCE ON ARTIFICIAL INTELLIGENCE IN HEALTHCARE (AIiH)* 4 - 6 September 2024, Swansea, UK https://aiih.cc (*2nd CALL FOR ABSTRACT*) Submission deadline: Monday 1 July (FIRM) *1. INTRODUCTION * https://