[Freesurfer] HBT/FS60/CA segmentation

External Email - Use Caution Dear Freesurfer Developpers, When I look at the FreeSurfer documentation on hippocampal segmentation, I see that it is possible to obtain different segmentations in addition to the 'traditionnal ' freesurfer 7 one: - HBT: the hippocampus is subdivide

[Freesurfer] TR: Issues at the "tailarach_avi" transformation step of recon-all

External Email - Use Caution De : Hensenne, Eva (Stud. FHML) Envoyé : mercredi 18 octobre 2023 14:41 À : freesurfer@nmr.mgh.harvard.edu Objet : Issues at the "tailarach_avi" transformation step of recon-all Dear Freesurfer Developers, I am curre

Re: [Freesurfer] TR: Issues at the "tailarach_avi" transformation step of recon-all

Hi Eva, The error is "gauss_4dfp: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory". Make sure your system has libquadmath installed, and it is in your LD_LIBRARY_PATH. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] HBT/FS60/CA segmentation

Hi Jasmine, This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities). At that point, you’re probably better off counting voxels and multiplying by their volume. Doug: is there a way to do this with FreeSurfer programs, as oppose

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

External Email - Use Caution I made the change you suggested but it didn’t appear to have any effect. I still get the same if: Syntax error with trac-all. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, October 11, 2023 10:12 AM To: Free

Re: [Freesurfer] HBT/FS60/CA segmentation

You can use mri_segstats, eg, mri_segstats --seg seg.mgz --sum summary.txt If the seg.mgz has an embedded color table that lists all the segmentatons, then the names will appear in the summary. If you have such a color table you can pass it with --ctab On 10/18/2023 10:34 AM, Iglesias Gonzalez

Re: [Freesurfer] lta_convert issue with ants Registration Matrix

External Email - Use Caution Hi Yujing, 90 I mean that i had use "lta_convert" in two setup, 1) Images in RAS Orientation (Worked Well) 2) Images in "LAS/PSR" Orientation (Issues Happened here) and Yes By definition nii, is defined in RAS+ so if we take a look at T_Vox2anatomica

[Freesurfer] .lta vs .dat questions

External Email - Use Caution Hi all, Can someone please explain the difference between .lta and .dat and why the registration looks different using the two file types? If bbregister outputs were already checked and edited (if needed) using the .dat file, is there a way to convert

Re: [Freesurfer] .lta vs .dat questions

Hi Corinna, Here is an explanation of register.dat - https://surfer.nmr.mgh.harvard.edu/fswiki/RegisterDat You can use lta_convert to convert it to .lta - https://ftp.nmr.mgh.harvard.edu/pub/docs/html/lta_convert.help.xml.html Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu O

Re: [Freesurfer] .lta vs .dat questions

External Email - Use Caution Thanks, Yujing. Do you know why the output of mri_vol2vol would be different if using the .lta vs the .dat file? And, if the .dat file was verified/modified using tkregister2, would the .lta file also be updated accordingly? Thanks Corinna On Wed, O

Re: [Freesurfer] .lta vs .dat questions

External Email - Use Caution Also - what does the "fscale" in the .lta file refer to? On Wed, Oct 18, 2023 at 1:40 PM Corinna Bauer wrote: > Thanks, Yujing. > > Do you know why the output of mri_vol2vol would be different if using the > .lta vs the .dat file? And, if the .dat fi

[Freesurfer] Removeing the email

External Email - Use Caution Hello, Please remove my email: hanieh@gmail.com from the Freesurfer mailing list. Thank you Hânieh Mohammadi , Ph.D (she/her) Postdoctoral researcher in Biomedical Engineering EPIC Center of the Montreal Hear