[Freesurfer] recon-all with T1 and T2 images

External Email - Use Caution Hello, I have processed the majority of my T1 images using the general recon-all command. After reviewing segmentation, a number of images have the pial surface included in the gray matter. I re-ran an image with the recon-all command combining the

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.

Re: [Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hi Ryan, This is weird! I am safely assuming that you sourced FreeSurfer, etc? What was the command you ran? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeigle

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.

[Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Hi, I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, and ? Could Someone point me to some documen

Re: [Freesurfer] mri_compute_volume_fractions

Hi Dhivya if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the volume frac

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Thank you so much for your quick reply ! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Sorry for bothering with more questions! I am getting an error saying , mri_compute_volume_fractions: could not load registration file from identity.nofile And my command is, mri_compute_volume_fractions identity.nofile mri/aseg.mgz test and if I

Re: [Freesurfer] Non-rigid registration approaches

External Email - Use Caution Hi Douglas, I applied a non-rigid registration to my nifti files using another software (IRTK) and then tried to run dt_recon in Freesurfer. Dt_recon is failing during Fitting Tensors and the error message it is displaying is "ERROR: DTIstructFromBFiles

Re: [Freesurfer] mri_compute_volume_fractions

oh, this must be Doug's code, not mine. Try using --regheader instead And also please send us the full command and all screen output from it in the future. cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > Sorry for bothering with more questio

Re: [Freesurfer] mri_compute_volume_fractions

External Email - Use Caution Thanks Bruce! I even tried with --regheader mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile It gives me below error, arg = 6 reading registration file mri/aseg.mgz regio_read_register(): Success Error reading inplaner

Re: [Freesurfer] mri_compute_volume_fractions

try mri_compute_volume_fractions --o test --regheader On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >External Email - Use Caution > > Thanks Bruce! > > I even tried with --regheader > > mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile > > It gives me below