Re: [Freesurfer] pass word for Ubuntu VM file FS_7_2_0_Ubuntu_18_04_06.ova.7z

External Email - Use Caution You may want to check your spam filters as it was already sent to you on 9/9/2022 with the subjectFS Ubuntu VM info Sending it again just now. - R. On Sep 13, 2022, at 00:35, PRASAD D prasad.d...@ptuniv.edu.in wrote:External Email - Use CautionDear

[Freesurfer] pass word for Ubuntu VM file FS_7_2_0_Ubuntu_18_04_06.ova.7z,

External Email - Use Caution Dear all, Does anyone have the password for Ubuntu VM file FS_7_2_0_Ubuntu_18_04_06.ova. kindly share the password with prasad.d...@ptuniv.edu.in thanks in advance. regards. D.Parasd Fulltime Scholar PTU university.

[Freesurfer] Extract Fetal Brain MRI

External Email - Use Caution Hi Dear, We are a research team at Rush University Medical Center. We are working on the Fetal MRI data. In this step,*we need to extract the "Fetal Brain MRI" from our images, which have "mother and other tissues"* as well. One of our options is

[Freesurfer] White matter normalization

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. I do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1

Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

External Email - Use Caution dear douglas, you are right a visual comparison is the thing to do. I hope I can ask you an advice on that. I used freeview to open the mri data + segmentation for both participants: freeview -v $subj/mri/brainmask.mgz

[Freesurfer] resample anatomical mask

External Email - Use Caution Dear experts, I would like to downsample the GM mask, which is at 1mm isotropic voxel size (freesurfer subject space), at 3mm isotropic. What is the most efficient way to do it with freesurfer? Thank you in advance. Marina

[Freesurfer] MNI coordinates of minimal thickness in ROI

External Email - Use Caution Dear Experts, I am looking for a way to extract information on the location (xyz coordinates in MNI space) of a vertex with the lowest thickness value within an ROI (label) for a group of subjects. I have previously ran recon-all and qcache on the

Re: [Freesurfer] mri_binarize error for thalamic nuclei during trac-all prep

External Email - Use Caution Hi Freesurfer Developers, I believe I found a work around for the mri_binarize error I was running into regarding the thalamic nuclei segmentation during trac-all prep as described in greater detail in my previous message (

Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale

External Email - Use Caution Hi Douglas, Thank you for answering me. I think may be the DOSS would work. Yuan 获取 Outlook for

Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

What you show for the lateral ventricle is not really concerning to me. Oftentimes there are differences on border voxels, and border voxels can easily make 5% or more of a structure. If you compare them visually, do you see big differences? On 9/12/2022 7:41 AM, Bernardoni, Fabio wrote:    

Re: [Freesurfer] Issues with recon-all

well, you're running 5.3, which we have not supported in years. My guess is that it has to do with the MNI tools not working in ubuntu. I don't know that you are going to be able to use 5.3 in this context On 9/12/2022 3:01 AM, Hitesh Pradhan wrote: External Email - Use Caution

Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale

HCs always have 0 medicationload so it is not possible to measure a load slope for them. Is it the case that a BD with load=0 is the same as HC? If so, then just have one class. If not, do you expect the age, edu, and tiv slopes to differ between the groups? If not, then use DOSS (default was

Re: [Freesurfer] recon-all error: ERROR: recon-all command failed with return_code: 1

It is not clear what is going wrong as there is not really an error message.Was there anything printed to the terminal that is not in the log file? The last thing it did was to write out mri/aparc.DKTatlas+aseg.mgz. Can you check that and see if it looks ok? Did you run out of space on the

[Freesurfer] volume differences between longitudinal and crosssectional preprocessing

External Email - Use Caution dear freesurfer experts comparing the results of longitudinal vs. crosssectional preprocessing for single time point participants I have noticed that there are some quite substantial differences (>5% for some sub cortical regions). I wonder whether

[Freesurfer] Issues with recon-all

External Email - Use Caution Hello Developers, I am facing the recon-all command which exits with premature exit. I have attached the recon-all log file. I have also attached my license file for your reference. 1. I am using UBUNTU 18 as my platform. 2. I have attached the