Re: [Freesurfer] [EXTERNAL] Re: Tracula 7.2 -bedp error

External Email - Use Caution Dear Tracula Team, I ran the command suggested below to merge the files: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri But this did not seem to work unfortunately, here is the output. Removing intermediate files Creating identity xfm

[Freesurfer] Dracula 7.2 -bedp error

External Email - Use Caution Dear Tracula team, I am running 7.2 on a computing cluster and the -prep stage completes without error. The dmri directory show the following files, below. However, after running the second step ( -bedp), the files under dmri.bedpostX do not appear

[Freesurfer] long_mris_slopes

External Email - Use Caution Hello, I am trying to do some preliminary analysis of a longitudinal dataset, following the tutorial. I am running FS on Ubuntu 20.04 and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I have finished processing the dataset; to prepare the

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution Lilla, It worked for the CC into the aseg. How would I get the CC into the aparc+aseg? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Zollei, Lilla,Ph.D. Sent: Thursday, October 21, 2021 3:39 PM To: Freesurfer support list Subject

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution We will give 7.2 a try as well. Lilla's suggestion did create/append the CC to the aseg using: set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Thx. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendi

Re: [Freesurfer] Dracula 7.2 -bedp error

Not sure why, could be a specific version of FSL. You can try running the step that merges everything separately: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri On a separate note: I have to do some emergency travel so I will not be monitoring the list through the next week. __

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

This won't be good for the cc.* tracts for sure (in the new version we have the entire CC covered with 7 subdivisions). TRACULA learns how often the n-th point along tract X falls in or next to label Y from the structural segmentation. If it's learned that a tract goes through label Y=254 half w

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution Correction Lilla, I think they are nih atlases in the 21-27mo age group.. We are analyzing the 2yo age group. Could we use the baby FS atlases at that age range since they have the CC segmented to generate the CC on our asegs with the method you sug

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution Lilla, But the asegs we're generated using the ABCD-hcp-DCAN infant pipeline, using manually refined ALBERTs atlases, not FS atlases. Jim . Get Outlook for Android

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

Jim, You could run set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list Subjec

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution Anastasia, Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts

Re: [Freesurfer] developer password of Freesurfer VBOx

External Email - Use Caution Sending the info to your private emails shortly. -R. On Oct 20, 2021, at 11:20, Joshua Ericson wrote:External Email - Use CautionI am having the same issue.  Please, provide the password to me as well.Thank

Re: [Freesurfer] developer password of Freesurfer VBOx

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 11:11, byu wrote:External Email - Use CautionI am radiologist of Shengjing hospital of China Medical University. I am now  attempting to start Freesu

Re: [Freesurfer] developer password

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 10:31, Joshua Ericson wrote:External Email - Use CautionI am attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it req