Re: [Freesurfer] Alignment of segmented brainstem in Freesurfer

External Email - Use Caution Thankyou, Sir. It really helped me a lot. On Sat, Apr 20, 2019 at 11:46 PM Bruce Fischl wrote: > What command did you use to apply the transform? If mri_convert add -rt > nearest to your command line. > The issue is that you are using trilinear

Re: [Freesurfer] ERROR: flirt in bbr Matlab Execution

Don't use --best anymore, it is depricated. There should be no need to specify an initialization (unless it is to initialize it with the header geometry). Under the hood, it will use mri_coreg (a shameless copy of spmreg). On 4/24/2019 7:07 PM, Pfannmoeller, Joerg Peter wrote: Hello, I have a

[Freesurfer] ERROR: flirt in bbr Matlab Execution

Hello, I have a problem with bbregister and the option --init-best. In the current dev version of freesurfer 6 the processing stops with the error message: terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt if I run bbr using Matlab and

Re: [Freesurfer] Fwd: mri_surfcluster ERROR

This is pretty weird. Can you try this version https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster On 4/24/19 2:56 PM, Javier Navas wrote: > > External Email - Use Caution > > > -- Forwarded message - > De: *Javier Navas* mailto:fjnav...@gmail.com>> > Date:

Re: [Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

External Email - Use Caution ​Hello Gonzola, I use a CentOS7 VM image (on virtualbox) originally downloaded from osboxes.org. After downloading and bringing up the image, I installed various packages for freesurfer. But apart from my image being CentOS7 (and not CentOS6), I

[Freesurfer] QDEC ROI Analysis

External Email - Use Caution Hello FreeSurfers, I had the same question as below, but did not see a response. Does anyone know if this feasible in QDEC? Best, Jessica - fabrizio

Re: [Freesurfer] Obtaining stats for a custom label

External Email - Use Caution Correction to the previous email: I can view the label in the rh.white, not lh.white.  Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Apr 24, 2019, at 10:50

Re: [Freesurfer] Obtaining stats for a custom label

External Email - Use Caution Hi Doug, I used the command below to convert a volume to a label file. The volume is a binary mask highlighting a subcortical ROI that I am projecting to the closest vertex. I can visualize the label on the fsaverage lh.white surface. mri_vol2label

Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file

External Email - Use Caution Thanks for looking into the matter Doug, and I now have gotten to the bottom of the problem based on your suggestion about dropping volumes. For context, I have been collecting functional runs from a Phillips scanner using a self-paced task, and

[Freesurfer] trac-all -prep b0 inhomogeneity correction error

External Email - Use Caution Hello Doug, When running trac-all -prep and including b0 inhomogeneity correction with epidewarp.fsl I get the following error. FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X Looking at the epidewarp.fsl source code I see that the error is

Re: [Freesurfer] mri_surfcluster ERROR

External Email - Use Caution Yes, the file ($SUBJECTS_DIR/fsaverage/surf/rh.white) exists and I can open it with freeview. The mri_surfcluster worked well in the past. However, I recently downloaded the fspalm and the mri_surfcluster attached for the fspalm. I do not know if it

Re: [Freesurfer] recon-all error

I don't think there was a file attached. Have you been able to processes any subjects in FreeSurfer? Or does it fail in this way on all subjects? On 4/24/2019 4:59 AM, Ebru Ayyürek wrote: External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a full

Re: [Freesurfer] mri_surfcluster ERROR

The "locale" error is probably not a problem. Does /media/Data/PEH/NEW_FS_analysis/fsaverage/surf/rh.white exist? What operating system are you using? On 4/24/2019 6:41 AM, Javier Navas wrote: External Email - Use Caution Dear freesurfer experts, I want to create an annot from the

Re: [Freesurfer] Obtaining stats for a custom label

How did you create the label? Is it a surface-based label? Ie, does it have valid vertex indices as the first item in each label point in the label file? On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello Freesurfer developers, I am using the code

Re: [Freesurfer] How to Display Specific Cortical Parcels (not the output of the recon-all) on Brain Surface

You will have to go through a few steps. 1. Sample your labels onto the surface with mri_vol2surf --mov yoursegmentation.mgz --regheader --s subject --hemi lh --interp nearest --o lh.mysegmentation.mgz 2. Convert the surface-sampled segmentation to an annotation using mris_seg2annot. Run it with

[Freesurfer] FreeSurfer 6.0 disk image for VirtualBox?

External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] recon-all error

hmmm, how long did you let it run? I've never seen this before. Can you upload your subject to our ftp site? cheers Bruce On Wed, 24 Apr 2019, 1013364183 wrote: External Email - Use Caution Dear freesurfer   We run the recon-all command of freesurfer, but when it runs to the

[Freesurfer] fswiki brainstem substructures: test data unavailable

External Email - Use Caution Hi, Section "6. Test data" of the article "Brainstem Substructures" at https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures mentions: > Processed data of a single subject (also used to demo the hippocampal > subfield segmentation) is

[Freesurfer] How to Display Specific Cortical Parcels (not the output of the recon-all) on Brain Surface

External Email - Use Caution Dear Freesurfer Experts, I have a predetermined cortical parcels in native space. I want to display them on brain surface, As shown in the last image of page bellow: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have

[Freesurfer] mri_surfcluster ERROR

External Email - Use Caution Dear freesurfer experts, I want to create an annot from the output of PALM, the vertexwise file corrected by TFCE-FWEp. The values of this files are in 'p-values'. However, the mri_surfcluster has some problems: it could not recognize the fsaverage

[Freesurfer] recon-all error

External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a full recon-all on the dicom/nifti file for test my freesurfer installation as described on the website https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall but I have an error like

[Freesurfer] recon-all error

External Email - Use Caution Dear freesurfer We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it will not run anymore, that is, the running terminal has been stuck in the following statement for more than 10 days.We want to ask why

[Freesurfer] Obtaining stats for a custom label

External Email - Use Caution Hello Freesurfer developers, I am using the code below to generate the stats table for the ROI. mris_anatomical_stats -l /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label -b subject rh white However, when I run