Re: [Freesurfer] Which files do I need to mri_deface to anonymized a subject?

Hi Tim you probably also want to do the files in the orig dir (like orig/001.mgz). cheers Bruce On Fri, 27 Sep 2019, Tim Schäfer wrote: External Email - Use Caution Dear FS experts, I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium

[Freesurfer] TRACULA - input Nifti instead of DICOM?

External Email - Use Caution Hello I was given a dataset already in Nifti format that I would like to run Tracula on. Is it possible to input Nifti files in the config file instead of DICOMs? How would this work? Best, Daniel Callow -- *Daniel Callow* *PhD Student, Neuroscience

[Freesurfer] What's the difference between FSFAST and SPM in the 1-st level GLM?

External Email - Use Caution Dear Freesurfer experts, May I ask what's the difference between FSFAST and SPM in the 1st level GLM? Now I use fsfast to pre-process my task-based imaging data, then model the data with FSFAST and SPM respectively. I expected to get very similar

Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

Nifti files don't store that info. You'd have to get the gradient table and b-values either from the dicom header or from the scanner. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel Callow Sent: Friday, September 27, 2019 11:32 AM To:

Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

External Email - Use Caution Gotcha. I was wondering if it would be possible to extract the bvecs and bval files directly from the Nifti file, however, it seems like based on the documentation that this is not possible and I will have to specify the bvals and bvecs and make sure

Re: [Freesurfer] Error during processing. mris_make_surfaces(10174, 0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated/

Hi, if you upload this entire subject to our ftp site we will take a look cheers Bruce On Fri, 27 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Hello FreeSurfer Developers, during the processing of patient data an error occurred. I don’t

Re: [Freesurfer] Error during processing data. mris_make_surfaces malloc: *** error for object 0x2431900024317: pointer being freed was not allocated.

ok, we'll see if we can replicate it. On Fri, 27 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Dear Bruce, I don't’ know exactly what happened during the processing.  I have 8 Gb of RAM of my Mac. When the freesurfer is working there is

Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

Yes. Please check out the instructions in the tutorial on how to specify your input DWIs and let us know if you have any questions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel

[Freesurfer] Add email to post in mailing list

External Email - Use Caution prl.saheli...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Converting .label coordinates to MNI

Hi Joel I believe they are stored in "tkreg ras" by default. In any case, mri_label2label should let you map them to pretty much any space you like. cheers Bruce On Fri, 27 Sep 2019, Berger, Joel wrote: External Email - Use Caution Hi friendly Freesurfers, I have seen

[Freesurfer] mri_surf2vol -lost cluster

Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsaverage surface with the following command: mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz --mni152reg This works well, but I'm losing a small temporal gyrus cluster

Re: [Freesurfer] [External] Re: Converting .label coordinates to MNI

External Email - Use Caution Thanks so much for the quick and clear reply Bruce. I'll look into doing that. Cheers, Joel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 27 September 2019 12:52:47 To: Freesurfer

[Freesurfer] Converting .label coordinates to MNI

External Email - Use Caution Hi friendly Freesurfers, I have seen this question asked, but can't find the answer. When exporting a label from tksurfer for a particular ROI for a subject, the coordinates in the .label document don't match up with any of the coordinates I can

[Freesurfer] Which files do I need to mri_deface to anonymized a subject?

External Email - Use Caution Dear FS experts, I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium server, and they require all data to be anonymized. I found mri_deface [1] and wondered which files I would have to apply it to,