[Freesurfer] Downloading OVA

External Email - Use Caution Hi, I'd like to download the OVA to run in VirtualBox, but the wiki article

[Freesurfer] recon-all error

External Email - Use Caution Hi, For some of my subjects I get the following error at the beginning of recon-all: mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN

[Freesurfer] Transformation of volume images

External Email - Use Caution Dear developers, please, may I ask you how I can transform volume images (containing discrete region labels) from the fsaverage space into the space of a given subject, and vice-versa? I tried the following command: mri_vol2vol --interp nearest --mov

[Freesurfer] Question about lesions output

External Email - Use Caution Hi freesurfer I did an experiment about lesions about the output of samseg. And the results are as follows: The volume of lesions in label 99 in seg.mgz result is 745 mm^3. The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok? Why are

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

External Email - Use Caution Dear Douglas, thank you for the reply. I am attaching it here. I usually create it (using BASH) as such: << echo “1 -1” > File_Name.mtxand have never had issues, however I have not used "[ ] " on my contrasts before... Thank you so so much for

Re: [Freesurfer] Problem with brainstem overlap after BBR

External Email - Use Caution I have found the answer, thank you very much! From: on behalf of "Douglas N. Greve" Reply to: Freesurfer support list Date: Thursday, 16 November 2023 at 15.27 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Problem with brainstem

Re: [Freesurfer] Question about lesions output of samseg

External Email - Use Caution Thanks The volume of lesions in label 99 in seg.mgz result is 745 mm^3. The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok? On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve wrote: > Internally, samseg uses partial volume to compute

Re: [Freesurfer] Question about lesions output of samseg

Internally, samseg uses partial volume to compute a more accurate volume. They should still be very close though. On 11/16/2023 6:46 AM, reza razmara wrote: External Email - Use Caution Hi freesurfer team I use samseg for lesion segmentation. In the result of .stats i see the

Re: [Freesurfer] Problem with brainstem overlap after BBR

I answered it yesterday. Check your inbox On 11/16/2023 4:08 AM, Spapens, Jeltje (NP) wrote: External Email - Use Caution Hello Freesurfer Developers, I have never received an answer to my problem, maybe it was lost in the e-mails. Kind regards, Jeltje Spapens *From: *"Spapens,

[Freesurfer] Question about lesions output of samseg

External Email - Use Caution Hi freesurfer team I use samseg for lesion segmentation. In the result of .stats i see the lesions volume. But when i extract lesions seprately as a new file we know that it uses the label 99 for extraction. But when i calculate the volume of this

Re: [Freesurfer] [EXTERN] Re: Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer

External Email - Use Caution Hi Yujing, Thanks for the response. We addressed the issues by modifying the labels of the vertices that represent specific areas. To do this, we employed the 'write_annotation' function in FS (MATLAB-based). Anyway, It's worth noting that the

Re: [Freesurfer] Problem with brainstem overlap after BBR

External Email - Use Caution Hello Freesurfer Developers, I have never received an answer to my problem, maybe it was lost in the e-mails. Kind regards, Jeltje Spapens From: "Spapens, Jeltje (NP)" Date: Wednesday, 8 November 2023 at 13.55 To: "Freesurfer@nmr.mgh.harvard.edu"