Re: [Freesurfer] Cutting an occipital patch

External Email - Use Caution It works, thank you! Noam ‫בתאריך יום ב׳, 17 באוק׳ 2022 ב-0:20 מאת ‪Douglas N. Greve‬‏ <‪ dgr...@mgh.harvard.edu‬‏>:‬ > Try this: > Click on the "brain with scissors icon" ("Cut"), select the points, then > hit "Cut Closed Line". > Now, make sure th

Re: [Freesurfer] [EXTERNAL]Re: mris_transform with flirt transformation wrong result

External Email - Use Caution That worked, thanks Doug. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, 17 October 2022 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL]Re: [Freesurfer] mris_transform with flirt transformation

Re: [Freesurfer] Fusion of PET and T1 weighted

yes, but how are you combining them? And what features after you do? On 10/16/2022 10:18 AM, Amar Shukla wrote: External Email - Use Caution Dear Sir, Fusion means combining the two modalities  that is T1 and Pet. Then extracting features from combined image. This is what I am thinki

Re: [Freesurfer] Question about sclimbic

This is a known bug. Please see https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes for a patch On 10/14/2022 1:46 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution I receive an error when I try to run the sclimbic module, do you have any sugge

Re: [Freesurfer] NoPVC PET

You need to add --save-input (just added a note to the wiki) On 10/14/2022 9:22 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to get a noPVC PET volume scaled by the intensity of the pons, then project it and apply standard surface-based analysis

Re: [Freesurfer] mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)

Can you confirm that /subjects/CI_01/mri/orig.mgz exists? Usually, your  SUBJECTS_DIR would not be directly in root, especially on a mac, but it is not impossible. On 10/14/2022 7:17 AM, Wandschneider, Britta wrote: External Email - Use Caution Hello, I am trying to map tumour+oedem

Re: [Freesurfer] Cutting an occipital patch

Try this: Click on the "brain with scissors icon" ("Cut"), select the points, then hit "Cut Closed Line". Now,  make sure the cursor is in the patch you want to keep, then hit "Fill Uncut Area" On 10/14/2022 3:14 AM, Noam Khayat wrote: External Email - Use Caution Hello, I need to

Re: [Freesurfer] Skullstripping

you can run recon-all with -autorecon1 instead of -all or you can run mri_synthstrip to get the brainmask or you can run mri_synthseg and binarize to keep the segments you want or you can run samseg and binarize to keep the segments you want mri_synthstrip will probably get you where you want to

Re: [Freesurfer] somatosensory cortex (S1)

Hi Eszter We provide estimates of architectonic boundaries like 1, 3a, 3b, 2 etc… as label maps in each subject’s label dir. They are either unthresholded (and have the estimated probability of being in that area for all vertices with p>0) or thresholded so that the label has the average surfac

Re: [Freesurfer] mris_transform with flirt transformation wrong result

Not sure about mris_transform, but you can use mris_applyreg --lta source-surf ltafile output-surf You will have to convert your flirt reg to lta (lta_convert --infsl flirt.mtx --outlta flirt.lta --src flirtinput.nii --trg flirtoutput.nii) On 10/13/2022 9:40 PM, Chris Adamson wrote: E

[Freesurfer] somatosensory cortex (S1)

External Email - Use Caution Dear FreeSurfer Team, I would like to do a ROI analysis focusing on the primary somatosensory cortex (S1) using Freesurfer and see the potential alterations after a (behavioral) treatment . I am wondering how I can do that? First, I picked and looked

Re: [Freesurfer] Fusion of PET and T1 weighted

External Email - Use Caution Dear Sir, Fusion means combining the two modalities that is T1 and Pet. Then extracting features from combined image. This is what I am thinking Sir. regards amar Shukla On Thu, 13 Oct 2022 at 11:19 AM, Amar Shukla wrote: > Dear Freesurfer Commu

[Freesurfer] Pass code to unzip VM

External Email - Use Caution Dear Researchers, I am emailing to request the pass code to unzip the FS_7_2_0_ubuntu_18_04_07.ova.7z file to use FreeSurfer on Windows. Thank you. Allesha Get Outlook for iOS

Re: [Freesurfer] Fusion of PET and T1 weighted

I don't know what you mean by "fusion" here. Can you explain more? On 10/13/2022 1:49 AM, Amar Shukla wrote: External Email - Use Caution Dear Freesurfer Community. I want to do image fusion (PET+T1) = T' weighted image. Then I want to go for the feature extraction from this T1 modal

Re: [Freesurfer] Extract single time frame

I'm not sure what this refers to because there is no history in the email. I'm guessing that you want to extract a certain range of frames from a multiframe file. If so try the  --fsubsample  option in mri_convert On 10/12/2022 2:33 PM, Proulx, Jean Sebastien wrote: > Hello, > > Specifying a sin

Re: [Freesurfer] Creating a seed sphere using MNI coordinate

Hi Reuben, On 10/5/2022 10:05 PM, Addison, Reuben wrote: 1. I am planning to add a seed sphere 6mm cortical and 4 millimeters subcortical and I want to do this with Fsfast using given MNI coordinates from a previous study. I am wondering if there is a command on fsfast to achieve t

Re: [Freesurfer] fft

No, not that I know of On 10/7/2022 5:39 PM, Proulx, Jean Sebastien wrote: > Hello, > > Is there an easy way to perform fast fourier transform (fft) or other > fancier spectral analysis with freesurfer tools (e.g. with mris_calc)? > > Thanks and > Have a good day! > Sebastien > >

Re: [Freesurfer] Specify random seed with recon-all

Sorry, we have not used that functionality in years, and worked pretty hard so that things would be deterministic. On 10/7/2022 4:03 PM, Elizabeth Kenneally wrote: External Email - Use Caution Hi FreeSurfer Developers, I’m trying to run FreeSurfer with a specified random seed with r

Re: [Freesurfer] Creating a lobar atlas

Why do you need to create a new atlas? Why not just compute the stats from wmparc.lobes.mgz ? On 10/6/2022 5:23 PM, James Brown wrote: External Email - Use Caution Dear colleagues Freesurfer experts, I would like to create an atlas (my atlas) for the white matter like "wmparc.mgz" s

Re: [Freesurfer] mri_glmfit error

Do you see where it says "ERROR: READ THIS"? And below that do you see that it asks for four things? Can you send those four things? On 10/5/2022 2:51 PM, fernanda rohrsetzer wrote: External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the fo

Re: [Freesurfer] Quality control of longitudinal recon-all output for >500 participants

If you run mri_segstats --qa-stats subject subject.qa.dat It will generate the QA .dat file. This will have 20 numbers in it. Run mri_segstats --help to see what they are. I usually use #20 (CNR) Run it for all your subjects, then sort by CNR, then examine the worse subjects On 10/4/2022 10:24

Re: [Freesurfer] Getting recon-all stats from SynthSeg 2.0 segmentations

we don't have a way to do this yet. If you want recon-all type stats, you can run synthseg storing the output in subject/mri, then look at the recon-all.log file to get the mri_segstats command that creates the aseg.stats file, modify the command line to use the synthseg output and change the .