Freesurfer January 2024

freesurfer@nmr.mgh.harvard.edu

70 participants
111 discussions

FW: Boundary based registration
by Spapens, Jeltje (NP) 01 Jan '24

01 Jan '24

External Email - Use Caution Hello Freesurfer developers, I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects. I also changed som flags such as -init-header and --cubic, but all seem to give the same results. bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat –trilin I would appreciate to hear your thoughts on this problem. Have a nice weekend and kind regards, Jeltje Spapens

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Use pial or white surface area of FreeSurfer?
by free_learner 01 Jan '24

01 Jan '24

External Email - Use Caution Dear experts, Surface area is a commonly used metric. Unlike thickness and volume, area could be calculated based on white surface or pial surface in FreeSurfer. I don’t know which one should be better used for analysis. I believe the pial surface area is more sensitive to brain changes such as gray matter atrophy. But the white surface area is the default in FreeSurfer and thus probably the one used in papers. Maybe I should use the mean area of white and pial surface? Best, Yang Hu

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Tksurfer option for horizontal scale bar
by Lee, Jeungchan 01 Jan '24

01 Jan '24

Hi Freesurfers, I’m using TkSurfer to visualize my results and want to add a horizontal color scale bar. I used [ -colorscalebarflag 1 ] to do so, but I only got a vertical bar. Is there any way (command options) to get a horizontal color scale bar? Thanks, jeungchan

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Brainnetome atlas
by Blanca Zufiria Gerbolés 01 Jan '24

01 Jan '24

External Email - Use Caution Dear all, I would like to extract the cortical thickness, subcortical volumes and eTIV from the Brainnetome atlas of subjects I have preprocessed with FreeSurfer v7.3. I understand this entails several steps. Could someone advise me how to do this? Best wishes, Blanca När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://secure-web.cisco.com/1UfjSvkpcEA-W18RIWXnAOlIhR9tz8hfZlA7NdpYFKSpWW…>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://secure-web.cisco.com/1VCHcReN3VOjcjz8kTVUawgcRo_JbylQUb1S4aWfBcPzFl…>.

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Help with transform matrix for SEEG
by Hyunchul Lee 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have SEEG electrode locations that have been digitized in MRI RAS space, and I'm trying to apply a transform matrix so that these electrodes will be registered with the same brain that I performed recon-all on using Freesurfer, so that I can do further analysis in MNE python. I understand that voxel space to MRI RAS space transform matrix is stored in vox2ras and the transform for voxel space to Freesurfer's surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since the electrodes are in MRI RAS space, I am applying a transform matrix that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However, this doesn't work out in real life, and I end up with electrodes half way outside the head. Am I using the correct matrices? Also, T1.affine appears similar to vox2ras but very slightly different. Just hoping that there would be an easier way.. Best regards, *Hyunchul Lee* MBBS PhD

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Clear background from command line
by Datta, Aditya 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, Is there any way to clear background for a volume file from the command line. I am attempting to overlay electrodes onto a T1 image, and I would like for the background of the electrode files to be clear when they are loaded from a script. Thanks, Aditya Datta Staff Research Associate II UCLA Department of Neurosurgery 670 Charles E. Young Dr. South, CHS 63-360 Los Angeles , CA 90095 650-435-9337 ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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MEMPRAGE dura flags
by Akkoyunlu, Beyza 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, I have longitudinal data with MEMPRAGE. I want to improve white-gray matter boundaries by using dura flag. But I’m a bit lost about how to do it. Your previous recommendations to use echoes with “mri_make_surfaces” function, yet the surfaces only needed-created in the base and long steps. Should I register the echoes to the respective anatomical’s long version and then use mri_make_surfaces? if not, do you have any suggestion about how to go for it? Thanks in advance Best, Beyza

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Cortical Thickness Measurement in Cortical Lesion ROI
by 李浩 01 Jan '24

01 Jan '24

External Email - Use Caution Dear Freesurfer Experts, I am currently engaged in a project where I need to measure the cortical thickness of a segmented cortical lesion (ROI) in the volume space. After running recon-all for my subjects, i employed 'mri_vol2surf' function to project my ROI from the native T1 space to indiviaul surface space. My command was as follows: mri_vol2surf —mov $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz --hemi rh --surf white --projfrac-avg -0.1 1 0.05 --interp nearest --o "$sub"_chronic-CMI_4-1_rh.mgh --regheader "$sub" --trgsubject “$sub” However, I encountered an issue where I could not locate the ROI in the individual surface space, as the values in "$sub"_chronic-CMI_4-1_rh.mgh were all zero. I suspect this might be due to a registration error or possibly the small size of my ROI (only 4 voxels). Do you have any suggestions on how to address this issue? Additionally, I am wondering whether it's possible to register the cortical thickness map from the surface space back to the individual volume space, then calculate the mean cortical thickness of my ROI there. Alternatively, is it feasible to convert the coordinates of my ROI's center point to the MNI152 coordinate and then surface-based coordinates and directly create an ROI in the surface space? Any feedback on these questions would be greatly appreciated. Thanks in advance. Bests, Hao Li

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Correlation Line Plot for FS Group Analysis
by Tejaswi D. Sudhakar 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I am to generate a plot to visualize the slopes between classes for group analysis. I would like to generate something similar to this freesurfer post: https://secure-web.cisco.com/10NQ6nNamVal7BE9lNMpStHRFgMjBEDJy0P_U59n_G56Yh… Is this available in freesurfer version 7? Thanks in advance, Tejaswi

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volumetric to surface using mri_vol2surf: tpl-MNI152NLin2009cAsym
by Lee, Jeungchan 01 Jan '24

01 Jan '24

Hi Freesurfers, I was wondering if there is a registration matrix (from volumetric to surface) for MNI152NLIN2009cAsym template. I was not able to find any (relevant) dat files in $FREESURFER_HOME/average/. I have some data in that space and would like to map them on the surface for visualization. Thanks, jeungchan

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Freesurfer January 2024