Freesurfer July 2024

freesurfer@nmr.mgh.harvard.edu

44 participants
44 discussions

ssistance needed: Aligning existing FreeSurfer segmentation with new T1 image
by Owusu-Ansah, Maame 25 Jul '24

25 Jul '24

External Email - Use Caution Dear FreeSurfer team, I'm working on a project where I need to align an existing FreeSurfer segmentation (from an older T1 image) with a the same T1 image of the same subject, but it is debiased and in a different atlas space. The goal is to leverage the manual edits and refinements made in the original FreeSurfer output while utilizing the improved image quality of the new T1 scan. Current approach: 1. Using mri_robust_register to align the old FreeSurfer T1 to the new T1 image 2. Applying the resulting transformation to all FreeSurfer volumes (mri/*.mgz files) 3. Transforming the surface files using mri_surf2surf 4. Running recon-all -autorecon2-cp -autorecon3 on the transformed data Main Issue: After applying our current approach, we've noticed that while the volume files (mri/.mgz) seem to align well with the new T1 image, the surface files (surf/.pial, surf/*.white, etc.) are not aligning properly. This misalignment is causing discrepancies in our cortical measurements and affecting downstream analyses. Questions: 1. Is our approach appropriate for maintaining the quality of the original segmentation while adapting to the new T1 image? 2. Why might the surface files be misaligned when the volume files seem to align correctly? 3. Are there alternative methods or additional steps we should consider to ensure proper alignment of both volume and surface files? 4. How can we ensure that manually edited regions in the original segmentation are preserved, especially for surface-based edits? 5. Are there specific quality control steps you'd recommend for verifying both volume and surface alignment? Any guidance, alternative approaches, or explanations you could provide would be greatly appreciated. Thanks, Maame ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Assistance needed: Aligning existing FreeSurfer segmentation with new T1 image
by Owusu-Ansah, Maame 25 Jul '24

25 Jul '24

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Issues for longitudinal pipeline-based process
by Yoonho Hwang 24 Jul '24

24 Jul '24

External Email - Use Caution Dear FreeSurfer developers, Hi, Prior to the FreeSurfer-based longitudinal analysis, it's inevitable that the scanner will change over time in a long follow-up study. We had multiple follow-up data for the same subjects [e.g., baseline and 1st follow-up (scanner 1), 2nd follow-up (scanner 2)]. I applied the longitudinal pipeline of FreeSurfer to the data as follows: 1. Cross-sectional process for each time point 2. Create template (recon-all -base long_base -tp long_tp1 -tp long_tp2 -tp long_tp3 -all -parallel -openmp 4) 3. Longitudinal process In process 2, I encountered the following warning, but completed the entire process without errors. ******************************************************************************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ******************************************************************************* There are resolutions of our data for each time point: - Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180) - 1st follow-up (scanner1, 512 x 512 x 180) - 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Can I ignore the warning? Or is there anything I need to fix before doing process 3 (longitudinal process)? Also, could you please give me any suggestions on longitudinal analyses? Thank you very much Sincerely, Yoonho

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Scalp mask
by Francesco Lomi 22 Jul '24

22 Jul '24

External Email - Use Caution Hi everybody, Do you know how to create a scalp mask file with freesurfer? Thank you in advance Francesco

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Negative voxel ranges
by ERNEST KISSI 22 Jul '24

22 Jul '24

External Email - Use Caution Dear fresurfer team, Please I want to extract the intensity of a voxel 48, -56, -34. But my voxel ranges of my image does not include negative values. Is there a way to make the ranges cover these values. Thanks 👍.

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Very large segmentation errors with recon-all
by Tornabene, Danilo 22 Jul '24

22 Jul '24

External Email - Use Caution Dear FreeSurfer developers, I've encountered very large, systematic errors in segmentation running recon-all on a MRI dataset of 76 subjects. In the screenshot attached, you can see how the white surface (shown in the right hemisphere) includes most of the cortex as well, while the pial surface (in the left hemisphere) extends into the CSF and often reaches the skull. In some of the subjects there is also a clear misalignment with the T1 images. I don't have a long experience with FreeSurfer, but my supervisor Prof. Cole tells me he has processed thousands of scans and never seen this kind of errors so we thought of reaching out to you for some help or explanation. The only thing we noticed is that this error happens on scans with a higher-than-usual resolution (voxels are 0.8x0.8x0.8 mm), could this be causing the problem? I have simply ran recon-all withouth any additional option or argument other than the input files and IDs and the output directory. Please find the shell log outputs for two sample subjects. The recon-all pipeline was completed with no hard errors, and the Euler numbers were mostly 2 with some 1. Best, Danilo Tornabene

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ConcatenateSubregionsResults
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Jul '24

22 Jul '24

External Email - Use Caution Hi Dr. Iglesias, The script ConcatenateSubregionsResults<https://surfer.nmr.mgh.harvard.edu/fswiki/ConcatenateSubregionsResults?acti…>.sh is not readily available, either in the page or the most latest version of FS, could you share? Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://www.bilh.org for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Open question to everyone about publicly available MRI datasets
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 18 Jul '24

18 Jul '24

External Email - Use Caution Hi everyone, Does anyone have any leads to publicly available 0.8 x 0.8 x 0.8 mm slice thickness GE structural scans, especially ones outside NDA.nih.gov? This is for a segmentation project. Thank you, Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://www.bilh.org for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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(no subject)
by 李梦君 17 Jul '24

17 Jul '24

External Email - Use Caution Dear Freesurfer Team I have extracted the left and right cerebral cortex from the aseg.mgz file in the 3d slicer. At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer the left and right cerebral cortex extracted from the aseg.mgz file was not in the same position with the lh.pial and rh.pial in the 3d slicer How should I put them in the same position in the 3d slicer Thanks Mengjun

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BUG: FTP Server data visible without credential
by Kavar Hardik 17 Jul '24

17 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am checking your website and I found your FTP server are configured without Credentials. FTP URL: https://surfer.nmr.mgh.harvard.edu/ftp/ POC attached with mail. Regards Kavar Hardik

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Freesurfer July 2024