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30070 discussions

Guidance on ADC Value Extraction and Rescaling Factor
by Taghizadeh Mortezaei, Nima 01 Jun '25

01 Jun '25

Hello everyone, I am currently working with ADC values extracted from inhomogeneity bias-corrected ADC MRIs obtained through SAMSEG and have encountered a few issues that I would greatly appreciate your insights on. 1. Units for ADC Values: When extracting ADC values for my ROIs, using 3D Slicer, I noticed that no unit was provided for the ADC values, neither in the software nor in the imaging visualization tools (PACS, VISAGE). I also checked the DICOM metadata for ADC and DWI MRIs but could not find any relevant tags related to ADC values, rescaling, or intersection. As a result, I am uncertain about the unit or scale used for the ADC values. 2. Discrepancy in ADC Value Range: The mean ADC values extracted from the bias-corrected image for my ROIs were in the range of 150-250. These values seem far away from the normal average ADC values for these structures. I suspected that the bias correction might have influenced these values, so I also extracted the values from the original ADC image. In this case, the values ranged from 1200-1500 for ROIs. However, I still could not identify any unit or rescaling factor. Considering that the average normal ADC values for my ROI are around 1000 to 1500 x 10-6 mm²/s, I have two questions: For extracting radiomics features (including ADC values) from the ADC image, would you recommend using the bias-corrected image or the original ADC image as the scalar volume? Based on the values I found, there must be a rescaling factor (like 10-6). Would you happen to know where I might find the rescaling factor, or how I could confirm it? I would greatly appreciate any guidance you could provide on these issues. Thanks, Nima

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Clarification on Label 24 – CSF in FreeSurfer
by Emma Rodrigues 01 Jun '25

01 Jun '25

External Email - Use Caution Dear FreeSurfer Experts, I hope this email finds you well. I'm reaching out to request clarification regarding label 24 – CSF in the FreeSurfer software. From my observations, this label appears to correspond to a region near the third ventricle. However, it does not seem to be included in any of the standard ventricular volume measurements. Additionally, I’ve noticed that in segmentations produced with SynthSeg, label 24 – CSF appears to correspond to the subarachnoid space, which adds some confusion. I’ve looked for documentation or forum discussions on this topic but have encountered mixed information. Could you please clarify what anatomical region label 24 – CSF represents in the original (pre-SynthSeg) version of FreeSurfer? Thank you in advance for your time and help. Best regards, Emma Rodrigues

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Opportunity to contribute to BRIDGE project
by Joana Braga Pereira 27 May '25

27 May '25

External Email - Use Caution Dear all, Please find an exciting opportunity below. For further information and queries please do not hesitate to contact Matthew (in CC: mathew(a)incf.org) ***About the Project*** The BRIDGE project (braindatagovernance.org <https://secure-web.cisco.com/1jTqF6FToUlilGFw1NR0zphQrV_aicG82sl_532pbnRBqZ…>), is tasked to develop international data governance frameworks (IDGFs) to facilitate the cross-border sharing of brain and mental health data, addressing the unique challenges posed by varying legal, ethical, and technical landscapes. It is well known that data accessibility, awareness, and training resources are far more prevalent in high-resource settings, leaving low- and middle-income countries at a disadvantage. This imbalance significantly hampers the global equity and inclusiveness of neuroscience research, particularly in mental health. To effectively address and minimize this disparity, BRIDGE is working to identify and thoroughly understand the barriers that exist at each stage of the research process across high-, middle-, and low-resource settings. For the Pathfinders Phase Two component of the project, volunteers will be asked to access several datasets (2-4) from different parts of the world and record the steps of downloading, minimally processing and analyzing each dataset.* All volunteers who complete the steps for their assigned datasets will be offered co-authorship on any subsequent manuscripts produced from their efforts.* In the coming weeks we will be ready to launch this phase of the BRIDGE project. We would like to enlist PhD students and Postdocs who have had previous experience handling human brain data to volunteer with us. All work can be completed remotely. Thank You! *Sign up here:* BRIDGE Pathfinders Sign Up <https://secure-web.cisco.com/15S3CEFy9BYdILHaaIpJeDfjDEOk6sCoiFJQ8UZ08hVw5U…> -- Mathew Birdsall Abrams, PhD, MPH Director, Science and Training International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15A SE-171 77 Sweden http://secure-web.cisco.com/1tA9CkZljq16-3xGKhpKZxhmE-bbjYthPUNQkWo7vGrtqAH… <https://secure-web.cisco.com/1Hl7aMSAc1sAxUQXCzDfC2Oo6Pjf2ySDEw_3gq3Ny7gpv0…>

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Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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June 2025 FreeSurfer course
by Sennott, Liam Ricker 21 May '25

21 May '25

Hello all, The next virtual FreeSurfer course will be held on June 9th, 10th, and 12th. Registration for this virtual FreeSurfer course is opening on Wednesday, May 21st at 10am Eastern Daylight Time. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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Re: [Freesurfer] Freesurfer 8 + PetSurfer talairach.m3z
by Simon Jones 18 May '25

18 May '25

External Email - Use Caution OK, thank you Yujing I'll see if we can update the installation Simon

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Freesurfer 8 + PetSurfer talairach.m3z
by Simon Jones 16 May '25

16 May '25

External Email - Use Caution Dear FS I tried to perform PetSurfer following recon-all pipeline using FreeSurfer 8. When I run gtmseg -s $sub I get error ERROR: cannot find talairach.m3z I was able to create the file talairach.m3z which is omitted from version 8 recon-all pipeline using mri_ca_register but I guess I should be converting the files in the subject/mri/transforms/synthmorph.1.0mm.1.0mm directory into talairach.m3z using mri_warp_convert. Is there an example of how to do that or are some other steps recommended? Thanks, Simon

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mri segstats "masksign abs" syntaxis option
by Gonzalo Rojas Costa 15 May '25

15 May '25

External Email - Use Caution Hi: Using "--masksign abs" option: which must be the syntax for "--maskthresh" option in mri_segstats command? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University Santiago Chile

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Question on Samseg Basic and Samseg for MS lesions
by Stefano Cerri 15 May '25

15 May '25

External Email - Use Caution Hi Arianna, 1) Yes. Please note that the method was tuned and mostly tested on MS patients. 2) These two versions of SAMSEG model WMH/ WM lesions differently and cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here <https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre…>). 3) Yes. Note that SWI data might not add valuable information to the lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data. Stefano Sent on behalf of Arianna Menardi: ---- Dear Experts, I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions. I am new to the approach so I have 3 main questions: 1. Can I use Samseg for MS lesions even if my patients present WM lesions but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images? Thank you for your help, Arianna The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Kb8pmdPdKdYdZdQofh1Zs9Y9vJBM9d8tTBbuN-azPwq2U… <https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELl…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011
by Payam Sadeghi Shabestari 15 May '25

15 May '25

External Email - Use Caution Hi FS team, I'm trying to obtain anatomical statistics for the regions defined in the Choi 2012 and Buckner 2011 parcellations, but I couldn't figure out how to get stats on them. I already did: for mask_option in "${mask_options[@]}"; do mri_vol2vol --mov $SUBJECTS_DIR/$subject_id/mri/norm.mgz \ --s $subject_id \ --targ $SUBJECTS_DIR/MNI152/buckner_atlas/17_network_${mask_option}_mask.nii.gz \ --m3z $SUBJECTS_DIR/MNI152/mri/transforms/talairach.m3z \ --noDefM3zPath \ --o $SUBJECTS_DIR/$subject_id/mri/cerebellum_17_network_${mask_option}_mask.nii.gz \ --inv-morph \ --interp nearest Thank you and best regards, Payam

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