Freesurfer February 2025

freesurfer@nmr.mgh.harvard.edu

48 participants
82 discussions

Question regarding high Disk IO during Local Gyrification Index calculations,
by Ha, Sung Min 22 Feb '25

22 Feb '25

External Email - Use Caution Hello, I am running (recon-all -localGI) command on around ~250 subjects concurrently right now on high performance computing cluster running SLURM using FreeSurfer 6.0. These subjects already have recon-all finished and I am running recon-all -localGI to additionally calculate LGI values per subject. The cluster manager got back to me stating that these jobs are causing massive amount of IOPs on the storage to the point of slowing down the entire cluster to unusable state. Is this expected behavior with LGI calculation? Is there any flag I can pass to recon-all to reduce the intermediate files being written and read during the calculations? Any help or advice would be greatly appreciated. Sincerely, Sung

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Hippocampus and amygdala segmentation
by Miguel Ángel Rivas Fernández 21 Feb '25

21 Feb '25

External Email - Use Caution Dear Eugenio, My name is Miguel. I am currently processing data of the ABCD Study using FreeSurfer. In our pipeline, we also include the specific FreeSurfer segmentations for the hippocampus and amygdala. As an additional step, we would like to use these segmentations as masks. However, I see that FreeSurfer exports several files, and I am not entirely sure which one I should use. From what I read on the wiki, the files with the suffix *FSvoxelSpace.mgz* are the segmentations that are in the same voxel space as the other FreeSurfer volumes, although it is noted that these segmentations are somewhat rougher. However, I see that there are several files with that name. For example, for the hippocampus segmentation in both hemispheres, we have: - *CA.FSvoxelSpace* - *FS60.FSvoxelSpace* - *FSvoxelSpace.mgz* - *HBT.FSvoxelSpace.mgz* I would like to have an image that contains all hippocampus and amygdala segmentations in a single image. In that case, which file should I use? Perhaps *FSvoxelSpace.mgz*? Another question arises, not only for the hippocampus segmentation but also for other segmentations. Is there a list on the FreeSurfer wiki that shows which region corresponds to each value in the segmentations? For example, in the file *lh.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz*, the value 2000 corresponds to structure X. I am also interested in this labeling for the thalamus and brainstem segmentations (for the hypothalamus, I see that they are listed in a table on the website: [ https://secure-web.cisco.com/1Ri4u8JcCgMmT8lkhPiOD8Jt189NZVInJMJiY327a8k4d2… ). Thank you very much! Miguel

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Re: [Freesurfer] *** buffer overflow detected ***
by fsbuild 21 Feb '25

21 Feb '25

External Email - Use Caution  Please list: > version of freersurfer you are running> OS name and version you are running> amount of RAM on your machine - R. On Feb 20, 2025, at 05:58, Brunno M. de Campos <brunno(a)unicamp.br> wrote:        External Email - Use Caution        Dear all,I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long).In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6".1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case.2 - If this is indeed the issue, do you know the peak memory required for such a process?Thank you!Brunno M Campos University of Campinas _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1YUhZcLLpg4GoPqDFoZq91udJaMJb659sWfNv6Mp1j4MmR…

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Re: [Freesurfer] Unable to download version 8.0.0
by fsbuild 20 Feb '25

20 Feb '25

External Email - Use Caution  The web pages are being updated in advance of the release, but the download links won’t go live until sometime after 8.0.0 has been officially announced on the mailing list. - R. On Feb 20, 2025, at 07:11, Ziming Cui-MSBA23A <zimingc3(a)uci.edu> wrote:        External Email - Use Caution        Hello all,  I'm trying to download version 8..0.0 of the “macOS X darwin_arm64 (64b) PKG installer”, but it says “Not Found” no matter what I try. Is there anything I can do? Best,By Ziming Cui_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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volumes and surfaces misalignment in freeview
by Paola Di Filippo 20 Feb '25

20 Feb '25

External Email - Use Caution Hi again everyone. I am using freesurfer 7.4.1. on ubuntu 22 with a virtual machine. I performed my first recon-all, without hard failures as the .log ended with "recon-all completed with no errors". Then, I have tried to launch freeview to visualize both volumes and surfaces for my subject, with the following command: freeview -v angcher.02.04.91.12.09.22/mri/T1.mgz angcher.02.04.91.12.09.22/mri/wm.mgz angcher.02.04.91.12.09.22/mri/brainmask.mgz angcher.02.04.91.12.09.22/mri/aseg.mgz:colormap=lut:opacity=0.2 -f angcher.02.04.91.12.09.22/surf/lh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/lh.pial:edgecolor=red angcher.02.04.91.12.09.22/surf/rh.white:edgecolor=blue angcher.02.04.91.12.09.22/surf/rh.pial:edgecolor=red but in freeview, surfaces are completely misaligned with volumes. This is an image to give you an idea of the problem (sorry for the quality, i'm controlling the computer on which i work remotely from home): [image: image.png] this is what i see in the terminal after launching the command: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info when i first tried freeview after downloading the program, i had the same problem with bert; when i launch this command: freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red this is what I get: [image: image.png] again, this is what I see in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info The only time when i didn't experience this problem is after downloading tutorial data and trying this command: freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz good_output/mri/brainmask.mgz good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 -f good_output/surf/lh.white:edgecolor=blue good_output/surf/lh.pial:edgecolor=red good_output/surf/rh.white:edgecolor=blue good_output/surf/rh.pial:edgecolor=red that gave me this outoput in freeview: [image: image.png] but still I get this in the terminal: Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info Warning: MatrixInverse failed. Did not find any volume info. any ideas on how could I fix this problem? many thanks in advance. --

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Unable to download version 8.0.0
by Ziming Cui-MSBA23A 20 Feb '25

20 Feb '25

External Email - Use Caution Hello all, I'm trying to download version 8.0.0 of the “macOS X darwin_arm64 (64b) PKG installer”, but it says “Not Found” no matter what I try. Is there anything I can do? Best, By Ziming Cui

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*** buffer overflow detected ***
by Brunno M. de Campos 20 Feb '25

20 Feb '25

External Email - Use Caution Dear all, I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long). In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6". 1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case. 2 - If this is indeed the issue, do you know the peak memory required for such a process? Thank you! Brunno M Campos University of Campinas

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Clarification on co-registration using bbregister
by Gabriella Monopoli 20 Feb '25

20 Feb '25

External Email - Use Caution Dears, I'm Gabriella, a PhD student in Neuroscience and Imaging. I am currently working on coregistering anatomical scans with DTI scans (FA and MD maps) using bbregister. However, there are some details in the pipeline that I find unclear. First, is it correct to use the DTI scan file directly as the --mov input? I came across discussions in the mailing list mentioning an intermediate step involving the lowb volume—specifically, performing bbregister first with the anatomical scans and the lowb volume, and then using mri_vol2vol to apply the registration matrix to the DTI map. I am unsure whether this step is always necessary or if it should only be performed when the direct coregistration (bbregister between the anatomical scan and the DTI map) is inaccurate. Additionally, regarding the initial registration parameter (--init-coreg), what criteria should be used to decide between the default option and alternatives such as --init-fsl? Thank you in advance for your time and assistance. I look forward to your response. Best regards, Gabriella

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Inquiry Regarding FreeSurfer Usage in Clinical Trials
by Yeh Shang Ming 19 Feb '25

19 Feb '25

External Email - Use Caution Dear Sir/Madam, My name is Shang-Ming (Tony) Yeh, and I work at an imaging CRO based in Japan. We are currently using FreeSurfer version 6.0.0 and are considering its use in a potential project. To support our evaluation, we would appreciate your insights on the following: 1. Clinical Trial Usage: - Has FreeSurfer been utilized in any clinical trials? - If so, have any of these trials been submitted for regulatory approval? 2. Comparative Studies: - Are there any publications that compare FreeSurfer with other similar software? If you have any relevant information or publications, we would greatly appreciate it if you could share them with us. Thank you for your time and support. We look forward to your response. Sincerely, Shang-Ming (Tony) Yeh

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CSF Volume difference between recon-all-clinical and SAMSEG
by Taghizadeh Mortezaei, Nima 18 Feb '25

18 Feb '25

Dear FreeSurfer Developers, I seek clarification regarding a discrepancy in cerebrospinal fluid (CSF) volume measurements obtained using different FreeSurfer tools. In my analysis, I measured CSF volume using both recon-all-clinical.sh and SAMSEG for the same subject. However, the results were significantly different: recon-all-clinical: 236,073.36 mm³ (~236 mL) SAMSEG: 471,854.76 mm³ (~472 mL) Additionally, I conducted SAMSEG on 10 neurologically healthy subjects, and in all cases, the CSF volume was at least twice the normal average CSF volume (~150 mL) reported in the literature. I would appreciate any insights into the following questions: Why is there such a large discrepancy between the two methods? Which method provides a more reliable estimate of total CSF volume? Why are the estimated CSF volumes significantly higher than the known physiological average? Thank you for your time and assistance! Best regards, Nima

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Freesurfer February 2025