Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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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problem with autorecon-pial
by Yildirim, Irem 18 Feb '25

18 Feb '25

External Email - Use Caution Hello, I am trying to fix the freesurfer results after running recon-all with fmriprep. The problem is in the pial surface, wm, and brain masks because of some inhomogeneity in the 7T MPRAGE data. I am fixing the brain mask following the instructions here: https://secure-web.cisco.com/1yEIcMRf9tPPRvYNsf-fTOA8sAaKck250MhUSiZCJA7LZQ… . After I fix the brain mask, I am trying to run the code for surfaces to be updated based on the updated brain mask with "recon-all -autorecon-pial" command. Every time I tried with different subjects, it updated the surfaces but not in a corrected way. The results for surfaces never really changed, and the mri/brain.mgz file was never even updated. One solution is to run recon-all -all with the options I want for skullstripping but it is time consuming for me and I usually prefer the fmriprep's pipeline for freesurfer. Can you help me find a way to fix this without having to rerun all the analysis? You can find an example log file where you can see the skullstripping with different settings starting on Line 3959 and the calling of autorecon-pial starting on Line 4245. Thank you, Irem FsTutorial/SkullStripFix_freeview - Free Surfer Wiki<https://secure-web.cisco.com/1yEIcMRf9tPPRvYNsf-fTOA8sAaKck250MhUSiZCJA7LZQ…> top | previous. Fixing a bad skull strip. To follow this exercise exactly, be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names. surfer.nmr.mgh.harvard.edu

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hounsfield units based in some aseg.mgz labels
by Gonzalo Rojas Costa 17 Feb '25

17 Feb '25

External Email - Use Caution Hi: I completed the co-registration of CT images to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD Hounsfield units (from corregistered sub-OAS30001_sess-d3132_CT.nii.gz) using aseg.mgz labels (of freesurfered OAS30001_MR_d0757) ? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] ERC_bayesian_segmentation is not shipped in the nightly dev build
by fsbuild 17 Feb '25

17 Feb '25

External Email - Use Caution That set of files is too large to be included in some packages.   Not sure what info you are following about pulling the files from GitHub, but for now you could try, - R. $ cd $FREESURFER_HOME/python/packages/ERC_bayesian_segmentation$ sudo wget https://secure-web.cisco.com/16qOF4aueY_oOax52PDUZUC7cA… wait for download to finish …$ sudo rm -rf  atlas_full  atlas_simplified$ sudo tar zxpf ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz$ sudo rm ERC_bayesian_segmentation/atlas_subdirs_20250217.tgz On Feb 17, 2025, at 11:27, Chourrout, Matthieu <m.chourrout(a)ucl.ac.uk> wrote:        External Email - Use Caution        Hi all, I was trying to run the dev version of FreeSurfer from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gGb7gF2nKiypt4FLjrahIBuWyn147VH1mU3Ia… the content from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://github.com/freesurfer/freesurfer/tree/dev/mri_histo_util/ERC_baye… not present in ${FREESURFER_HOME}/python/packages/ As instructed, I've put atlas_full/ and atlas_simplified/ inside ${FREESURFER_HOME}/python/packages/ERC_bayesian_segmentation/ when trying to run mri_histo_atlas_segment_fireants but had to manually create the subdir. can't open file '/share/apps/freesurfer-dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory Can the files from ERC_bayesian_segmentation/ in GitHub be manually pulled out into this directory? Which files are required? Best regards, Dr Matthieu Chourrout Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural CircuitsUCL Mechanical EngineeringMaterials, Structure and Manufacturing at Harwell (MSMaH)Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JEBloomsbury Campus, University College London_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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hounsfield units for some aseg.mgz labels
by Gonzalo Rojas Costa 17 Feb '25

17 Feb '25

External Email - Use Caution Hi: I completed the co-registration of CT to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD hounsfield units of some aseg.mgz labels? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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ERC_bayesian_segmentation is not shipped in the nightly dev build
by Chourrout, Matthieu 17 Feb '25

17 Feb '25

External Email - Use Caution Hi all, I was trying to run the dev version of FreeSurfer from https://secure-web.cisco.com/1WtBzDJVBe2-2xc-ZyLSEcxaAxh0X5-CzPpHRJlz_acv5L… but the content from https://secure-web.cisco.com/1MMHkQC0FfiJGDyWJmsuvvc_IYxIL5eyKAe0D4iNTL8uZ9… is not present in ${FREESURFER_HOME}/python/packages/ As instructed, I've put atlas_full/ and atlas_simplified/ inside ${FREESURFER_HOME}/python/packages/ERC_bayesian_segmentation/ when trying to run mri_histo_atlas_segment_fireants but had to manually create the subdir. can't open file '/share/apps/freesurfer-dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py': [Errno 2] No such file or directory Can the files from ERC_bayesian_segmentation/ in GitHub be manually pulled out into this directory? Which files are required? Best regards, Dr Matthieu Chourrout [orcid logo 16px] <https://secure-web.cisco.com/1-n5OFLL4s4yFn7XM1MH7qpzWv10xwrOxrYPwOpqLI0AgP…> Research Fellow on Correlative X-ray Imaging for the Large-scale Imaging of Neural Circuits UCL Mechanical Engineering<https://secure-web.cisco.com/10kRa1voAealTFL-mjMLpqi2JdO0FO-HEtTDRw-L3blsf8…> Materials, Structure and Manufacturing at Harwell (MSMaH)<https://secure-web.cisco.com/1xdgUA8Zer-mG8V0D7hnqtYAAE7M6hmti3ln6qu7pf_60k….> Rm 4.17 Malet Place Eng. Building, Torrington Place, London, WC1E 7JE Bloomsbury Campus, University College London

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Re: [Freesurfer] recon-all failed
by fsbuild 16 Feb '25

16 Feb '25

External Email - Use Caution  You can read from but not write to where freesurfer is installed under /usr/local/freesurfer as your normal userid.   Just change the setting of SUBJECTS_DIR to be, e.g., in your home directory or some location you can always write to as your normal userid.  It’s a good idea not to modify the distribution installed under /usr/local/freesurfer.  To change to your home directory, … setup the freesurfer environment which by default sets SUBJECTS_DIR to be under /usr/local/freesurfer ....$ cd $HOME… or …$ cd$ mkdir subjects$ cd subjects… copy in you subject data …$ export SUBJECTS_DIR=$HOME/subjects…. then re-run your command(s) ... - R. On Feb 15, 2025, at 12:52, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:        External Email - Use Caution        hi everyone,i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine.now i am trying to run my first recon-all, but this is the error I get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ recon-all -subject angcher.02.04.91.12.09.22 -sd /usr/local/freesurfer/7.4.1/subjects  -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511174521774361.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511942168418847.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511945768618951.dcm -all  mkdir: cannot create directory '/usr/local/freesurfer/7.4.1/subjects/angcher.02.04.91.12.09.22': Permission denied fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn ERROR: cannot find angcher.02.04.91.12.09.22 recon-all: version check failed fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn how could i solve this problem?thanks in advance _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1QY3rGdqJouwjNSkdy2O1DaMbRHvOVLBCmyyP7lydP63wt…

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recon-all failed
by Paola Di Filippo 15 Feb '25

15 Feb '25

External Email - Use Caution hi everyone, i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine. now i am trying to run my first recon-all, but this is the error I get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ recon-all -subject angcher.02.04.91.12.09.22 -sd /usr/local/freesurfer/7.4.1/subjects -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511174521774361.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511942168418847.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511945768618951.dcm -all mkdir: cannot create directory '/usr/local/freesurfer/7.4.1/subjects/angcher.02.04.91.12.09.22': Permission denied fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn ERROR: cannot find angcher.02.04.91.12.09.22 recon-all: version check failed fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn how could i solve this problem? thanks in advance --

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Unusual Cortical Thickness Measurements in Specific Regions
by hmarzban＠student.ubc.ca 14 Feb '25

14 Feb '25

External Email - Use Caution Hello developers I am encountering unexpected cortical thickness values in the following regions: lh_G_Ins_lg_and_S_cent_ins_thickness lh_S_intrapariet_and_P_trans_thickness lh_S_oc_middle_and_Lunatus_thickness lh_S_oc-temp_med_and_Lingual_thickness lh_S_oc_sup_and_transversal_thickness Upon calculating the means for these regions, I observed significant differences compared to my control group. However, I am uncertain whether these discrepancies are attributable to the illness under study or to potential segmentation errors. I am seeking advice on steps or considerations to address this issue. Can you provide insights into potential causes and solutions? Thank you for your assistance. Regards Hengameh

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Amygdala nuclei atlas
by Krista Wahlstrom 14 Feb '25

14 Feb '25

External Email - Use Caution Good morning, Freesurfer team! I'm interested in using the amygdala atlas created by Saygin ZM & Kliemann D et al., 2017 (High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas). I understand this atlas is integrated into the Freesurfer software; however our research team uses an alternative software for human brain imaging processing. I'm wondering if it's possible to gain access to the code for your segmentation of the amygdala so we can implement this atlas into our own imaging processing pipeline. I wasn't able to find the amygdala atlas code on the Freesurfer GitHub, but it's possible I wasn't looking in the correct repository. Any help would be much appreciated! Thanks, Krista **************************************** Krista Wahlstrom, Ph.D. University of Utah Department of Psychology Cognition & Neural Science | CNS Postdoctoral Research Associate INMAN Laboratory<https://secure-web.cisco.com/1j4sHQVeR_3rCIIA29tFpHoNp8Sc-LeT178BzyiKrItw-c…> [cid:120e0f87-08bb-457c-aa0d-d302467fcd28] [cid:a613c0be-3f3e-45da-96b4-05a0c1cf72cb]

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