External Email - Use Caution Hi Lilla,
and is there a reason why ? I mean are these regions (labels) not detectable in the infants or did you just not include them ? Since the adult freesurfer pipeline could segment them I am wondering why they are not labeled in the infant atlas… Yours Frank ---------------- adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: frank.zoell...@medma.uni-heidelberg.de<mailto:frank.zoell...@medma.uni-heidelberg.de> Web: https://secure-web.cisco.com/1RqQnv7kxvO9_w5Srsw77gD-ZtwN2XNsKEWYAXYh8x70-333ftNPvVUWcsAOtTEsrGagJ_83isR_4MTegJ2X6Kfj-IcBySpyk280wyPai7Niv5XnSyfWCoJEsJymIkcwRKv3-rUT0K2Hr21teSY0DgFMEXcGvWhZaRibNTeOnxeyduhFOuoUMopwgs83BBQ5pR_CqIIacNe8p9TmDmjoSGC14In3Cu7XLVGV9tN7qg7XML4loywQgATD6zZYKbpqKz8SmORsV6itXQZeN2D-xpZzDxAcTw2gg5FMJjxw7k6F2GQx5tpl0_EdNM0aoU6ZdmbLI6vrVRVZ7Duw4f1ZLpQ/https%3A%2F%2Fwww.umm.uni-heidelberg.de%2Fmiism%2Fcomputer-assisted-clinical-medicine%2F Von: <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von "Zollei, Lilla,Ph.D." <lzol...@mgh.harvard.edu> Antworten an: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Datum: Donnerstag, 24. Oktober 2024 um 03:59 An: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] infantFS: expected outputs Dear Frank, You are correct. The list of segmentation labels is not 100% the same. For the infantFS segmentation labels you can refer to Table 1 in https://secure-web.cisco.com/1vWMGdCD3mZXs2SmPbxmXci6igleKzDLTd49jV-LXb9OvpO3PWHpHxIQ7902fDIxqLNii6Ea3nBWyvAg-2fBHU0A4N58PFGH6PTBOJahsyRml9Tv7EkAhiRZXMXIsQok9IwFG-EVEhx1WGLne53gqNTsJgFOkKEgbA1FWFZ2Tis4cTGr7cVM9Nwen0J9DpIRT5EKVyYTpe86pdtsZd3LwVdHj1jaXj91nZJWRsoowMTkvh6qYwkySjdWutbKjhnKOZb_tlIYIpbqR_T26jq9F10xf7fZQEfUdzRvryzoprUM8djaNviMRe2o0I3VBuQEIP7ApEzUJsktR62pVQ_-Htw/https%3A%2F%2Fpmc.ncbi.nlm.nih.gov%2Farticles%2FPMC7415702%2F Best, Lilla ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zoellner, Frank <frank.zoell...@medma.uni-heidelberg.de> Sent: Monday, September 23, 2024 4:31 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear Lilla, Besides the differences in the files, when looking at the segmentations we wondered why there are some labels zero in the aseg stats file. These are : Left-Inf-Lat-Vent CSF Right-Inf-Lat-Vent Brain-Stem Left-vessel Left-choroid-plexus Right-vessel Right-choroid-plexus 5th ventrikel WM-hypointensities We also did a cross check and had run the same subject with the normal freesurfer pipeline and here there have been segmentations for the above structures. Maybe you have an idea what is happening here ? or are these not included in the atlas? Thanks in advance Yours Frank ----------- adjunct Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent System in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Phone: +49 (0)621 3835121 Fax: +49 (0)621 3835123 Email: frank.zoell...@medma.uni-heidelberg.de<mailto:frank.zoell...@medma.uni-heidelberg.de> Web: https://secure-web.cisco.com/1RqQnv7kxvO9_w5Srsw77gD-ZtwN2XNsKEWYAXYh8x70-333ftNPvVUWcsAOtTEsrGagJ_83isR_4MTegJ2X6Kfj-IcBySpyk280wyPai7Niv5XnSyfWCoJEsJymIkcwRKv3-rUT0K2Hr21teSY0DgFMEXcGvWhZaRibNTeOnxeyduhFOuoUMopwgs83BBQ5pR_CqIIacNe8p9TmDmjoSGC14In3Cu7XLVGV9tN7qg7XML4loywQgATD6zZYKbpqKz8SmORsV6itXQZeN2D-xpZzDxAcTw2gg5FMJjxw7k6F2GQx5tpl0_EdNM0aoU6ZdmbLI6vrVRVZ7Duw4f1ZLpQ/https%3A%2F%2Fwww.umm.uni-heidelberg.de%2Fmiism%2Fcomputer-assisted-clinical-medicine%2F Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Zollei, Lilla,Ph.D. Gesendet: Sonntag, 22. September 2024 16:12 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs Hi Marlene, This is correct. Even though infant_recon_all is trying to mimic the output folder structure and follows the FreeSrufer naming convention, it does not generate all of the files that the adult version does. Lilla ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Marlene Staginnus <ms2...@bath.ac.uk<mailto:ms2...@bath.ac.uk>> Sent: Monday, September 16, 2024 9:57 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] infantFS: expected outputs External Email - Use Caution Dear FreeSurfer Team, Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://secure-web.cisco.com/1mA29bmjZg8MZLmt_5OWSzYbAcnPRT4qfP6KTFLCwUY69AAk14nzzR4mQXFFauyLEgAAKu6XqvrbLnDPHDS2M27R_IpwK7YdeBueCVeFKnZIa-OK88PNybtZAt4Os97_joXKnpilISTfl0dKHF8ZhC-E04ru1zoEi6pIokRFi39VR5VQfxkZmnywyNfoqUoPr_kdsQWUh4c-uEX88vKW0OyLcOlOunC8-tWuBIzFvDE-2tSLyorwRYtaUfBtBz26tXCmKmPJqsXj6CIue-fCElKpO0idSlx3TZ5vJuWuyb1FuIs4RCIWPJXEU08Al803p-lGHtuctAlBAYeLOMe6LMw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllOutputFiles) for the adult pipeline? I am asking as after testing the pipeline using the example participant provided on openneuro (https://secure-web.cisco.com/1eG9UEoGKfhMXUoWW953Ozv01X5SscPRanNwg37dq-iV0qiGfMJtdAWxL5nAP5c2o0nO72Wk9LdCMA2ArqcCWcdzDwrqmnZC8mqaXu9DnWJ2Oa6xY7iDxAzT6eLCSwao0JMLl3SjamvtgkinK5_UeSbBWJ2m9lUgL1R-jGyLsbIhx5OTa5Gnt-lrRkhfp9yiQ9opQM8lT-z2tgTr6lrbg1kCuBfdzeQsIrhKl5jsFJEyOlhHzD-SkND_cMxc6WVmHvlbIk-SR2-rP6tPuub6dLnzL4FpIq_WpmhoPtMpOMwf8zFwEMI0HUysriDAGV-oQ/https%3A%2F%2Fopenneuro.org%2Fdatasets%2Fds004776%2Fversions%2F1.0.0, I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf. Is this correct or might there be something going wrong on my end? 1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499 2) Platform: CentOS release 7 3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux 4) infant_recon_all log: see attached Thank you in advance! Best wishes, Marlene
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