Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

pass code for FreeSurfer virtual machine
by Rana Ghamari 22 Jun '23

22 Jun '23

External Email - Use Caution Dear Freesurfer help team This is Rana Ghamari and I have just downloaded Ubuntu compressed image with the FreeSurfer. Would you mind giving me a pass code to open the zipped file? Best regards Rana

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sending email to post to FreeSurfer mailing list
by Rana Ghamari 22 Jun '23

22 Jun '23

External Email - Use Caution ghamarirana(a)gmail.com

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GM Threshold too low
by Michael Mc Laughlin 21 Jun '23

21 Jun '23

External Email - Use Caution How can I set the threshold used for Gray matter? I have a T1 mprage scan and a large amount of gray matter is clearly not being included (see attached). There is a lot of help on setting the GM/WM threshold but I can't find anything about setting the GM/CSF threshold. [image: image.png]

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Re: [Freesurfer] Freesurfer binary for Centos 9
by fsbuild 21 Jun '23

21 Jun '23

External Email - Use Caution I would suggest someone try installing the CentOS8 RPM file and if that succeeds, then you could try running freesurfer.   However, freesurfer has not been tested running on “CentOS9 stream” or the current RHEL 9 release and I would not expect it to build natively there.   We are looking at what OS’s should be supported and will consider your request. - R. On Jun 21, 2023, at 05:05, Knut J Bjuland <knutjorgen(a)outlook.com> wrote:        External Email - Use Caution        Dear Freesurfer surfer experts,Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1?Best regards, Knut Jørgen Bjuland _______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Vbox password
by neda_afzalian 21 Jun '23

21 Jun '23

External Email - Use Caution Would you please send me the unzip pass for freesurfer again? The last one did not work

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Inconsistent number of ROIs in ?.aparc.DKTatlas.stats
by Karoui, Hajer 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivity matrices across subjects (various numbers of ROIs {27, 28, 29, 30, 31,32}. For all subjects from other cohorts, patients and controls, it was 31 ROIs). I tried inspecting which ROIs usually cause this difference between the two hemispheres, it differs from subject to subject, but here is a comprehensive list of all the problematic ROIs that came up. Please not this is a cohort of healthy controls this issue is coming up for. I ran this on a set of patients with Multiple Sclerosis, and I got a consistent number of 31 ROIs. {'insula', 'parahippocampal', 'caudalmiddlefrontal', 'parsorbitalis', 'paracentral', 'transversetemporal', 'parsopercularis', 'superiortemporal', 'postcentral', 'isthmuscingulate', 'inferiortemporal', 'superiorparietal', 'parstriangularis', 'middletemporal', 'rostralanteriorcingulate', 'lateraloccipital', 'entorhinal', 'posteriorcingulate', 'lingual', 'pericalcarine', 'inferiorparietal', 'precentral', 'cuneus', 'fusiform', 'lateralorbitofrontal', 'caudalanteriorcingulate', 'superiorfrontal', 'medialorbitofrontal', 'precuneus', 'supramarginal', 'temporalpole', 'rostralmiddlefrontal'} Any idea what this might be due to? This is quite a big issue for our pipeline so any help would be appreciated. Thanks, and looking forward to your response. Hajer Karoui Data Manager & Researcher | MS & PD Tissue Bank Imperial College London Department of Brain Sciences LinkedIn<https://secure-web.cisco.com/1OeYrjhIt9Fk085_UN6qcwoS-MNLucvE34f-51vAnmxH5x…> [cid:4345924b-28e1-4b07-947d-e7b515fc02ea]

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Inconsistent number of ROIs in ?.aparc.DKTatlas.stats
by Karoui, Hajer 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I hope my email finds you well. I am running into a major issue when I run recon-all -all on the OASIS1 cohort. I am getting an inconsistent number of ROIs for the same subject between the lh and rh, resulting in different sizes of connectivity matrices across subjects (various numbers of ROIs {27, 28, 29, 30, 31,32}. For all subjects from other cohorts, patients and controls, it was 31 ROIs). Please find below a quick example, subject OAS1_0384 is fine, whereas OAS1_0167 and OAS1_0159 are not. [cid:ab6e09d5-0731-49fd-8841-b7f1c6c698e8] I tried inspecting which ROIs usually cause this difference between the two hemispheres, it differs from subject to subject, but here is a comprehensive list of all the problematic ROIs that came up. Please not this is a cohort of healthy controls this issue is coming up for. I ran this on a set of patients with Multiple Sclerosis, and I got a consistent number of 31 ROIs. {'insula', 'parahippocampal', 'caudalmiddlefrontal', 'parsorbitalis', 'paracentral', 'transversetemporal', 'parsopercularis', 'superiortemporal', 'postcentral', 'isthmuscingulate', 'inferiortemporal', 'superiorparietal', 'parstriangularis', 'middletemporal', 'rostralanteriorcingulate', 'lateraloccipital', 'entorhinal', 'posteriorcingulate', 'lingual', 'pericalcarine', 'inferiorparietal', 'precentral', 'cuneus', 'fusiform', 'lateralorbitofrontal', 'caudalanteriorcingulate', 'superiorfrontal', 'medialorbitofrontal', 'precuneus', 'supramarginal', 'temporalpole', 'rostralmiddlefrontal'} I attached a few examples. Any idea what this might be due to? This is quite a big issue for our pipeline so any help would be appreciated. Thanks, and looking forward to your response. Hajer Karoui Data Manager & Researcher | MS & PD Tissue Bank Imperial College London Department of Brain Sciences LinkedIn<https://secure-web.cisco.com/1JO7xNCIyxfajee8Ev2WuUyu6FQChzXcn1tXpNtESmlpj8…> [cid:5bdd6a0d-136c-4240-862a-c9df55fc7797]

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request for password
by Yifei Fan 21 Jun '23

21 Jun '23

External Email - Use Caution Dear freesurfer, I'm a medical physics student at the University of Manchester, I just downloaded the FS_7_2_0_ubuntu_18_04_06.ova.7z on my mac computer. please send me a password. Best, Yifei

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Pass code Request
by Freya Bowden 21 Jun '23

21 Jun '23

External Email - Use Caution Hello, I am installing Freesurfer on a Windows 10 device and I have been asked for a passcode to open the 7z file. Please can I request this? Thank you, Freya

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Freesurfer binary for Centos 9
by Knut J Bjuland 21 Jun '23

21 Jun '23

External Email - Use Caution Dear Freesurfer surfer experts, Will Freesurfer surfer be built for Centos 9 as the cluster I am using has now been upgraded to Centos 9? Is there a source package for Freesurfer 7.4.1? Best regards, Knut Jørgen Bjuland

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Freesurfer June 2023