Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

source freesurfer error
by Pedro henrique barradas 29 May '23

29 May '23

External Email - Use Caution Hi everyone! I am trying to run freesurfer on a windows machine using ubuntu but I am having trouble with the source command When I try to source freesurfer i get the following message: source #FREESURFERHOME/SetUpFreeSurfer.sh -bash: source: filename argument required source: usage: source filename [arguments] Thank you very much

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FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer
by Rob Kudyba 26 May '23

26 May '23

External Email - Use Caution In a HPC cluster where freesurfer is loaded ad hoc as a module, running module avail results in the following warning: /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. I don't think ts related but here is my .bashrc file: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then . "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" else export PATH="/path/to/anaconda3-2021.11/bin:$PATH" fi fi unset __conda_setup The modulefile for Freesurfer contains: module-whatis "adds freesurfer to your environment variables" set root /path/to/freesurfer setenv "FREESURFER_HOME" "/path/to/freesurfer" setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects" prepend-path PATH $root/bin if { [ module-info mode load ] } { system "source /path/to/freesurfer/SetUpFreeSurfer.sh" } I see that SetUpFreeSurfer.sh has this: # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh After running module unload freesurfer several directories remain in $PATH: echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO <https://secure-web.cisco.com/1oVSBML06vH3hcXfhl4P1X2gg9xkRWHiWCsxRgOqnwVIMA…> mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?

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Request for pass code
by Juri Kim 26 May '23

26 May '23

External Email - Use Caution Hi, I am writing to ask if I can get the pass code to open the image to open the FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you! Sincerely, Juri Kim.

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Fwd: The results of your email commands
by Rob Kudyba 26 May '23

26 May '23

External Email - Use Caution does this message mean my email was rejected? Also the link to subscrobe on https://secure-web.cisco.com/1C8Ww8WKzb-WR8JygU7XB0JN4vWN1-1IzwWYF8eJpyXmp6… are broken as they should point to the https version, e.g., the link to subscribe http://secure-web.cisco.com/1Rs_mL5ODuvETF1LGNBWxqNLByNtjtuyy843X-XuQN3-Jxn… ---------- Forwarded message --------- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> Date: Fri, May 26, 2023 at 11:25 AM Subject: The results of your email commands To: <rk3199(a)columbia.edu> The results of your email command are provided below. Attached is your original message. - Results: Ignoring non-text/plain MIME parts - Unprocessed: c3RlciB3aGVyZSBGcmVlc3VyZmVyIGlzIGxvYWRlZCBhZCBob2MgYXMgYSBtb2R1bGUuIFJ1bm5p bmcgbW9kdWxlCmF2YWlsIHJlc3VsdHMgaW4gdGhlIGZvbGxvd2luZyB3YXJuaW5nczoKCi9wYXRo L3RvL2FuYWNvbmRhMy0yMDIxLjExL2Jpbi9tcGljYzogbGluZSAyODU6Cng4Nl82NC1jb25kYV9j b3M2LWxpbnV4LWdudS1jYzogY29tbWFuZCBub3QgZm91bmQKIEVSUk9SOiBFbnZpcm9ubWVudCB2 YXJpYWJsZSBGUkVFU1VSRkVSX0hPTUUgbXVzdCBiZSBkZWZpbmVkIHByaW9yIHRvCnNvdXJjaW5n IEZyZWVzdXJmZXIuCi9wYXRoL3RvL2FuYWNvbmRhMy0yMDIxLjExL2Jpbi9tcGljYzogbGluZSAy ODU6Cng4Nl82NC1jb25kYV9jb3M2LWxpbnV4LWdudS1jYzogY29tbWFuZCBub3QgZm91bmQKIEVS Uk9SOiBFbnZpcm9ubWVudCB2YXJpYWJsZSBGUkVFU1VSRkVSX0hPTUUgbXVzdCBiZSBkZWZpbmVk IHByaW9yIHRvCnNvdXJjaW5nIEZyZWVzdXJmZXIuCgpJbiBteSAuYmFzaHJjIGZpbGU6CgogPj4+ IGNvbmRhIGluaXRpYWxpemUgPj4+CgogISEgQ29udGVudHMgd2l0aGluIHRoaXMgYmxvY2sgYXJl IG1hbmFnZWQgYnkgJ2NvbmRhIGluaXQnICEhCgpfX2NvbmRhX3NldHVwPSIkKCcvcGF0aC90by9h bmFjb25kYTMtMjAyMS4xMS9iaW4vY29uZGEnICdzaGVsbC5iYXNoJyAnaG9vaycKMj4gL2Rldi9u dWxsKSIKCmlmIFsgJD8gLWVxIDAgXTsgdGhlbgoKICAgIGV2YWwgIiRfX2NvbmRhX3NldHVwIgoK ZWxzZQoKICAgIGlmIFsgLWYgIi9wYXRoL3RvL2FuYWNvbmRhMy0yMDIxLjExL2V0Yy9wcm9maWxl LmQvY29uZGEuc2giIF07IHRoZW4KCiAgICAgICAgLiAiL3BhdGgvdG8vYW5hY29uZGEzLTIwMjEu MTEvZXRjL3Byb2ZpbGUuZC9jb25kYS5zaCIKCiAgICBlbHNlCgogICAgICAgIGV4cG9ydCBQQVRI PSIvcGF0aC90by9hbmFjb25kYTMtMjAyMS4xMS9iaW46JFBBVEgiCgogICAgZmkKCmZpCgp1bnNl dCBfX2NvbmRhX3NldHVwCgoKVGhlIG1vZHVsZWZpbGUgZm9yIEZyZWVzdXJmZXIgY29udGFpbnM6 Cgptb2R1bGUtd2hhdGlzICJhZGRzIGZyZWVzdXJmZXIgdG8geW91ciBlbnZpcm9ubWVudCB2YXJp YWJsZXMiCgpzZXQgICAgICAgICAgICAgIHJvb3QgICAgICAgICAgL3BhdGgvdG8vZnJlZXN1cmZl cgoKc2V0ZW52ICAgICJGUkVFU1VSRkVSX0hPTUUiICAgICIvcGF0aC90by9mcmVlc3VyZmVyIgoK c2V0ZW52ICAgICJTVUJKRUNUU19ESVIiICAgICAgIi9wYXRoL3RvL2ZyZWVzdXJmZXIvc3ViamVj dHMiCgpwcmVwZW5kLXBhdGggICAgIFBBVEggICAgICAgICAgICAgICAgICRyb290L2JpbgoKaWYg eyBbIG1vZHVsZS1pbmZvIG1vZGUgbG9hZCBdIH0gewoKc3lzdGVtICJzb3VyY2UgL3BhdGgvdG8v - Ignored: ZnJlZXN1cmZlci9TZXRVcEZyZWVTdXJmZXIuc2giCgp9CgoKSSBzZWUgdGhhdCBTZXRVcEZyZWVT dXJmZXIuc2ggaGFzIHRoaXM6CgoKIyBDYWxsIGNvbmZpZ3VyYXRpb24gc2NyaXB0OgoKc291cmNl ICRGUkVFU1VSRkVSX0hPTUUvRnJlZVN1cmZlckVudi5zaAoKCkFmdGVyIHJ1bm5pbmcgbW9kdWxl IHVubG9hZCBmcmVlc3VyZmVyIHNldmVyYWwgZGlyZWN0b3JpZXMgcmVtYWluIGluICRQQVRIOgoK CmVjaG8gJFBBVEgKL3BhdGgvdG8vZnJlZXN1cmZlci9mc2Zhc3QvYmluOi9wYXRoL3RvL2ZyZWVz dXJmZXIvdGt0b29sczovcGF0aC90by9mcmVlc3VyZmVyL21uaS9iaW46L3BhdGgvdG8vZnJlZXN1 cmZlci9mc2Zhc3QvYmluOi9wYXRoL3RvL2ZyZWVzdXJmZXIvdGt0b29sczovcGF0aC90by9mcmVl c3VyZmVyL21uaS9iaW4KCgpTbyAkRlJFRVNVUkZFUl9IT01FIGFuZCAkU1VCSkVDVFNfRElSIGFy ZSBiZWluZyB1bnNldCBidXQgYWxsIG9mIHRoZSBvdGhlcgplbnYgdmFycyBhcmUgbm90LiBJcyB0 aGVyZSBhIHdheSB0byB1bnNldCB0aGUgdmFycyBmcm9tCkZyZWVTdXJmZXJFbnYuc2g/IEEgdGhy ZWFkCm9uIFNPCjxodHRwczovL3NlY3VyZS13ZWIuY2lzY28uY29tLzFyOC1DLWhlMlRkSWpHVUVG dnJpdjBNZUNOWVZPRlVVcW05ekhTTkN2RTg0NEpSZGNEaUgtelRvelMxTUs0WW1MWWJXVzVvd1Ju MV9qRzJwSTdhUkdNTDFWeFo2TXdQeXlYLWw2OFNWczhDTGhfT2dYYk52cXFiYkt4YzZIMndKT3JS MmxGdzg4SjdlMHVISG9oZUNwV3B0V2MxYzZUaDZaQzNXaGVucTFvTDJwMFdGcWVaOFE0RDFmem4x bFZWNFZjR3JKaWZnM21XSkFWajJhT2M5OU1TUjNyVEpfdWFMXzJrR2NmUGI4SXNlOWJ5N0wzY2Nr c21VUW5HcFZxWkxYVU9hMnl4MVFnb2tHYVNRWDA0bkpTZUVibGwxMXEtS1FOd3VYM3FybmsycmJq WlRQYUpzTEotZEhDRkl0Z1ZjNkV5MmVkalcxajFBQklTcmgtTTJJQUEvaHR0cHMlM0ElMkYlMkZz dGFja292ZXJmbG93LmNvbSUyRnF1ZXN0aW9ucyUyRjY5Mjc0MzQ3JTJGb3ZlcndyaXRlLWFuZC1y ZXN0b3JlLWVudmlyb25tZW50LXZhcmlhYmxlcy1pbi1iYXNoLXdpdGgtZW52aXJvbm1lbnQtbW9k dWxlcz4KbWVudGlvbnMgdXNpbmcgdW5zZXRlbnYgYnV0IHBlcmhhcHMgdGhlcmUncyBhbiBlbHNl aWYgdGhhdCBjYW4gYmUgYWRkZWQgdG8KdGhlIG1vZHVsZWZpbGU/Cg== - Done. 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/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7V… < https://secure-web.cisco.com/1Ia6Ud55puWRILt2_mnFiSQklsfT7C9EDW3db8NhTcmq7V…> . 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. ---------- Forwarded message ---------- From: Rob Kudyba <rk3199(a)columbia.edu> To: Freesurfer-request(a)nmr.mgh.harvard.edu Cc: Bcc: Date: Fri, 26 May 2023 11:24:40 -0400 Subject: FS in a HPC cluster via module file: ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer External Email - Use Caution In. HPC cluster where Freesurfer is loaded ad hoc as a module. Running module avail results in the following warnings: /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. /path/to/anaconda3-2021.11/bin/mpicc: line 285: x86_64-conda_cos6-linux-gnu-cc: command not found ERROR: Environment variable FREESURFER_HOME must be defined prior to sourcing Freesurfer. In my .bashrc file: >>> conda initialize >>> !! Contents within this block are managed by 'conda init' !! __conda_setup="$('/path/to/anaconda3-2021.11/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" ]; then . "/path/to/anaconda3-2021.11/etc/profile.d/conda.sh" else export PATH="/path/to/anaconda3-2021.11/bin:$PATH" fi fi unset __conda_setup The modulefile for Freesurfer contains: module-whatis "adds freesurfer to your environment variables" set root /path/to/freesurfer setenv "FREESURFER_HOME" "/path/to/freesurfer" setenv "SUBJECTS_DIR" "/path/to/freesurfer/subjects" prepend-path PATH $root/bin if { [ module-info mode load ] } { system "source /path/to/freesurfer/SetUpFreeSurfer.sh" } I see that SetUpFreeSurfer.sh has this: # Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh After running module unload freesurfer several directories remain in $PATH: echo $PATH /path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin:/path/to/freesurfer/fsfast/bin:/path/to/freesurfer/tktools:/path/to/freesurfer/mni/bin So $FREESURFER_HOME and $SUBJECTS_DIR are being unset but all of the other env vars are not. Is there a way to unset the vars from FreeSurferEnv.sh? A thread on SO <https://secure-web.cisco.com/1r8-C-he2TdIjGUEFvriv0MeCNYVOFUUqm9zHSNCvE844J…> mentions using unsetenv but perhaps there's an elseif that can be added to the modulefile?

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Tracula dpath Missing Files
by Lauren Stephens 25 May '23

25 May '23

External Email - Use Caution Dear Freesurfer Experts, We have been working to run a test data set through tracula and have seemingly had success, however when we ran trac-all -path it completed without error but the files created did not go into a dpath folder. The files that were created went into the dmri and dlabel folders. We are specifically looking for the dpath/merged_avg<nsubj>_<inter>_<intra>.mgz file. We are using Freesurfer 7.3.2 on an iMac Pro running Ventura 13.3.1 in a bash shell. I have attached the dmrirc file. I have also attached the trac-all.log. Thank you for any help you can provide. Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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change ants N4 bias field correction parameter in recon-all pipeline
by 刘梦醒 25 May '23

25 May '23

External Email - Use Caution Hello FreeSurfer Developers, Some T1s we collected have higher intensity in the occipital cortex. The default recon-all failed skull stripping and wm/gm segmentation in that part of the brain. After several tests, we found that doing ants N4 bias field correction with a shrink factor of 1 could fix the problem in most cases. We are aware that the same correction is included in recon-all, while with default parameters. We wonder if there is one way to specify the parameter for the bias correction in recon-all? If not, what would you recommend in this situation? A bias correction before recon-all, and still do another correction inside recon-all? The freesurfer we use is 7.1.1. Thanks! best, Mengxing

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fsl fmri thresh_zstat1.nii file showing in fsaverage pial surface
by Gonzalo Rojas Costa 25 May '23

25 May '23

External Email - Use Caution Hi: I processed an fMRI task using FSL. I got the standard image coregistered result... How can I show the thresh_zstat1.nii file in fsaverage pial surface? Sincerely, Gonzalo Rojas Costa

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conjunction
by Maria Czarnecka 25 May '23

25 May '23

External Email - Use Caution Dear experts, Another question: How do I do conjunction analysis? I have my contrasts on 1lvl, I have the second level, I need a conjunction of two contrasts. I would guess "mergecontrasts-sess", unfortunately, it doesn't seem to work. [image: image.png] Could you help me with that issue? Kind regards, Maria Czarnecka

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fsfast percent signal change
by Maria Czarnecka 25 May '23

25 May '23

External Email - Use Caution Dear experts, I struggle with the functional analysis in Freesurfer. How can I calculate the percent signal change in a specific contrast in an ROI? I will be grateful for your suggestions (especially if you point toward a specific function). Kind regards, Maria Czarnecka

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MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper Submissions
by Vin 25 May '23

25 May '23

External Email - Use Caution Dear Researchers! We are excited to announce that the paper submissions for the #MICCAI Workshop on Machine Learning in Clinical NeuroImaging are now open! This workshop aims to bring together experts from the fields of machine learning and clinical neuroimaging to explore innovative solutions and advancements in this rapidly evolving domain - https://secure-web.cisco.com/153XVXhlclD9QnxOpu0soPhfDZvJxzhlZhJnF7G7lphKNy… If you have been working on cutting-edge research related to machine learning techniques applied to clinical neuroimaging data, we invite you to submit your work for consideration. This is a remarkable opportunity to showcase your expertise and contribute to the advancement of the field. Benefits: - Accepted papers will be presented during the workshop, providing an opportunity for valuable discussions and feedback from experts in the field. - The top 3 papers will receive recognition and prize money of 1.500 USD will be awarded to the authors of these top papers. - Accepted papers will be published in conference proceedings, Springer (MLCN 22 Proceeding: https://secure-web.cisco.com/1sY98crGbyMWOD79iNBAx2CRjs0I14tuhCQ66l3fHKjsh5…) Join us in exploring the frontiers of machine learning in clinical neuroimaging and help shape the future of this exciting field. We encourage you to spread the word among your colleagues and fellow researchers who may be interested. For more information, including the workshop schedule, submission guidelines, and important dates, please visit our workshop website - https://secure-web.cisco.com/153XVXhlclD9QnxOpu0soPhfDZvJxzhlZhJnF7G7lphKNy… . We look forward to your submissions and your presence at the workshop. Best regards, MLCN Organizing Committee

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Freesurfer May 2023