[Freesurfer] Measure statistics from manually segmented cortical GM
External Email - Use Caution Dear Freesurfer Team, My name is K Eswar, and I am reaching out to seek assistance regarding a project I am currently working on. I have manually segmented the cortical gray matter of a fetal brain MRI (nii.gz and stl formats) and now need to perform various analyses such as measuring curvature, volume, area, and thickness. As I am relatively new to using FreeSurfer, I am seeking guidance on how to effectively utilize the software for these analyses. Could you please provide me with some guidance or resources on how to proceed with this task using FreeSurfer? Any assistance or advice you could offer would be greatly appreciated. Thank you very much for your time and assistance. I look forward to hearing back from you soon. Kind regards K Eswar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
[Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis
External Email - Use Caution Dear FS community I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. I have recently come across a paper on MRI segmentation using a function called- samseg. From the webpage( https://secure-web.cisco.com/1AJdw_iZ93Ctl2bXUM-tS9sQoJ_9a6-0RHBNEGqz7c8Pz8GSVQSAS9NvPicCtOfOlcCk2usfSQaphR2x5O9OtMVeO3byxBTtWanL1Lo6pkUBbO7WBqlr0s2GXTavc8OsJmxaGyjxPXbpYGjyC-R9lbgqfpPqvPSFBqUm2C1CcpmZtpG68WfRTj09GXjjGFDeJvf9e1rMz7DTEq_IjhzeX_ueSNnY8PVK6WlzPVLcJT-wzuUaplRF9gMRJevnnNwDO9_ahhh74NOapQ6VO_0eaM8Vbsa9FN4_n6ghVPXg-ptwtkfgZtPfaTd8CDM1lEKjcGz9EsuNtBKF8XpvLnJQS3g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FExvivoRecon) I realized that there is a different approach altogether to processing these fixative brains. However, as a first step, when I tried the samseg function, I noticed that the function exited with errors. The steps where it fails are: Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Killed I am using the Ubuntu 22.04 version with RAM 32GB Freesurver version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 I would greatly appreciate it if you could help me with MRI segmentation and cortical surface analysis on these brains. Thanks for your time and consideration. Regards K Eswar Project Scientist Sudha Gopalakrishnan Brain Centre IIT Madras, India ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mri_synth functions errors
External Email - Use Caution Dear Yujing It worked. Thank you so much for your time Regards K Eswar On Tue, Oct 10, 2023 at 7:48 PM Huang, Yujing wrote: > External Email - Use Caution > > Can you try to source your Freesurfer environment? > > > > For tcsh or csh, > > setenv FREESURFER_HOME /freesurfer > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > > > For bash, > > export FREESURFER_HOME=/freesurfer > > source $FREESURFER_HOME/SetUpFreeSurfer.sh > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *K Eswar > *Sent:* Monday, October 9, 2023 1:59 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] mri_synth functions errors > > > > *External Email - Use Caution* > > Hello Freesurfer Developers, > > > > I am attempting to process mri_synthseg,mri_synthsr,mri_synthstrip and it > shows the following error > > > > For mri_synthseg and mri_synthsr: > > Traceback (most recent call last): > File "/home/sgbc/freesurfer/python/scripts/mri_synthseg", line 10, in > > import surfa as sf > ModuleNotFoundError: No module named 'surfa' > > > > For mri_synthstrip > > Traceback (most recent call last): > File "/home/sgbc/freesurfer/python/scripts/mri_synthstrip", line 5, in > > import torch > ModuleNotFoundError: No module named 'torch' > > > > I am using linux operating system_Ubuntu 22.04.2 LTS > > > > I have recently installed infant freesurfer and I don't know if the > problem is following to it as I expect path might have been changed > > > > I tried looking for these errors in the forum, however I did not find the > fix. > > > > Thank you for your time and consideration > > > > Kind regards > > K Eswar > > Project scientist > > Sudha Gopalakrishnan Brain Centre > > IIT Madras, India > > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1o3NhQvsyUZN14AJJUYOPPUJZEm-DEbIFlgFLPay6GD988EPgNrH5tsHnoQoHm0LsNgfXpHl2SXR5ca794sBaGaxjHln6pI8v1aJFJwfERshzrPMzjMP2GOm7T7B31Cb7STLuKCfr4v_VvSzGRNjcTVz4n9nLwyHwCR6bGkbHFBJjZ0jfHZDHIDqKx_pJC87wGaqHtjTbTcxkmaA0j62CyMA-K7hcYMXGTG5VavFHS3G-6bTZhAITfF0MD_JsOIelNlHkfE5Du8vpxMsFh5sv1aTinoAGTUXWKVuxsJjKUr9EMBhfpwYGkr96_zIK201g6dSHHBSXz_XoufYn23D1fQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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/1_4WCKJ7ICCWnkoSI-xXque6QvTKszuVpzK2WIpue65TMQsWQjNZ-yZeopjseJRe6IBmgmu8Ir_TgOAUE7CIHU6WBGn0hqCmFfflbW5enB3Tw7dnwVGieNYtiidbnBerxjuochqt-wtU1a6C4H2miqOd26smJO2et8RKooKHGcG5Tha_NC7lWoSfp1Y5ZY0GqDmqyQlw_GuDashDQjCrgyIAVyMaPUx1PwZPSQseyViahmmsH-8hb6VgXtc8MvlzLeuXCTwWSrMsMGkvm8dY_unCi8A6PTA0XB6u8wPBcLZWhf9XNMOxb5HUMaS6eNGOs8MFrYmqrDSQczw0a_bLxkw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1_4WCKJ7ICCWnkoSI-xXque6QvTKszuVpzK2WIpue65TMQsWQjNZ-yZeopjseJRe6IBmgmu8Ir_TgOAUE7CIHU6WBGn0hqCmFfflbW5enB3Tw7dnwVGieNYtiidbnBerxjuochqt-wtU1a6C4H2miqOd26smJO2et8RKooKHGcG5Tha_NC7lWoSfp1Y5ZY0GqDmqyQlw_GuDashDQjCrgyIAVyMaPUx1PwZPSQseyViahmmsH-8hb6VgXtc8MvlzLeuXCTwWSrMsMGkvm8dY_unCi8A6PTA0XB6u8wPBcLZWhf9XNMOxb5HUMaS6eNGOs8MFrYmqrDSQczw0a_bLxkw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mri_synth functions errors
External Email - Use Caution Hello Freesurfer Developers, I am attempting to process mri_synthseg,mri_synthsr,mri_synthstrip and it shows the following error For mri_synthseg and mri_synthsr: Traceback (most recent call last): File "/home/sgbc/freesurfer/python/scripts/mri_synthseg", line 10, in import surfa as sf ModuleNotFoundError: No module named 'surfa' For mri_synthstrip Traceback (most recent call last): File "/home/sgbc/freesurfer/python/scripts/mri_synthstrip", line 5, in import torch ModuleNotFoundError: No module named 'torch' I am using linux operating system_Ubuntu 22.04.2 LTS I have recently installed infant freesurfer and I don't know if the problem is following to it as I expect path might have been changed I tried looking for these errors in the forum, however I did not find the fix. Thank you for your time and consideration Kind regards K Eswar Project scientist Sudha Gopalakrishnan Brain Centre IIT Madras, India ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
