Freesurfer December 2024

freesurfer@nmr.mgh.harvard.edu

45 participants
62 discussions

Help
by Katherine Sawyer 20 Dec '24

20 Dec '24

External Email - Use Caution Hello, When trying to run recon-all I keep getting the following error message: mri_convert: Command not found. ERROR: Executable 'mri_convert -all-info failed! Is it missing from the distribution?' I just wondered what would be causing it and how to fix it? When running initially, I got the error mris_fix_topology: Command not found. My IT department, deleted and reinstalled FreeSurfer and now I am getting the mri_convert error instead. They deleted 7.4.1 and installed 7.4.0 and this issue is now occurring. The commands seem to be missing from the FreeSurfer bin folder for some reason? I am wondering what could be the cause and solution – or if I’m doing something incorrectly. I imagine it is a local problem for me rather than a wider issue. Thank you. Best wishes, Katherine Sawyer

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help
by 黄月虹 20 Dec '24

20 Dec '24

External Email - Use Caution > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2024-12-20 20:43:35 (星期五) > 收件人: huangyuehong(a)stu.hznu.edu.cn > 主题: Welcome to the "Freesurfer" mailing list (Digest mode) > > Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! > > To post to this list, send your email to: > > freesurfer(a)nmr.mgh.harvard.edu > > General information about the mailing list is at: > > https://secure-web.cisco.com/1swppzx-gPFP5tp-8ifqBZJJEUBqvLwkRhk8kiEa60foCl… > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://secure-web.cisco.com/1bcCMKQylUb-M5LSlt1J5Omoavz14P715YF9qvRBX66EmE… > > > You can also make such adjustments via email by sending a message to: > > Freesurfer-request(a)nmr.mgh.harvard.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > zoumwove > > Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > 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/1p5RAyh3XrOw6sVI1Ck5SYeNw6BwVQxZCzFaDAXlXgTsRK… <https://secure-web.cisco.com/1p5RAyh3XrOw6sVI1Ck5SYeNw6BwVQxZCzFaDAXlXgTsRK…> . > 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.

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Fw: Welcome to the "Freesurfer" mailing list (Digest mode)
by 黄月虹 20 Dec '24

20 Dec '24

External Email - Use Caution > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2024-12-20 20:43:35 (星期五) > 收件人: huangyuehong(a)stu.hznu.edu.cn > 主题: Welcome to the "Freesurfer" mailing list (Digest mode) > > Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! > > To post to this list, send your email to: > > freesurfer(a)nmr.mgh.harvard.edu > > General information about the mailing list is at: > > https://secure-web.cisco.com/19G_vD1R-PUdgNSk-6dsP4CrmgiHrLgcB0Dp1Zo8hH5MKa… > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://secure-web.cisco.com/1HutEKVL-PtiSBcic7igKoljqCRrwKDzjjkZWKX5gj0t5c… > > > You can also make such adjustments via email by sending a message to: > > Freesurfer-request(a)nmr.mgh.harvard.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > zoumwove > > Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > 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/1wMY0l8vtjTZjVQnTI7Y9HDtuIA5QahRy5daIdbXO9NY3L… <https://secure-web.cisco.com/1wMY0l8vtjTZjVQnTI7Y9HDtuIA5QahRy5daIdbXO9NY3L…> . > 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.

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mri_convert: Command not found
by Katherine Sawyer 20 Dec '24

20 Dec '24

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obtain vertex neighborhood
by Jiaen Liu 18 Dec '24

18 Dec '24

External Email - Use Caution Hi Freesurfer users I search the FS documents but can't find a way to extract the vertex neighborhood for a particular vertex. I'd like to use data associated with the vertices in the neighborhood. In 3D space, we often use such kernels for filtering. Thanks! Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://secure-web.cisco.com/18PydljEg7EKeNzVJZ2fExAIRqZx618rAX7iZIcyZK6dZt…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Subject: query about mri_vol2surf
by Pandey, Shraddha 17 Dec '24

17 Dec '24

External Email - Use Caution Hello FreeSurfer Experts, I am using mri_vol2surf to map a volume onto a surface, with the registration .dat file generated via bbregister. I would like to understand how the input volume is being sampled to generate the surface and how to visualize the sampled points. mri_vol2surf --src "$input_volume" --out "$output_surface" --srcreg "$output_reg_file" --hemi lh --projfrac 0.2 Specifically, how can I display the input_volume along with the sampled points at a projfrac of 0.2 on Freeview? Thank you in advance for your help! Shraddha

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amygdala nuclei from segmentHA_T1 registration issue
by Stephanie Williams 17 Dec '24

17 Dec '24

External Email - Use Caution The amygdala nuclei labels from segmentHA_T1.sh seem to behave differently in standard freesurfer registration commands than other labels from aparc+aseg.mgz: I can't get the amygdala nuclei to register to my functional space correctly despite no issues with aparc+aseg labels. Are additional steps needed to correct header or orientation information when using amygdala nuclei labels? I'm extracting labels from one of the amygdala FSVoxelSpace files. Below is an example of the command I use to extract labels + register to functional space that isn't working. These commands work great with labels from aparc+aseg.mgz but end up in completely incorrect positions for any of the segmentHA-T1 amygdala nuclei. There is no error message, the issue is just that the output masks are in the wrong location. mri_extract_label rh.hippoAmygLabels.HBT.FSvoxelSpace.mgz 7001 labels/nuclei1_rh.nii mri_vol2vol --mov myfunc --targ labels/nuclei1_rh.nii --reg func2anat.dat --inv --o nuclei1_funcspace.nii The label file from the extract label command looks correct when overlaid on the anatomical. The issue seems to arise after vol2vol command -- the output mask is in the wrong area (eg amygdala nuclei are in the cerebellumafter vol2vol). The same vol2vol command works fine with the whole amygdala label from aparc+aseg, + I have checked the registration .dat file from bbregister is correct. Any advice would be appreciated! I've checked the header information using fslhd and the orientations from masks that worked (aparc+aseg) and didn't work (rh.hippoAmygLabels) appear identical. *I've abbreviated the name of the input to mri_extract_label command for simplification, the full name is: rh.hippoAmygLabels-T1.v22.HBT.FSvoxelSpace.mgz

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Issues with hippocampal segmentation code (segmentHA_T2) and missing ConcatenateSubregionsResults in 7.3.1
by Chumin, Evgeny Jenya 17 Dec '24

17 Dec '24

External Email - Use Caution Hello, I am attempting to run hippocampal segmentation with freesurfer 7.3.1, using the segmentHA_T2.sh script with a high-resolution hippocampus T2 sequence as additional scan input. The code runs fine, but oddly it places the outputs into the mri subfolder rather than into stats (output file names shown below). mri/ rh.amygNucVolumes-T2HighResHippo.v22.txt rh.hippoSfVolumes-T2HighResHippo.v22.txt rh.hippoAmygLabels-T2HighResHippo.v22.CA.FSvoxelSpace.mgz rh.hippoAmygLabels-T2HighResHippo.v22.CA.mgz rh.hippoAmygLabels-T2HighResHippo.v22.FS60.FSvoxelSpace.mgz rh.hippoAmygLabels-T2HighResHippo.v22.FS60.mgz rh.hippoAmygLabels-T2HighResHippo.v22.FSvoxelSpace.mgz rh.hippoAmygLabels-T2HighResHippo.v22.HBT.FSvoxelSpace.mgz rh.hippoAmygLabels-T2HighResHippo.v22.HBT.mgz rh.hippoAmygLabels-T2HighResHippo.v22.mgz The stats folder also contains output .stats files for hippocampus and amygdala, but they only have one sentence in them: " # Amygdala nuclei volumes as created by segmentHA_T2.sh " These are the names of the files in the stats directory: stats/ amygdalar-nuclei.lh.T2.v22.T2HighResHippo.stats amygdalar-nuclei.rh.T2.v22.T2HighResHippo.stats hipposubfields.lh.T2.v22.T2HighResHippo.stats hipposubfields.rh.T2.v22.T2HighResHippo.stats It seems to me that the output files are initialized in the stats directory, but the values themselves get written to files in the mri directory. When I go to compile the data across subjects, the ConcatenateSubregionsResults script is missing from the installation (I have confirmed this both for 7.3.1 and 7.4.1 installations). I found the following thread in archive with a similar issue of this file missing: https://secure-web.cisco.com/1D6pNu3LKBDnQ_g29D1J9DrkaQ4h3xi6d3NHKg1r8YUImC… In this thread Antoine shared a direct download for the ConcatenateSubregionsResults, then Jackson shares a batched version of the script to resolve an issue with it looking for files in the /mri directory (which is where those files are written in my case anyways). Either by using the unbatched script or using the batched script and manually moving the files from the mri to the stats, I am able to run the script but run into another issue. The output file contains in the first row the values for the first subject and then for all subsequent subject rows it has region labels. I looked at each subject's output and it looks like this: Hippocampal_tail 547.477135 subiculum-body 198.862009 CA1-body 108.611407 subiculum-head 162.383267 hippocampal-fissure 132.385149 presubiculum-head 100.360234 CA1-head 477.119333 presubiculum-body 85.674081 parasubiculum 58.297345 molecular_layer_HP-head 180.316933 molecular_layer_HP-body 231.129446 GC-ML-DG-head 132.306221 CA3-body 66.096743 GC-ML-DG-body 115.076547 CA4-head 108.334300 CA4-body 105.624384 fimbria 86.764321 CA3-head 89.481195 HATA 52.204101 Whole_hippocampal_body 997.838938 Whole_hippocampal_head 1360.802930 Whole_hippocampus 2906.119003 My guess is that the labels are being incorrectly pulled from the second column and the values from the first column. Doe anyone have any insight on how to resolve this? I could always pull what I need manually, but if this is an issue with the code it would be nice to see it resolved. Many thanks! Jenya C. Indiana University School of Medicine

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needed: tools to work with synthmorph deformations in ANTS and FSL pipelines.
by Josh 17 Dec '24

17 Dec '24

External Email - Use Caution mri_synthmorph is simply an amazing SOTA tool that I want to incorporate into all my pipelines. However, I am unsure how to convert the combined affine+nonlinear deformation image into a format that can be worked with by ants or FSL. Optimally, synthmorph + lta_convert + mri_convert would provide tools to: 1. separate affine and nonlinear components of the registration (useful in certain applications) 2. convert freesurfer transforms to current standard formats (FSL and ITK ants) -Josh

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Single voxel grey-white matter boundary binary mask
by Tamir Eisenstein 16 Dec '24

16 Dec '24

External Email - Use Caution Dear FreeSurfer experts, Is it possible using the FS tools to create a grey-white matter boundary binary mask in volume space (e.g., a nifti file) that will be a single voxel thick along the entire grey-white matter boundary? Many thanks, Tamir Dr Tamir Eisenstein, Ph.D. Postdoctoral Researcher FMRIB, Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences John Radcliffe Hospital, Oxford OX3 9DU University of Oxford tamir.eisenstein(a)ndcn.ox.ac.uk<mailto:julien.fars@ndcn.ox.ac.uk> eisentamir(a)gmail.com<mailto:julien.fars@gmail.com> tel: +44 7938790763

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Freesurfer December 2024