Freesurfer September 2024

freesurfer@nmr.mgh.harvard.edu

48 participants
58 discussions

Re: [Freesurfer] installation on Linux server incompatible with python2?
by fsbuild 09 Sep '24

09 Sep '24

External Email - Use Caution  You could try first installing rocky8, then install freesurfer, then *upgrade* the machine to rocky9, though you still may not have python2 after the upgrade.   We have not run into any issues so far running the freesurfer rocky8 binaries on rocky9. You could try using the —skip-broken switch when you install the RPM directly on rocky9. You could try downloading/building python2 directly on the Rocky9 machine, i.e., see this thread with same issue on CentOS9,https://stackoverflow.com/questions/71256853/how-do-i-install-pytho… - R. On Sep 9, 2024, at 17:48, Gowin, Joshua <JOSHUA.GOWIN(a)cuanschutz.edu> wrote:        External Email - Use Caution        Hello FreeSurfer community,    We are trying to install FreeSurfer on a new server that uses Rocky Linux 9.4 (Blue Onyx). Unfortunately, python2 is not available on this Linux version, but we believe it is necessary to run FreeSurfer.Are there possible FreeSurfer builds that do not require python2? Or would it be better to run FreeSurfer from a container image based on Rocky 8, which still has Python2 available?Or, are there other solutions that would be better for us?  We’d be grateful for any suggestions for our set up.  Josh  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

installation on Linux server incompatible with python2?
by Gowin, Joshua 09 Sep '24

09 Sep '24

External Email - Use Caution Hello FreeSurfer community, We are trying to install FreeSurfer on a new server that uses Rocky Linux 9.4 (Blue Onyx). Unfortunately, python2 is not available on this Linux version, but we believe it is necessary to run FreeSurfer. Are there possible FreeSurfer builds that do not require python2? Or would it be better to run FreeSurfer from a container image based on Rocky 8, which still has Python2 available? Or, are there other solutions that would be better for us? We'd be grateful for any suggestions for our set up. Josh

1 0

UNABLE TO MAKE EDITS AFTER SIMNIBS
by Cesar Zabdiel Gutierrez Mendoza (czgtrrzm) 09 Sep '24

09 Sep '24

External Email - Use Caution Hello to all, I am attempting to do a simple editing on Freesurfer where I just want to do manual voxel editing. I am working off of the “Ernie” model from SimNibs. I ran charm on simnibs to get a mesh. After I received the mesh, I used the “labeling_tissues_upsampled.nii.gz” and attempted to edit. When I attempt to edit, there simply is not a response on the screen itself. I left click and drag but it does not let me edit. P.S. I have been able to edit other models when I do not run it through SIMNIBS. Anyone got tips about running things through SIMINBS? Could it be permission error? Could it be something else? Let me know. Using an M1 Macbook Air. On newest software Please let me know if you have suggestions!

1 0

How do we account for different scanner/acquisition parameters in the FreeSurfer longitudinal pipeline?
by Yoonho Hwang 08 Sep '24

08 Sep '24

External Email - Use Caution Dear FreeSurfer team, We are using the Freesurfer longitudinal pipeline, and we had questions about accounting for different scanners and acquisition parameters. We are looking at 3 different timepoints with 2 different scanners (scanner 1 was used for time points 1 and 2, scanner 2 was used for time point 3). Timepoint 1 (scanner1, 512 x 512 x 244 or 512 x 512 x 180) Timepoint 2 (scanner1, 512 x 512 x 180) Timepoint 3 (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Q1: Does creating the subject template based on median and intensity scaling help address the issue of different scanners and acquisition parameters when conducting longitudinal analyses? If it is not sufficient to address the scanner/acquisition issue, do you have any recommendations as to next steps to account for this? We have seen others use LongCombat harmonization or linear mixed effects models to address this issue, is that something you would consider as well? Q2: In a similar vein, when we received the warning below in the "base" step of longitudinal analysis, we were wondering how much it was affecting our results. Would it be helpful to resample the images? Do you have suggestions on other avenues we could consider to address this warning and have robust and reliable results? ************************************************************ ******************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ************************************************************ ******************* Thank you Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

1 0

Re: [Freesurfer] Using a newer version of FS for longitudinal processing
by fsbuild 08 Sep '24

08 Sep '24

External Email - Use Caution This from the bottom of the page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads- R.Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).- R. On Sep 8, 2024, at 18:28, Bronwyn Overs <b.overs(a)neura.edu.au> wrote:        External Email - Use Caution        Hi Freesurfer mailing list,I have over 600 structural MRI images, across three time-points, for which cross-sectional processing was completed on a Linux server using Freesurfer v5.3. That server is now closing down and we need to process these images using the longitudinal processing stream. Is it viable to process all of the longitudinal base and long images on a different system using a newer version of Freesurfer? Kind regards, Bronwyn OversResearch Assistant<neura-logo-email.png> Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 neura.edu.au  Twitter | Facebook | Subscribe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh..harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Using a newer version of FS for longitudinal processing
by Bronwyn Overs 08 Sep '24

08 Sep '24

External Email - Use Caution Hi Freesurfer mailing list, I have over 600 structural MRI images, across three time-points, for which cross-sectional processing was completed on a Linux server using Freesurfer v5.3. That server is now closing down and we need to process these images using the longitudinal processing stream. Is it viable to process all of the longitudinal base and long images on a different system using a newer version of Freesurfer? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

1 0

Combining left and right hemisphere segmentation files
by Mengjie Huang 07 Sep '24

07 Sep '24

External Email - Use Caution Dear FreeSurfer developers, Hi, I am currently working with the hippocampal subfields and amygdala segmentation pipeline, which produces separate output files for each hemisphere, such as `lh.hippoAmygLabels-T1.v21.mgz` and `rh.hippoAmygLabels-T1.v21.mgz`. I was wondering if there is a way to modify the pipeline or to combine these two files into a single file that contains the segmented regions for both hemispheres? Thank you in advance for your guidance. Best regards, Mengjie

1 0

mri_easy_reg separating transform into affine and nonlinear components: debugging the code
by Joshua K Lee 06 Sep '24

06 Sep '24

External Email - Use Caution I've really impressed with mri_easy_reg and I was hoping to use it in a similar way as ANTs built_template scripts, which requires separation of affine from nonlinear transforms for their unbiased template updating algorithm. However, mri_easy_reg only returns a single transform object, combining affine and nonlinear components. I added an argument as an option for producing separate transforms ``` def main(): parser.add_argument("--separate_transforms", default=None, help="(optional) Produce Affine and NonLinear Fields Separately, if 'a' produce combined transform too. If 'b', do not produce combined transform") ``` then include ``` if args.separate_transforms is not None: sepAII3 = II2 sepAJJ3 = JJ2 sepAKK3 = KK2 sepAaffine = torch.tensor(np.matmul(Mflo, atlas_aff), device='cpu') sepARAS_X = affine[0, 0] * sepAII3 + affine[0, 1] * sepAJJ3 + affine[0, 2] * sepAKK3 + affine[0, 3] sepARAS_Y = affine[1, 0] * sepAII3 + affine[1, 1] * sepAJJ3 + affine[1, 2] * sepAKK3 + affine[1, 3] sepARAS_Z = affine[2, 0] * sepAII3 + affine[2, 1] * sepAJJ3 + affine[2, 2] * sepAKK3 + affine[2, 3] ``` and ``` if args.separate_transforms is not None: #create separate nonlinear naked field ndepth, nheight, nwidth, _ = f2r_field.shape # Create meshgrid indices for each dimension nII, nJJ, nKK = np.meshgrid(np.arange(ndepth), np.arange(nheight), np.arange(nwidth), indexing='ij') # Convert numpy arrays to PyTorch tensors nII2 = torch.tensor(nII, dtype=torch.float32, device='cpu') # or device='cuda' if using GPU nJJ2 = torch.tensor(nJJ, dtype=torch.float32, device='cpu') nKK2 = torch.tensor(nKK, dtype=torch.float32, device='cpu') # Now use these tensors as inputs to your interpolation function nFIELD = fast_3D_interp_field_torch(f2r_field, nII2, nJJ2, nKK2) nII3 = nII2 + nFIELD[:, :, :, 0] nJJ3 = nJJ2 + nFIELD[:, :, :, 1] nKK3 = nKK2 + nFIELD[:, :, :, 2] ``` ``` and saves them if args.separate_transforms is not None: print("args.separate_transforms is not None") # Correctly combine the prefix with the filename fwd_field_dir = os.path.dirname(args.fwd_field) fwd_field_basename = os.path.basename(args.fwd_field) nonlinear_fwd_field = os.path.join(fwd_field_dir, nonlinear_prefix + fwd_field_basename) print(f" Saving nonlinear field to: {nonlinear_fwd_field}") try: nonlinear_field = torch.stack([nII3, nJJ3, nKK3], axis=-1) print(f" Nonlinear field shape: {nonlinear_field.shape}") save_volume(nonlinear_field, Raff, Rh, nonlinear_fwd_field, n_dims=3) print(" Nonlinear field saved successfully") except Exception as e: print(f" Error saving nonlinear field: {str(e)}") # Do the same for the affine field affine_fwd_field = os.path.join(fwd_field_dir, affine_prefix + fwd_field_basename) print(f" Saving affine field to: {affine_fwd_field}") try: save_volume(torch.stack([sepARAS_X, sepARAS_Y, sepARAS_Z], axis=-1), Raff, Rh, affine_fwd_field, n_dims=3) print(" Affine field saved successfully") except Exception as e: print(f" Error saving affine field: {str(e)}") ``` full python file attached. but it doesn't work. When I try applying them to floating image one at a time, the images go haywire. On the left is after applying the affine transform my code generated, on the right is applying the nonlinear transform onto the image on the left. [cid:2ae2ee64-8c83-49f5-b455-3348a9ec5983] I know this is an unusual request, but thanks for any help Josh Josh Lee Assistant Professional Researcher Department of Psychiatry and Behavioral Sciences University of California, MIND Institute jkilee(a)ucdavis.edu

1 0

SAMSEG - hanging for FLAIR lesion segmentation
by Stefano Cerri 06 Sep '24

06 Sep '24

External Email - Use Caution Hi Sravanthi, Can you check that "template_coreg.mgz" produced by samseg is aligned with your FLAIR image? There might be an issue with the initial template registration. If that is not the case, can you provide the full SAMSEG log? A warning might have been issued before it hung there. Stefano [Freesurfer] SAMSEG - hanging for FLAIR lesion segmentation <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Sravanthi Upadrasta <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Thu, 05 Sep 2024 04:46:51 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> External Email - Use Caution Hi, I am encountering an issue with Samseg while extracting lesion information from a CUBE FLAIR image. The process hangs for a long time and I have to forcekill the process after almost 2 hours. I did not have this issue with same subject T1w and T2 FLAIR images. Freesurfer - 7.2.0 Ubuntu 20.04 Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Could you help me troubleshoot this? Thanks, Sravanthi. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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.

1 0

Re: [Freesurfer] cortical thickness measurements
by AJ 05 Sep '24

05 Sep '24

External Email - Use Caution Hi, I am trying to determine which imaging type is ideal for cortical segmentation and thickness measurement: MPRAGE, MP2RAGE, or MEMP2RAGE on a 3T Philips scanner. Any helpful comments would be greatly appreciated. Thank you AJ

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2024