Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

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

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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 ]

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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

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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

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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.

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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

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SAMSEG - hanging for FLAIR lesion segmentation
by Sravanthi Upadrasta 05 Sep '24

05 Sep '24

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.

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Re: [Freesurfer] License issues
by fsbuild 04 Sep '24

04 Sep '24

External Email - Use Caution   The system you are running freesurfer 5.3 on likely uses older system libraries that are incompatible with reading current 7.X licenses.  Or 7.X licenses use different (newer) encryption libraries found only on more recent linux systems.   So a license file you download now is not expected to work on a system where 5.3 runs with its original license.  If you still need to run 5.3 (released in 2013/2014), then you should run it on the system where it works using its original license from that time period.  If that system is not available, then you could try hosting a CentOS virtual machine with Freesurfer 5.3 installed on the Linux system where you run 7.4.1.   You can download a compressed archive of a VirtualBox CentOS disk image with Freesurfer 5.3 installed from,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfe… You would need to install the VirtualBox application on your current Linux machine to run it. We discourage posting license files to public lists. - R. On Sep 4, 2024, at 03:27, Le Prieult, Yéléna <Yelena.LePrieult(a)med.uni-heidelberg.de> wrote:        External Email - Use Caution        Good morning,  I’m using the TASH toolbox for my project and the recommended version of freesurfer for this toolbox is 5.3. I used freesurfer 7.4.1 for the recon-all command, not knowing I needed a different version for the rest of the processing. I used a license that I downloaded month ago and it worked perfectly for freesurfer 7.4.1 but this license doesn’t work with freesurfer 5.3. I downloaded a new license and it didn’t work. I tried changing the permission of access on the license.txt, checked the license key, set properly all environments as FREESURFER_HOME and SUBJECTS_DIR, etc and everything is in order but it still doesn’t work. I even redownloaded another license and tried again but I still encounter the same error: ERROR: Invalid Freesurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martino Center, go to https://surfer.nmr.harvard.edu to get a valid license file (it’s free). If you are inside the NMR-Martinos Center, make sure to osurce the standard environment. Attached to this email you can have a look over the license I have. Thank you in advance for your reply. Best regards, Yéléna <license.txt>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Obtaining Detailed Lateral Ventricle Segmentati
by Necati Emre Şahin 04 Sep '24

04 Sep '24

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am currently working with FreeSurfer and I have encountered a situation that I would like your guidance on. Specifically, I have noticed that FreeSurfer outputs the lateral ventricle in two parts, namely "Left-Lateral-Ventricle" and "Left-Inf-Lat-Vent." However, from an anatomical perspective, I am interested in obtaining the results for the four parts of the lateral ventricle separately: the anterior horn, central part, posterior horn, and inferior horn. I understand that the "Left-Inf-Lat-Vent" might correspond to the inferior horn. Is FreeSurfer capable of providing the segmentation for the lateral ventricle in these specific sub-regions? If not, could you recommend any method or workaround that would allow me to obtain these detailed segmentations? Additionally, if it is not possible to directly obtain these sub-regional volumes, is there a way to derive the ventricle volumes within each lobe (e.g., frontal, parietal, occipital, temporal) using FreeSurfer or any other tool? Your assistance in this matter would be greatly appreciated. Thank you for your time and support. Best regards, Necati Emre Sahin. iPhone’umdan gönderildi

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License issues
by Le Prieult, Yéléna 04 Sep '24

04 Sep '24

External Email - Use Caution Good morning, I'm using the TASH toolbox for my project and the recommended version of freesurfer for this toolbox is 5.3. I used freesurfer 7.4.1 for the recon-all command, not knowing I needed a different version for the rest of the processing. I used a license that I downloaded month ago and it worked perfectly for freesurfer 7.4.1 but this license doesn't work with freesurfer 5.3. I downloaded a new license and it didn't work. I tried changing the permission of access on the license.txt, checked the license key, set properly all environments as FREESURFER_HOME and SUBJECTS_DIR, etc and everything is in order but it still doesn't work. I even redownloaded another license and tried again but I still encounter the same error: ERROR: Invalid Freesurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martino Center, go to https://surfer.nmr.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to osurce the standard environment. Attached to this email you can have a look over the license I have. Thank you in advance for your reply. Best regards, Yéléna

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