Freesurfer April 2025

freesurfer@nmr.mgh.harvard.edu

40 participants
53 discussions

Feasibility and Accuracy of Using SAMSEG with ADC Maps
by Taghizadeh Mortezaei, Nima 13 Apr '25

13 Apr '25

Dear FreeSurfer team, I am currently using FreeSurfer v7.4.1 and I want to ask is it feasible to run SAMSEG directly on ADC maps derived from diffusion MRI for segmenting normal brain anatomy? Alternatively, would it be more accurate to perform segmentation on a T1-weighted image and then transfer the labels to the co-registered ADC image? Thank you very much for your time and support. Best regards, Nima

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Re: [Freesurfer] Updates/bug fixes available for the 8.0.0 release
by fsbuild 11 Apr '25

11 Apr '25

External Email - Use Caution For ubuntu Linux the release string should be 8.0.0 and not 8..0.0, i.e., On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh On Apr 11, 2025, at 20:24, fsbuild <fsbuild(a)contbay.com> wrote:On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8..0.0  bash  fs8_updates.sh

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trac-preproc: orientLAS and mri_info issue with unsigned shorts
by Mirro, Amy 11 Apr '25

11 Apr '25

External Email - Use Caution Hi, Thanks so much for all your work on Freesurfer. I am currently running tracula v7.4 and I am coming across the following error. I believe this error is occurring during the orientLAS call in trac-preproc (the output is copied from my log file): orientLAS /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz I think the error in orientLAS might be due to the mri_info calls inside orientLAS (starting around here: https://secure-web.cisco.com/1yGfA9jbEQb9uMtyDf5LggAJmO-aUQoPIO34H0YN-0Lu0i…) When I attempt to run mri_info on my niftis, I get the following warning : "INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k -1 -0 0" I think that when mri_info returns this warning inside the orientLAS code, it causes orientLAS to fail, since the xyzR, xyzA, and xyzS variables are not set as expected. Do you have any suggestions on how I could solve this? Is there perhaps a way to suppress the warning in mri_info? Or is there a straightforward way to convert unsigned short data? Thanks, Amy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mris_register external atlas
by Stefanie Bradley 10 Apr '25

10 Apr '25

External Email - Use Caution Hi there, I am trying to register my Freesurfer subject's cortical surface into a common space to use the parcellations from a pediatric atlas (UNC 4D cortical surface atlas). With Freesurfer version 8.0.0 in a Linus OS, I am using mris_register as: mris_register -1 individual_subject/lh.sphere 4D_atlas/lh.sphere individual_subject /lh.sphere.FS.reg. I am getting an error where it says it requires a smoothwm file from the atlas files, though I only have curvature and sphere files from the atlas. Is there a way to register the atlas files to my subjects and then put the parcellations onto my subject's cortical surface? Thanks, Stefanie

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 09 Apr '25

09 Apr '25

We have always untarred up to 7.1.0 and used it successfully. This was the good thing about FreeSurfer that did not require a client side installation. I am the administrator and I can tell you that installation of this software via root is infeasible for 100 computers. Given your comment about 7.4.1 tarball being not installer, we want to know--has the installation mechanism changed since 7.4.1? Best, Tashrif

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 09 Apr '25

09 Apr '25

External Email - Use Caution  We are no longer supporting or releasing tar archives for the reasons explained in the previous email. Various sites install freesurfer package(s) on central machine(s)  for everyone to use/mount read only over the network in order to avoid installing and maintaining the same package on 100’s of machines.   However, my understanding is tools like puppet, chef, yum-cron, etc. can if need be automate doing the actual package installs site wide across multiple machines. - R.On Apr 9, 2025, at 15:44, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:I just checked that the only additional step you recommend is: > apt-get install ./freesurfer_ubuntu22-7.4.1_amd64.deb Sourcing the rest have remained the same. So why can you not also upload the tar ball? -TashrifFrom: Billah, Tashrif Sent: Wednesday, April 9, 2025 3:31 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC We have always untarred up to 7.1.0 and used it successfully. This was the good thing about FreeSurfer that did not require a client side installation. I am the administrator and I can tell you that installation of this software via root is infeasible for 100 computers. Given your comment about 7.4.1 tarball being not installer, we want to know--has the installation mechanism changed since 7.4.1? Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 09 Apr '25

09 Apr '25

External Email - Use Caution  It’s not practical for us to support freesurfer running on a system w/o a successful install via the rpm or deb file freesurfer installers, i.e., the tar archives were not installers.   Use of the installer packages is the standard way to help ensure the files a distribution needs to run are present on the system.  Or the install will fail if the freesurfer requirements conflict with what's currently installed on the system.   If you don't have permission, then please ask someone in your IT/support department to try installing the freesurfer package. - R. On Apr 9, 2025, at 13:56, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi fsbuild, I understand your suggestion about installing version 8. But, can you upload this release as a tar.gz file like you guys have always done for prior releases? Remember that end users will not have root permissions to install an rpm file. Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 09 Apr '25

09 Apr '25

Hi fsbuild, I understand your suggestion about installing version 8. But, can you upload this release as a tar.gz file like you guys have always done for prior releases? Remember that end users will not have root permissions to install an rpm file. Best, Tashrif

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Re: [Freesurfer] FreeSurfer 8 on Ubuntu 24.04
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution Please see the recent post,https://secure-web.cisco.com/1KCHTNX-B1zP9SDBeZBUF4EyohuSTVWQnK565FzMy… On Apr 8, 2025, at 13:23, Nagesh Adluru <adluru(a)wisc.edu> wrote:        External Email - Use Caution        Dear FreeSurfer development team, Could you kindly let us know if FreeSurfer 8 native installer for Ubuntu 24.04 would be released sometime in the near future? Thank you so much for the help and guidance. Please let us know if you have any questions or suggestions. Sincerely,Nagesh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by fsbuild 08 Apr '25

08 Apr '25

External Email - Use Caution  If your path /software/rocky9/… means you are trying to run a 7.4.1 release on Rocky9 Linux, then I would not expect it to work.  Starting with the 8.0.0 release, there is a Rocky8 installer that I think will also work on Rocky9.   Please see the release page at,https://secure-web.cisco.com/1cdkdm-VjSPKz6eCLzOVZPN9EdLt6weq_jIU-Vi8uL0… - R. On Apr 8, 2025, at 16:49, Billah, Tashrif <tbillah(a)bwh.harvard.edu> wrote:Hi all, In freesurfer-7.4.1, the nu_correct command gives this error: ```Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /software/rocky9/freesurfer-7.4.1/mni/share/perl5 /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/MiscUtilities.pm line 36.Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/share/perl5/MNI/Spawn.pm line 35.Compilation failed in require at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 38.BEGIN failed--compilation aborted at /software/rocky9/freesurfer-7.4.1/mni/bin/nu_correct line 3``` We are in Redhat 9 OS. Is this expected? Could you recommend a solution? Best,Tashrif_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer April 2025