Freesurfer

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30056 discussions

Re: [Freesurfer] Tksurfer and freeview
by fsbuild 07 Aug '24

07 Aug '24

External Email - Use Caution  The tksurfer command is deprecated and no longer supported.  You could try using freeview directly or run tksurferfv which may use some of the same options as tksurfer, but runs freeview instead.  $ tksurferfv --help This is a script that runs freeview with arguments like tksurfer. Not all tksurfer functionality is replicated. tksurferfv subject hemi surface ... -tksurfer : use tksurfer instead of freeview Can have multiple annotations -all : load white, pial, inflated -vgl : runs freeview with /usr/pubsw/bin/vglrun -no-vgl : does not run freeview with /usr/pubsw/bin/vglrun -no-outline : do not show annots as outline -vtxno vtxno : put cursor on vtxno on the first surface -neuro : use neurological orientation instead of radiological -rotate-around-cursor (-rca) : in 3d view, rotate around cursor (use -no- to turn off) -linear, -linearopaque, -piecewise, -min_to_max (default) : overlay heat scale --keep-sphere-vol-geom : do not ignore sphere volume geometry when loading sphere On 8/7/24 16:01, Hengameh (hennn2023(a)gmail.com) wrote: Hi Ed, I am currently encountering the same issue. Could you please assist in fixing this issue?Thank you for your help. Hengameh  Sent from Mail for Windows 

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Extract surface vertex IDs from significance map
by Dan Levitas 07 Aug '24

07 Aug '24

External Email - Use Caution I may have spoken too soon. It appears that the —olab flag option in mri_surfcluster provides .label files with vertex IDs for each cluster. Dan

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Extract surface vertex IDs from significance map
by Dan Levitas 07 Aug '24

07 Aug '24

External Email - Use Caution I have been using the Matlab LME tutorial to assess several time*group interaction effects in my dataset. I successfully created *sig.mgh files and used *mri_surfcluster* to generate cluster summary (*thickness.clustersummary.txt), which include each cluster's highest peak vertex. I would like to extract all vertices for each cluster to more closely examine the interaction effect of cortical thickness, but am unsure how to do so. The *mri_surfcluster* function doesn't appear to have an option for this, is there some other function or series of steps I can take to achieve this? Thanks, Dan

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Question/potential bug regarding mri_convert and .gca files
by Siegel, Nys Tjade 07 Aug '24

07 Aug '24

External Email - Use Caution Dear Freesurfer community, I'm trying to extract labels from a .gca atlas volume using the following command: mri_convert atlas.gca -nth 1 labels.mgz (from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat) I've found a .gca file in the /average folder for which this works (RB_all_2020-01-02.gca), but for the cortical parcellations I'm actually interested in (e.g. lh.DKTatlas40.gcs), I get the following error: ERROR: cannot determine file type for lh.DKTatlas40.gcs I'm pretty confused, because the documentations, as well as other support requests, are pretty clear on that my problem should be solved using the mentioned command. Notably, mri_convert -u, does not list GCA under the supported file-types, maybe this is a versioning issue? I'm using freesurfer 7.2.0 with Ubunutu 22.04.4. Any help is much appreciated. Best regards, Nys Tjade Siegel

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Postdoctoral Fellow in human 7T and advanced neuroimaging at Emory University
by Wu, Junjie 06 Aug '24

06 Aug '24

External Email - Use Caution Please find attached an ad for a Postdoctoral Fellow in human 7T and advanced neuroimaging at Emory University. Thank you!

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WMH-Synthseg Bad CPU type in Executable
by Vaughn, Stephen 06 Aug '24

06 Aug '24

External Email - Use Caution Hello! I am trying to run the WMH synthseg command. I have successfully downloaded the Atlas files, but when I ran the mri_WMHsynthseg command, I encountered the error: /Applications/freesurfer/dev/bin/fspython: line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable /Applications/freesurfer/dev/bin/fspython: line 30: /Applications/freesurfer/dev/python/bin/python3: Undefined error: 0 >From the other archived emails, I found individuals reporting this from Qdec, tksurfer, and tkmedit because their macOS updated to 64 bit, is that what is happening here? Is there a work around or do I need to use a different computer with 32bit OS? Thanks! Please be aware that e-mail communication can be intercepted in transmission or misdirected. Please consider communicating any sensitive information by telephone, fax, or mail. The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to hipaa.security(a)yale.edu and destroy this message.

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Comparison of "segment_subregions" and "recon-all"
by Yoonho Hwang 06 Aug '24

06 Aug '24

External Email - Use Caution Dear Bruce Fischl and Douglas Greve, Hi all, After completing the "recon-all" process, I have completed the "segment_subregions" process. There is a difference between the total volume (hippocampus, amygdala, thalamus, brainstem) using "asegstats2table" and the total volume (hippocampus, amygdala, thalamus, brainstem) using "segment_subregions". Is there a standard for how much difference is acceptable? Thank you very much 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>*

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Re: [Freesurfer] mri_easyreg --help error: zsh : illegal hardware instruction mri_easyreg --help
by fsbuild 05 Aug '24

05 Aug '24

External Email - Use Caution  Hello Yaozhi, You probably installed the Intel Mac binaries to run on your Silicon Mac with an M1, M2, or M3 arm64 chip.  But not all Intel binaries will run on the newer arm64 Macs.   If you want to run that command you will need to download and install the silicon Mac nightly freesurfer build. To remove your current freesurfer install, you can try running the uninstall script from the command line under what you set FREESURFER_HOME to, $ cd $FREESURFER_HOME$ sudo bash uninstall.sh Once you have removed your current freesurfer installation, you can download and try installing the arm64 pkg, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesu… Right click with the mouse on the .pkg file and select “Open with —> install.app (default)".  Then follow the prompts in the installer windows. - R. On Aug 5, 2024, at 21:45, Yang, Yaozhi <yangyaozhi(a)ufl.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am trying to use easyreg from the paper--- A ready‑to‑use machine learning tool for symmetric multi‑modality registration of brain MRI and the paper says that I can use freesurfer to get the easyreg function. But after I download freesurfur in my macbook, and run mri_easyreg –-help on the terminal, I get the error saying that zsh : illegal hardware instruction mri_easyreg --help. So can you help me with that? How can I use easyreg method? Thank you very much! Best,Yaozhi_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_easyreg --help error: zsh : illegal hardware instruction mri_easyreg --help
by Yang, Yaozhi 05 Aug '24

05 Aug '24

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use easyreg from the paper--- A ready‑to‑use machine learning tool for symmetric multi‑modality registration of brain MRI and the paper says that I can use freesurfer to get the easyreg function. But after I download freesurfur in my macbook, and run mri_easyreg –-help on the terminal, I get the error saying that zsh : illegal hardware instruction mri_easyreg --help. So can you help me with that? How can I use easyreg method? Thank you very much! Best, Yaozhi

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Questions about FreeSurfer's longitudinal pipeline prior to longitudinal analysis
by Yoonho Hwang 05 Aug '24

05 Aug '24

External Email - Use Caution Dear Martin Reuter and Bruce Fischl, Hi all, When we use the longitudinal pipeline of FreeSurfer, I know there are three steps: 1. cross-sectional, 2: base, 3: long. When we create the subject template, it uses median and intensity scaling in the second step ("base") based on the paper ("Within-subject template estimation ~"). Considering the base, many processes are initialized in the third step ("long"). Q1) I know when we run the base, isn't there a process to use a function such as mri_convert to adjust the image size for each time to be the same? Could creating the subject template based on the median and intensity scaling minimizes the impact of longitudinal analysis on MRI from different scanners and acquisition parameters? Q2) In the base, I encountered the following warning, but completed the entire process without errors. ******************************************************************************* 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 ... ******************************************************************************* There is matrix size for each time point: Baseline (scanner1, 512 x 512 x 244 or 512 x 512 x 180) 1st follow-up (scanner1, 512 x 512 x 180) 2nd follow-up (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Could I ignore the warning? Or is there anything I need to fix before running the long)? Also, could you please give me any suggestions on longitudinal analyses? Thank you very much 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>*

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