Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

mri_robust_register --minsize
by Proulx, Jean Sebastien 06 Mar '23

06 Mar '23

Hello, I am trying to register a full volume to a single slice, and I follow example 3 of mri_robust_register's help. I get the following error: Input image is smaller than min dimension: 1 < 16 Input dimensions (after conformalizing) MOV: 64 64 64 Input dimensions (after conformalizing) DST: 64 64 1 Specify larger minimum ... This error stays after adding --minsize 1 or --minsize, despite mri_robust_register recognizing the flag, as suggested by this terminal output: --minsize: Smallest dimension > 0 . Registration ran ok when replacing the single-slice with a 40-slice volume. Any idea on what is going on here? Thanks a lot for the good work and Have a good day! Sebastien

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Visualizing transparent surface with non transparent annotations
by Leonardo Tozzi 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Experts, I would like to use Freeview to achieve the following. I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose to visualize to not be transparent. Is there a way to achieve this? Thank you, Leonardo Tozzi, MD, PhD Director of Computational Neuroscience & Neuroimaging Program Stanford Center for Precision Mental Health and Wellness Stanford University ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/10OmKEEhtSQzpfvnfJVDeLBEHHi9OqaBVJ9LAvZsQvsNWt…> [signature_1282923475] <http://secure-web.cisco.com/1I3hXNj6irLn6oQYZFgxz73In-4_EGzX-NMOPCnUJP3yv02…> [signature_911042299] <https://secure-web.cisco.com/10-8-bEWGWgfQnDhesaI2ZU2QywWqHHyTXTPc8TI7RfrgI…>

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Re: [Freesurfer] Mac OS 13 Ventura
by fsbuild 06 Mar '23

06 Mar '23

External Email - Use Caution Hello Elmira, You can try downloading an installing the 7.3.2 package file, freesurfer-darwin-macOS-7.3.2.pkg, from https://secure-web.cisco.com/19NKhoH2W5uSEES-6x2_z8s-Qx5RJB0qwAFyHKCorvYwKi… Once downloaded, right-clicking on the package file and then selecting open should work.  There should also be a link to setup instructions on that page. - R. On 3/6/23 10:41, Elmira Hassanzadeh (elmitt(a)gmail.com) wrote:         External Email - Use Caution         Hi everyone, Could someone please direct me to the workaround instructions on installing Freesurfer on Mac M1 ultra on OS 13.0 Ventura? Thank you,Elmira _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zSwVL2DeoKToXwAT4D4C9uxaS2pmJaYLtLmu4lG8MhZTN… 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/1GDd7p1A6AR5iRMjhtYjllNXrg_98JDGa0HS424tO6n1Pr… <https://secure-web.cisco.com/1KQsyVOY-H0bVeMnNv1GKX_2WfslJnmFqbrvM1nSvqzHZ26pGC-7wtfjj_oFyeyd6EOcKzzyw2j5MuM_0Is3SC2iOXFJRLXPeShQvA2lDk50bVoZ1VsEIy8Mg6Zjy7CRx0WBxpPgL1F7FK8Bkv2xp7dieYZcUQmH_WgLH4jlur0Di011ddDKa80eFIdPt-6cATmzYD1iDuOD5pdevpdpFqk6f_9bH1omfJ6Izf3JRL59dY_BPXLOcpe0TlTIuc-GOxVB0a5xcxMuXb06MGJTX7DRmY682xG3NAhMFSuBew8Mclo6_oo9ytRR28MkYNCNTMeeQv_AQBcEy8rD0_jBozg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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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Segment the centrum semiovale
by Julie Ottoy 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer team, I was wondering if FS has a way to segment the centrum semiovale? The freesurfer colorLUT table mentions "Centrum semiovale is also labled with 5001 (left) and 5002 (right)." (see https://secure-web.cisco.com/16ntnqYurxLXfYvZCsM5evs9fxRFquoTnxIkD0H4vCmJ3w… ) What does the "also" refer to in this description? Do the following rois represent the centrum semiovale ? : 5001 Left-UnsegmentedWhiteMatter 20 30 40 0 5002 Right-UnsegmentedWhiteMatter 20 30 40 0 Thank you for your help!

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Fwd: Pass code to open FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Idaiane Batista de Assunção Leme 06 Mar '23

06 Mar '23

External Email - Use Caution Dear, Please, request to pass code to open the file FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1qzfDfJY51va9DLVmDRvNTPE9nvtJPVCJT2gEoxA_oJfVO…> Kind regards, -- Idaiane Batista de Assunção Leme Biomédica, PhD

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Password request for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Michael Wagner 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Team, I'm about to install Freesurfer in a VirtualBox VM under Windows., following the instructions in https://secure-web.cisco.com/1Vo2zDB0YAGmcpr2LU_XN4jEZ1O0S0gevSS9oIAxajv6Iy… I believe I will need a password to unpack FS_7_2_0_ubuntu_18_04_06.ova.7z (currently downloading). Later on, I might also need a license file: "Once the VM starts and you have added your FreeSurfer license file, you can start a terminal" Can you please help me with either of these? Thanks, Michael

1 0

Omar: VirtualBox image password request
by Omar Salah Mohammed Mostafa Ahmed 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I'd like to request the password for FS_7_2_0_ubuntu_18_04_06.ova.7z in order to install the virtual image and run Freesurfer in a Virtualbox VM. Thank you! Omar Ahmed

1 0

infant freesurfer - input and output questions
by Inga Harting 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I'm new to infant freesurfer. I was initially relieved when a first run of a test patient went through after I created mprage.nii.gz using mri_convert. 1. Today I wanted to rerun it, but it gives me an error message although the "original" file mprage.nii.gz is sitting unchanged right there in the directory (ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz!). Could you help me find my error? I've copied the output on my screen below. 2. I wanted to look at the results using freeview and following along the lines of FS tutorial on FS output. However there is no T1.mgz in /mri and brainmask.mgz is referred to norm.mgz which is empty. Does this indicate the analysis went through but didn't work? 3. Is there a tutorial for infant freesurfer which I've missed and which might answer (some of) my questions? Best, Inga. -- Inga Harting private email: inga.harting(a)gmx.de Dpt. Neuroradiology Heidelberg University Medical Center INF400, 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de -- error for infant_revon_all-- inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ pwd /home/inga/Inga/Daten/test/pmd2-0 inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ ls -la insgesamt 33808 drwxrwxrwx 11 inga inga 4096 Oct 19 12:10 . drwxrwxr-x 10 inga inga 4096 Oct 19 12:10 .. drwxrwxrwx 2 inga inga 4096 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.218 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.219 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.223 drwxrwxrwx 2 inga inga 16384 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.224 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.5.181722182500.1102.1434102017.91 drwxrwxrwx 2 inga inga 32768 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101403.1.4.2 drwxrwxrwx 2 inga inga 40960 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101419.123.4.2 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.80.4248871915.8240.1434101490.1.4.2 drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 iFS_output_2022-10-05 -rw-rw-r-- 1 inga inga 34372241 Oct 5 14:36 mprage.nii.gz -rw-rw-r-- 1 inga inga 1350 Oct 5 10:39 scan.log inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ infant_recon_all --s pmd2-0 --age 4 InfantReconAll scripts DIR /usr/local/freesurfer/bin PWD /home/inga/Inga/Daten/test/pmd2-0 ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz! inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ -- output from infant freesurfer /mri (result of first run) -- inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0/iFS_output_2022-10-05/mri$ ls -la insgesamt 4824 drwxrwxr-x 3 inga inga 4096 Oct 5 15:44 . drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 .. -rw-rw-r-- 1 inga inga 232837 Oct 5 15:44 aparc+aseg.mgz -rw-rw-r-- 1 inga inga 39 Oct 5 15:44 aseg.count.txt -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.mgz -rw-rw-r-- 1 inga inga 186080 Oct 5 15:44 aseg.nii.gz -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.presurf.mgz -rw-rw-r-- 1 inga inga 606165 Oct 5 15:44 brain.finalsurfs.mgz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brainmask.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brainmask.nii.gz -> norm.nii.gz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brain.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brain.nii.gz -> norm.nii.gz -rw-rw-r-- 1 inga inga 102107 Oct 5 15:44 filled.mgz -rw-rw-r-- 1 inga inga 1000069 Oct 5 15:44 lh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 598075 Oct 5 15:44 lh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 53037 Oct 5 15:44 lh.ribbon.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.nii.gz -rw-rw-r-- 1 inga inga 1011650 Oct 5 15:44 rh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 372114 Oct 5 15:44 rh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 54091 Oct 5 15:44 rh.ribbon.mgz -rw-rw-r-- 1 inga inga 93026 Oct 5 15:44 ribbon.mgz drwxrwxr-x 2 inga inga 4096 Oct 5 15:44 transforms -rw-rw-r-- 1 inga inga 62243 Oct 5 15:44 wm.mgz --

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infant Freesurfer - subcortical/white matter segmentation
by Inga Harting 06 Mar '23

06 Mar '23

External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de

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Infant freesurfer issue
by Sayre, Christopher 06 Mar '23

06 Mar '23

External Email - Use Caution Hello all, I am having an issue when trying to run infant_recon_all. The error that I am getting is /opt/apps/software/FreeSurfer.7.2.0-centos7_x86_64/bin/atlassubjects.csh No such file or directory. I have searched through the bin folder xç xfor the atlassubjects.csh and indeed it does not exist. I have looked at the github for FreeSurfer and I was able to find the file under the infant folder. Am I missing something here or can anyone offer anything that would assist me in resolving this error? Thanks, Chris Sayre

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