Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

Re: [Freesurfer] Tksurfer Error
by fsbuild 29 Jun '22

29 Jun '22

External Email - Use Caution The tksurfer command is deprecated/no longer supported. You could try using freeview directly or run tksurferfv, which may take the same options as tksurfer but run freeview to display things. - R.. On Jun 29, 2022, at 16:33, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl in the following directories:    /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4   This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:./library./tix8.1./library./tix8.1/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1  How can I fix this error? Thanks, Rachel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: Pass code to expand archive for VirtualBox
by Cody Slater 29 Jun '22

29 Jun '22

External Email - Use Caution Hello, I am following the instructions to install the VirtualBox for Freesurfer 7.2.0 and would like access to the code for expanding the archive. Regards, Cody Slater

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Error Opening File
by Rachel Wagner 28 Jun '22

28 Jun '22

External Email - Use Caution Hello, I am getting the following error when trying to convert a file on my desktop: developer@developer-VirtualBox:~$ mri_convert home/developer/desktop/brain.mgz brain.nii mri_convert home/developer/desktop/brain.mgz brain.nii reading from home/developer/desktop/brain.mgz... error: mghRead(home/developer/desktop/brain.mgz, -1): could not open file developer@developer-VirtualBox:~$ Am I doing something incorrectly? Thanks! Rachel

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Converting File Type
by Rachel Wagner 28 Jun '22

28 Jun '22

External Email - Use Caution Hello, I have an img and an mgz file I would like to convert to a nii file. How can I do so? Thanks! Rachel

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passcord for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Ryo Kitada 28 Jun '22

28 Jun '22

External Email - Use Caution Dear FreeSurfer developer teams, Could you send me the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Cheers, Ryo.

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7Zip Password
by Richard Ronayne 27 Jun '22

27 Jun '22

External Email - Use Caution Hi there, I am trying to unzip FS_7_2_0_ubuntu_18_04_06.ova.7z to run in VirtualBox. Could you please reply to this email with the password for the 7Zip file? Thank you for your time. Kind regards, Richard

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Pass Code for the Virtual Image with FreeSurfer
by Hyun Song 27 Jun '22

27 Jun '22

External Email - Use Caution Hello FreeSurfer developers, I am attempting to set up and run the Freesurfer 7.2.0 release with the virtual image as described in https://secure-web.cisco.com/12fbDRySJWvFNE95kfnxYyknT6iNKMuI4NW2jBTJerlb-r… <https://secure-web.cisco.com/1Yywe94avXxYd05IrWZqd84sqbEs04TfWQqAXcGEXEEWs6…>. Would you please send me the pass code to expand the 7zip file? Thanks much, Best, Hyun

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mri_label2vol fill-ribbon segmentation fault
by Benjamin Deck 27 Jun '22

27 Jun '22

External Email - Use Caution Hi there, Having issues with the following command: mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz produces the following error: Number of labels: 0 Annot File: lh.yeo_2011.annot Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz Outut Volume: lh.sub-DAEK_annot_nat.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: sub-DAEK Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects 7.2.0 Template RAS-to-Vox: -------- -1.25000 -0.00000 -0.00000 160.00000; -0.00000 -0.00000 -1.25000 160.00000; -0.00000 1.25000 -0.00000 160.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 0.512 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -1.25000 0.00000 0.00000 160.00000; 0.00000 0.00000 -1.25000 160.00000; 0.00000 1.25000 0.00000 160.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white nvertices = 253237 Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness Loading annotations from lh.yeo_2011.annot annotidmax = 48 nlabels = 48 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz Mapping Segmentation fault But when I run the same command without fill-ribbon the process runs to completion. Not sure if this is a memory issue or something else. Ben -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1iKwJbETCAUSlHWE3gbz9IWJ4YvkeL0JhP2fGTP_IRLe0Y…> Virus-free. http://secure-web.cisco.com/1sIn3vnwCXrSMS_IlIv6nc9WGBmrAG1JrUsifsa6xR7SIRw… <https://secure-web.cisco.com/1lKwnHJD_3HKNZFq3yBeIxnL1wagOdiYUAdM7xFJLwCTPp…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Fwd: Pass code request for 7z
by Lesly Manresa 27 Jun '22

27 Jun '22

External Email - Use Caution Hi, I am writing to request the pass code to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Thanks, Lesly

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MeanItensities- PET
by Bouchra Guelib 27 Jun '22

27 Jun '22

External Email - Use Caution Hi, I wonder if someone can help me to do something similar to that: " the mean intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical regions were assessed the mean intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical regions were assessed to obtain SVU". Also, I found an article that mentioned that " the estimated total intracranial volume (eTIV) is calculated, which is used later for normalization of the volumetric measures". My questions are: 1) In " gtm.stats.dat" not all subcortical regions are mentioned, why? 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could not figure out what I should do after this step to obtain the mean intensity and compute SVU. 3) why do they use eTIV, should I use it, and if yes how! best regards. -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

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Freesurfer June 2022