Freesurfer January 2023

freesurfer@nmr.mgh.harvard.edu

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un-subscribe
by Noam Khayat 09 Jan '23

09 Jan '23

External Email - Use Caution Hello, Please remove me from the free surfer forum mailing list. Thank you, Noam Khayat

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recon-all terminates with error
by MANSON ERIC NAAB 09 Jan '23

09 Jan '23

External Email - Use Caution Dear FreeSurfer experts, I am a first time FreeSurfer user trying to run a recon-all for a sT1_W image. However, recon-all terminates with an error "tag image orientation not found" I need help on how to resolve this. Kindly find the recon-all.log file.

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Freeview label thickness: making the label outline thicker?
by Greta Tuckute 08 Jan '23

08 Jan '23

Hi developers, I am using Freeview to plot overlays on inflated surfaces with labels: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=OVERLAY_NAME.mgh:overlay_color=colorwheel,inverse,truncate:overlay_threshold=1,5:label=lh.primary.label:label_outline=1:label_color=0,0,0 This command will nicely plot the left fsaverage surface with the overlay of interest as well as the label in a black outline. My question is: the label outline is incredibly thin. I can’t seem to find a command line flag that adjusts this? In the Freeview GUI, there is a place to adjust “Edge thickness” but no matter which value I try, it does not have any effect. Is there any way to do this? Attached Freeview screenshot and label file for reference. Thanks so much for all your great work, Greta External Email - Use Caution

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Re: [Freesurfer] freeview: set file as read only
by fsbuild 07 Jan '23

07 Jan '23

External Email - Use Caution You could try the usual file system commands to set permissions before opening, e.g., read only,  $ chmod 444 myvolume.mgz Or on the command line prior to running freeview, $ chmod 444 myvolume.mgz  &&  freeview myvolume.mgz You could put commands like those into a script with the file name as an argument. - R.On Jan 7, 2023, at 17:00, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com> wrote:        External Email - Use Caution        Hello,Is there a way to set a loaded volume as read only in freeview on the command line?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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STC - Multiband
by Asa Borzabadi Farahani 06 Jan '23

06 Jan '23

External Email - Use Caution Hi, I am using multiband = 4 and according to the dicom files, my slice timing is as below.\ My question is if it is correct to do “-stc –odd “ & “-ngroups 4” in the preproc-sess command? Thank you so much "SliceTiming": [ 0, 0.655, 0.13, 0.785, 0.26, 0.9175, 0.3925, 1.0475, 0.5225, 0, 0.655, 0.13, 0.785, 0.26, 0.9175, 0.3925, 1.0475, 0.5225, 0, 0.655, 0.13, 0.785, 0.26, 0.9175, 0.3925, 1.0475, 0.5225, 0, 0.655, 0.13, 0.785, 0.26, 0.9175, 0.3925, 1.0475, 0.5225, ],

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FreeSurfer VirtualBox 7z-archive code, Ubuntu login credentials, and license file
by Jouhikainen, Pasi J 05 Jan '23

05 Jan '23

External Email - Use Caution Hello, I am an undergraduate neuroscience student at the University of Iowa. I have just started as a research assistant in a cognitive neuroscience laboratory on campus, and the principal investigator has asked me to start getting familiar with FreeSurfer. To practice, I downloaded the FreeSurfer VirtualBox VM image. This seemed like a good way to get started, especially since I have quite of bit of experience working with VMs in the past (including with VirtualBox). Based on the documentation, I would like to request the following three things: (1.) The pass code that is needed to open the 7zip archive (FS_7_2_0_ubuntu_18_04_06.ova.7z) (2.) The password for the user 'developer' that is needed to login to the Ubuntu VM. (3.) A valid 'license.txt' license file to be placed in the ~/Downloads directory inside the VM. If this is not the right email address for such a request, or if there is a different way to obtain those items other than via email, please excuse my mistake and let me know how I should proceed. Thank you in advance! Pasi Jouhikainen

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mri_glmfit with doss isn't working. v7.2
by miracle ozzoude 05 Jan '23

05 Jan '23

External Email - Use Caution Hello, I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like to regress out the effects of groups + other variables by using doss. However, whenever I specify doss with the mri_glmfit command, it gives me an error message (see below). I saw that others have experienced similar issues without any solutions. How can we solve this? Any insight is appreciated. Best, Paul mri_glmfit command: mri_glmfit --y ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres --nii.gz design.mtx: 0 0 0 0 0 0 0.5 Terminal output: gdfRead(): reading dti_RPQ_3.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 46.9333 9.86216 1 Sports 0.0666667 0.249444 2 Games 1.13333 1.62754 3 Days_TBI 1903.2 907.81 4 RPQ_3 7 2.28035 Class Size and Means of each Continuous Variable 1 PPCS_Male 3 33.3333 0.3333 2.3333 1337.3472 6.6667 2 PPCS_Female 12 50.3333 0.0000 0.8333 2044.6632 7.0833 ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you need at least 6 members

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Aseg stats question
by Rosalia Dacosta Aguayo 05 Jan '23

05 Jan '23

External Email - Use Caution Dear Freesurfer team, I have found a warning about not using amygdala, hippocampus and brainstem volumes from asegstats file. I wonder if that is true. Best wishes, Rosie

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Thalamic segmentation tool: question about input files from recon
by Verónica E 05 Jan '23

05 Jan '23

External Email - Use Caution Dear all, I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has been already preprocessed with FreeSurfer 5.3, but I want to rerun the recon step on the newer FreeSurfer version. My question is, which recon output images does the thalamic segmentation use as input? It would make a considerable difference for us if we could only rerun up to e.g. the normalization instead of the whole recon (e.g. to get the aseg.mgz file) in FreeSurfer 7. Sincerely, Verónica

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Additional question in "SynthSR and SynthSeg" FreeSurfer list - RE. 2022.12.15
by Yoonho Hwang 05 Jan '23

05 Jan '23

External Email - Use Caution Dear Douglas N. Greve, Thank you for quickly replying. Although I ask many questions, To reply to the mail kindly and quickly is very grateful for me. It became clear how to analyze it. Nevertheless, *there is an additional question*. Q) 4. When I process T1WI data with Freesurfer dev version, is it installed based on the new version in HPC per version update for freesurfer? A) I don't know what you mean. hcp=? *Additional question)* HPC is high-performance computing (computer cluster). I knew that in order to use the latest SynthSR and SynthSeg, I had to use the latest freesurfer developer version, and the developer version continues to be updated on a daily basis. When the freesurfer development version is updated, should I repeat the process of removing and re-installing the freesurfer development version to use the latest SynthSR and SynthSeg? And then, can you tell me what I need to do to measure the brain morphological property (e.g., cortical thickness and volume, etc) after using synthSR and synthSeg? Thank you very much. Best regards, 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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Freesurfer January 2023