Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Tcl_Init error on Ubuntu
by Kevin Nguyen 20 Sep '21

20 Sep '21

External Email - Use Caution Hey FreeSurfer community! I am running into a problem when trying to use the command "qdec --table $SUBJECTS_DIR/cross.qdec.table.dat" on my data. The following error message is shown: """ Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /home/kevin/freesurfer/lib/tcl8.4 /home/kevin/lib/tcl8.4 /home/kevin/freesurfer/library /home/kevin/library /home/kevin/tcl8.4.6/library /home/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Error initializing Tcl. """ I suppose there are version issues between the FreeSurfer version of Tcl (8.4.6?) and my own version (8.6). I would very much appreciate any help with that error:) Also, I am very new to Unix and FreeSurfer. I am running the latest FreeSurfer version as well as Ubuntu 20.04.3 LTS. Thanks in advance for your help! Best, Kevin

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Segmentation of thalamic nuclei: LGN volume
by Marco Aiello 20 Sep '21

20 Sep '21

External Email - Use Caution Dear Freesurfer experts, I'm running (FS 7.1.1) segmentThalamicNuclei.sh on T1 scan from recon-all. On a sample of about 100 subjects I've found an average volume of 250 mm^3 and 290 mm^3 for LGN-left and LGN-right, respectively. Consistent with literature, I would expect an LGN volume around the order of 100 mm^3. Do you have any suggestions to address this issue? Best, Marco An example of left thalamic nuclei stats on a subject: # Left Thalamic nuclei volume statistics as created by segmentThalamicNuclei.sh 1 1 0 179.160119 AV 2 2 0 89.639229 CeM 3 3 0 40.504433 CL 4 4 0 298.704524 CM 5 5 0 29.204221 LD 6 6 0 323.610060 LGN 7 7 0 172.804240 LP 8 8 0 16.699212 L-Sg 9 9 0 370.292762 MDl 10 10 0 1028.359432 MDm 11 11 0 99.816768 MGN 12 12 0 16.307111 MV(Re) 13 13 0 4.583480 Pc 14 14 0 46.055844 Pf 15 15 0 8.414055 Pt 16 16 0 274.769665 PuA 17 17 0 276.059756 PuI 18 18 0 197.470981 PuL 19 19 0 1329.257389 PuM 20 20 0 540.769724 VA 21 21 0 48.461021 VAmc 22 22 0 879.500725 VLa 23 23 0 1143.223136 VLp 24 24 0 33.606403 VM 25 25 0 1224.126516 VPL 26 26 0 8671.400807 Whole_thalamus

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Re: [Freesurfer] Ubuntu VM password
by fsbuild 16 Sep '21

16 Sep '21

External Email - Use Caution Sending the info your email shortly. -R. On Sep 16, 2021, at 07:32, tom.liebmann(a)yahoo.com wrote:        External Email - Use Caution        Like a number of similar posts, I am trying to work with the Ubuntu image for running FreeSurfer on my Windows machine.  Without the Administrator password, I cannot run the image.  Can you please provide the password for access.  Thank you very much for the service and the support.Kind regards,-Thomas_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu VM password
by tom.liebmann＠yahoo.com 16 Sep '21

16 Sep '21

External Email - Use Caution Like a number of similar posts, I am trying to work with the Ubuntu image for running FreeSurfer on my Windows machine. Without the Administrator password, I cannot run the image. Can you please provide the password for access. Thank you very much for the service and the support. Kind regards, -Thomas

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Re: [Freesurfer] Freesurfer 7.1.0 VirtualBox password
by fsbuild 15 Sep '21

15 Sep '21

External Email - Use Caution Sending the info to your local email shortly. - R. On Sep 14, 2021, at 12:58, Camila Fernandes da Silva <camila.fernandes.silva(a)usp.br> wrote:        External Email - Use Caution        Dear admin, I instaled Freesurfer 7.1.0 using the VirtualBox in my Windows 10.It does not allow me to use it, It asks the developer password.Could you please help me?Thank you so much!-- Atenciosamente,Camila FernandesLicenciatura em Física - IFUSP_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Samseg Choroid Plexus Segmentation T1 and T2-FLAIR separate argument
by Robb, William Hudson 15 Sep '21

15 Sep '21

External Email - Use Caution Hello, I am attempting to segment the choroid plexus using T1 and T2-FLAIR images as inputs to Samseg. On our T1 images, the choroid plexus is hardly visible, but it is much more visible on T2-FLAIR. Samseg seems to be failing to segment the choroid plexus on some images, but does a good job on others. For the pallidum, there is a flag “--pallidum-separate” which seems to privilege the T2-FLAIR for pallidum segmentation. Is there a similar argument or option that could be used to separate the segmentation of the choroid plexus to privilege the T2-FLAIR, such as “--choroid-separate”? Thank you, Hudson Robb

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ERROR: mri_ca_register with non-zero status 1
by Yanyu Xiong 15 Sep '21

15 Sep '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recond-all on multiple subjects with T2 used to help improve pial reconstruction. However, I got the following error message for many subjects: ERROR: mri_ca_register with non-zero status 1 I have attached the recon-all.log in case it's of any use.

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mri_vol2surf clarification
by Alice Giubergia 15 Sep '21

15 Sep '21

External Email - Use Caution Dear Freesurfer's experts, I am dealing with time course extraction from preprocessed (prerpoc-sess) task functional data; I was able to extract the time courses from the fsaverage sampled surfaces fmcpr.up.sm3.fsaverage.lh.nii.gz thanks to mri_segstats, but I was wondering how to handle the data sampled to the MNI space fmcpr.up.sm5.mni305.2mm.nii.gz. I think I should run mri_vol2surf to get a surface but I don't get the kind of registration option should I use. mri_vol2surf --src fmcpr.up.sm5.mni305.2mm.nii.gz I would appreciate any suggestion, many thanks, Alice

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Calculating GMV
by Brigitte Pace 15 Sep '21

15 Sep '21

External Email - Use Caution We are trying to calculate the volume of grey matter of the significant clusters within each region identified by our initial analyses. Is there a procedure already written in matlab to accomplish this calculation? Right now we've calculated the mean thickness across all subjects for each vertex, and then averaged those thickness across each region (or across each significant portion of a region). Then took the areas from the regions (calculated through Freesurfer’s mri_surfcluster program, which for the whole regions will obviously only get a single cluster, and total area of that cluster) and multiplied them by the mean thicknesses to get total area. It should be possible to do the same thing to get the significant volumes. Does the above procedure seem like the most straightforward? Or does freesurfer have a program to do this more efficiently? -- Brigitte Pace, M.A. Doctoral Student Clinical Psychology, Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine

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recon-all crash errors (fMRIPrep)
by Rubina Chandnani 15 Sep '21

15 Sep '21

External Email - Use Caution Hi there, I'm getting in touch because I'm consistently running into a repeated recon-all error. I've tried so many suggestions (from Neurostars) and I was wondering if you can maybe suggest an alternative to running the Freesurfer license. I used this code on Ubuntu 20.04 on Windows (it worked smoothly for 17 participants and failed on the remaining participants I need to run pre-processing): fmriprep-docker /mnt/c/Users/rubin/BIDS /mnt/c/Users/rubin/derivatives participant --participant-label sub-M1121053 --fs-license-file /mnt/c/Users/rubin/fs-license/license.txt --low-mem More specifically, I get these errors (please see 4 attachments). I also tried gzipping the files (with .gz at the end of the files) but even that failed. Are there any suggestions that you can offer that would help resolve these errors? I look forward to hearing from you. If there is anything you need from my end, please do get in touch with me. Thank you and best regards, Rubina Chandnani

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Freesurfer September 2021