Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

FS_7_2_0_Ubuntu_18_04_06.ova.7z password
by Marcel Heers 24 Nov '22

24 Nov '22

External Email - Use Caution Can you please share the password for the above mentioned VirtualBox with me? Thanks in advance! Marcel

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Permission denied error
by Adam Tartaglia 23 Nov '22

23 Nov '22

External Email - Use Caution Hello, Immediately after running recon-all, I get an error that says cannot create directory, permission denied. I am not sure as to why this is happening. My license is in the correct location. Thank you for your time, - Adam

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Semi-automatic tool for QC of 41 TRACULA paths?
by Blujus, Jenna 23 Nov '22

23 Nov '22

External Email - Use Caution Hi all, I recently ran the longitudinal TRACULA pipeline in a large dataset (>600 participants) using Freesurfer v7.3.2. Each participant in this dataset has two time points of data. I've finished running trac-all -path, so each dataset has 42 reconstructed WM tracts. I see in the tutorial that visual QC is recommended to check path outputs for partial reconstruction errors. Given our large dataset (1200 scans x 42 tracts), I was wondering what QC procedures you would recommend. I know that visual inspection is the gold standard, but are there any automatic or semi-automatic procedures you would recommend? Thank you, Jenna

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How to set original orientation to be sagittal view?
by Haiyun Chen 22 Nov '22

22 Nov '22

External Email - Use Caution Hello Freesurfer Experts, How can we set the original orientation of an image file such that when the image is opened in a different application the original orientation is a sagittal viewport? For the file aseg.mgz in the below directory based on your tutorial, could you please tell a specific command to convert aseg.mgz to a file with sagittal viewport as the original orientation? tutorial_data_20190918_1558/practice_with_data/Subj001/mri/aseg.mgz Thank you in advance! Best regards Haiyun

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infant_recon_all surface correction
by Laura Mazzocchi 22 Nov '22

22 Nov '22

External Email - Use Caution Dear Experts, I am working with FreeSurfer infant_recon_all and I need to correct the pial surface for most of the analyzed subjects. I would like to implement this correction by fixing the intensity normalization using control points, as well as for the adult subjects with tkmedit, but I can not understand if it is then possible to re-run the infant_recon_all pipeline (or how) after the cp definition, since it seems to me that it does not exist the possibility to add -autorecon2-cp and -autorecon3 flags to infant_recon_all, like with the pipeline for adults. So, I am asking if you have some suggestion to do that. I have already tried to normalize the intensity with flag --intnormFSL, specific for infant_recon_all. The result is better but not the best. Is there any other possibility? For example: - to launch mri_nu_correct.mni --i $infile --o $nufile Then, should I add the --masked flag at the infant_recon_all command by passing $nufile as input? Which is the difference between this one and the --intnormFSL option? - Is there something similar to the adult -autorecon2-cp also for infants? - Do you think that the application of AntsN4BiasFieldCorrectionFs is a good idea? And what about the possibility of applying newborn FLAIR sequence to the Bias Field corrected images? - Could it be better to create my own atlas and to use that to obtain a better segmentation? Thank you very much for any kind suggestion. Best Regards, Laura Mazzocchi --- La ricerca neurologica ha bisogno anche di te SOSTIENI LA FONDAZIONE MONDINO CON IL TUO 5 X MILLE http://secure-web.cisco.com/1OcBqU8Yy68wxtJrh1xuYaYanoYCq1G_wyTWR4VlJonLrJ1…

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Re: [Freesurfer] Issue with rotation during longitudinal base creation
by Huang, Yujing 22 Nov '22

22 Nov '22

Hi Nathan, Can you confirm that the error was from mri_robust_template? Not sure what your command line options. I think these options ‘—inittp <>’, ‘--fixtp’, ‘—seed <>’ might help. Best, Yujing -------- Forwarded Message -------- Subject: [Freesurfer] Issue with rotation during longitudinal base creation Date: Wed, 12 Oct 2022 16:54:29 +0000 From: Nathan Kindred (PGR) <N.Kindred1(a)newcastle.ac.uk><mailto:N.Kindred1@newcastle.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Hi, I have been processing longitudinal data using the longitudinal processing stream but for some subjects I am having getting this error when creating the base: Input rotation's max deviation from rotation is: 0.000258493 MyMatrix::RotationMean input(s) not rotation What would be the best way to fix this? Best, Nathan

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Requesting pass code for Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0
by Adam Tartaglia 21 Nov '22

21 Nov '22

External Email - Use Caution Hello, Can I get the pass code for the Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0 release installed on it? Thank you, - Adam

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Passcode for Freesurfer 7.2.0
by Adam Tartaglia 21 Nov '22

21 Nov '22

External Email - Use Caution Good morning, Would you please send me the pass code for opening the archive of FS 7.2.0? Thank you, - Adam

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Re: [Freesurfer] aparcstats2table segmentation fault error
by fsbuild 20 Nov '22

20 Nov '22

External Email - Use Caution You don’t need to manually set MINC_BIN_DIR or the MINC_LIB_DIR variables as those should get set when you source the freesurfer setup script. Try manually running the bash shell, set FREESURFER_HOME, and check you can see that directory, $ bash$ export FREESURFER_HOME=/home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0$ ls $FREESURFER_HOME< … output deleted but you should see the top of the tree including the SetUpFreeSurfer.sh script you are going to source … > Then source the setup script, $ source $FREESURFER_HOME/SetUpFreeSurfer.sh< … output deleted … > Then try running the command in debug mode and see if you get the help output.  If you see the help output, then the command ran. $ bash -x `which aparcstats2table` --help + '[' '!' -e  /home/ericlyn/local/easybuild/software/2020/Core/freesurfer/7.2.0']'+ exec /homes/1/rd521/freesurfer/dev/bin/fspython /homes/1/rd521/freesurfer/dev/python/scripts/aparcstats2table —help< … help output deleted ... > - R. On Nov 15, 2022, at 22:07, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell.  I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try$ mv .local local… reset FREESURFER_HOME, source the setup script again, and see if running the command works.- R.On Nov 15, 2022, at 19:59, Eric Yin <eric.yin(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. <9ECE8F5D2E7645A5962B55E842687C47.png> I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). <4E289904EB384B21861CA9E16B7DD234.png> Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. <64B17BE84D1E4AFBBF7FFCE28ED15CD7.png> Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time._______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1FgpEnfiQUT43jn39cU5NylGOXNr2K7trxyVjQ… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] aparcstats2table segmentation fault error
by fsbuild 20 Nov '22

20 Nov '22

External Email - Use Caution Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks like you are using a “dot” directory named “.local” in your path for FREESURFER_HOME which is usually reserved for hidden subdirs in the shell.  I would not name any subdirectory to begin with a "dot" for normal use with the shell, so try $ mv .local local … reset FREESURFER_HOME, source the setup script again, and see if running the command works. - R. On Nov 15, 2022, at 19:59, Eric Yin <eric.yin(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. <9ECE8F5D2E7645A5962B55E842687C47.png> I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). <4E289904EB384B21861CA9E16B7DD234.png> Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. <64B17BE84D1E4AFBBF7FFCE28ED15CD7..png> Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer November 2022