Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

Group analysis
by Hengameh Marzbani 14 Mar '20

14 Mar '20

External Email - Use Caution Hello Freesurfer developers, 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary (summary of clusters (text))which is obtained from mri_glmfit-sim. Is there a way to do this? 2- I don't see any clusters when I use cluster-based correction for multiple comparisons (for example mri_glmfit-sim \ --glmdir lh.Area.glmdir \ --sim mc-z 10000 2 mc-z.abs\ --sim-sign abs --cache 4 neg \ --cwp 0.05\ --2spaces). How much is it significant if I report the uncorrected clusters? 3- Are there new ways of looking at the whole brain together (not left and right hemisphere separately)by Qdec and FSGD? 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use? 5- How can I demean and normalize the covariates when I use FSGD? what flag should I use? Thanks you in advance! Best regards, Hengameh

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tracula error too many ('s
by Renew Andrade 14 Mar '20

14 Mar '20

External Email - Use Caution Dear FreeSurfer experts: I mentioned an error that I still cannot fix. I don’t think is the “\” because as you can see in the file attached everything seems correct. I cannot fix the issue with TRACULA I attach the configuration file so you can check in effect is correct. Sincerely, Andrade.

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Error in segmentSubjectT1_autoEstimateAlveusML
by Pascale Patenaude 14 Mar '20

14 Mar '20

External Email - Use Caution Hello FreeSurfer developers, When trying to run segmentHA_T1.sh with the dev version of FreeSurfer to accomplish hippocampal subfield and amygdala subnuclei segmentation (see FreeSurfer module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) I get this error: Open file failed because file '/tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' Attempt to execute SCRIPT kvlWriteImage as a function: /tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m Error in segmentSubjectT1_autoEstimateAlveusML (line 1547) This tmp/MCR_3413898417/.mcrCache8.4/segmen0/autofs directory does not exist. I also have the matlab runtime required for this FreeSurfer module installed. Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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dmri_pathstats segment
by Wang, Lily 13 Mar '20

13 Mar '20

Hi, I am trying to get voxel by voxel stats for fmajor on a threshold that's not the 0.2 default because when I looked at merged nii, fmajor is constructed correctly but on a different threshold. This is the command I used: dmri_pathstats --intrk fmajor_PP_avg33_mni_bbr/path.pd.trk --dtbase ../dmri/dtifit --outvox new_fmajor --pthr 0.4 And I am getting in the terminal: INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 940 streamlines as length outliers INFO: Have 1460 total streamlines (min/mean/max length: 75/101/117) INFO: Have 1460 non-truncated streamlines (min/mean/max length: 75/101/117) Segmentation fault (core dumped) Am I running the command incorrectly? Thank you, Lily

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Re: [Freesurfer] Freesurfer Set-Up Help
by fsbuild 13 Mar '20

13 Mar '20

External Email - Use Caution Hello Liam, Have you tried following the “Setup Instructions” under, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. ? For the 6.0.0 release: If you are on the Mac, running the .pkg installer should give you the distribution under /Applications/freesurferThen you would set FREESURFER_HOME to /Applications/freesurfer If you are on Linux, you need to choose a location to install it.  It is typically put under /usr/local, and if you expand the archive there, you will get /usr/local/freesurfer, e.g, assuming the archive is in your downloads folder$ cd /usr/local$ sudo tar zxpf ~/Downloads/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gzThen you would set FREESURFER_HOME to /usr/local/freesurfer - or follow what is under the section “Setup & Configuration” - R. On Mar 13, 2020, at 21:24, Liam Sullivan <maillts28(a)gmail.com> wrote:        External Email - Use Caution        Hi there,I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process.Once Freesurfer is set-up, I will be using it to measure hippocampal volumes post-ablation.I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. And if possible, if someone is able to chat with me via phone, that would be even better.Thank you.Best,Liam_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer Set-Up Help
by Liam Sullivan 13 Mar '20

13 Mar '20

External Email - Use Caution Hi there, I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process. Once Freesurfer is set-up, I will be using it to measure hippocampal volumes post-ablation. I have followed the instructions online to the best of my ability but can't seem to figure this out. Any assistance would be very much appreciated. And if possible, if someone is able to chat with me via phone, that would be even better. Thank you. Best, Liam

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FreeSurfer Cortical Parcellation using isoDWI image only?
by Yixin Ma 13 Mar '20

13 Mar '20

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if it's possible to run FreeSurfer Cortical Parcellation by just using the isoDWI image. If it's possible, it will reduce the scan time and avoid misregistration between T1 and DWI. I started from just input the masked isoDWI (mask generated from MRtrix3) for -reconall command, and attached is a screenshot of the image of NU.mgz, which shows a clear delineation of WM/GM matter. So I think it's promising, although the recon-all stopped because of the wrong contrast. My ideas on tackling this problem are: 1) generate a corresponding "fake" T1-weighted image by either adjusting the value directly or using a brain Atlas and deformable registration to create one. 2) Tweak some parameters in FreeSurfer. Any suggestions or comments on my ideas are appreciated. Thank you very much and all the best, Yixin Ma [image: Screen Shot 2020-03-12 at 3.06.22 PM.png]

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Functional connectivity analysis ERROR: cannot find.../dof
by Renew Andrade 13 Mar '20

13 Mar '20

External Email - Use Caution Dear FreeSurfer experts: I cannot fix the problem that I mention in the subject. I put the output of the terminal below. I was doing functional connectivity analysis walkthrough tutorial and I followed until group analysis when applying "isxconcat-sess”. I cannot proceed because the “.dof” files are in "/sessx/rest/*” where x is a number from 0 to 9 and * indicates location. So I don’t know why this files are here and not in the analysis subdirectory i.e. “fc.lpccseed.lh”. What is the problem? How should I fix it? Thank you for all the help!! Sincerely, Andrade.

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error when running recon-all
by ZhangBo 13 Mar '20

13 Mar '20

External Email - Use Caution Hi team, I encountered an error when running the test "Candal" dataset. For some patients' files, I found the error information in the log file. So, after "recon-all" finished, I re-run recall for these files with errors. However, error still happened? What's wrong? Thanks. log file for a patient is in the attachment. Best wishes. Bo

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freeview error
by Ortug, Alpen 12 Mar '20

12 Mar '20

Hello FreeSurfer Experts, I'm attempting to install Freesurfer. I am trying to test my installation. $>recon-all -i sample-001.nii.gz -s bert -all ............ $>recon-all -s bert finished without error at Wed Mar 11 19:09:43 EDT 2020 done However, after this I am getting an error message when I try to open in Freeview. It is attached. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Ubuntu 19.10 3) uname -a: Linux antalya 5.3.0-40-generic #32-Ubuntu SMP Fri Jan 31 20:24:34 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 4) error file: see attached Many thanks Best Alpen ORTUG, PhD Post-doctoral Research Fellow Division of Newborn Medicine Boston Children's Hospital Harvard Medical School 401 Park Dr. Boston, MA 02215, USA

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Freesurfer March 2020