Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Thalamic segmentation questions
by Manoj Saranathan 29 Jan '19

29 Jan '19

External Email - Use Caution The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations. My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned? Thanks, manoj ________________________________ From: Manoj Saranathan Sent: Tuesday, January 29, 2019 5:11 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Thalamic segmentation questions The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations. My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned? Thanks, manoj ________________________________ From: Manoj Saranathan Sent: Tuesday, January 29, 2019 5:06 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Thalamic segmentation questions The thalamic registration produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice with manual segmentation. The 'reslice like' option of mri_convert does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually register and propagate the warps if they are not aligned. Thanks, manoj Manoj Saranathan Associate Professor, Dept. of Medical Imaging University of Arizona Ph: 520-626-6531

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LME
by Tefera, Getaneh B 29 Jan '19

29 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh --

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Running Freesurfer on Linux VM on Google Cloud Platform (GCP)
by Yi-Fang Chuang 29 Jan '19

29 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm recently attempting to run Freesurfer for structural MRI on VM on Google Clound Platform with the hope that recon-all runtime can be shortened in a great deal. My own Desktop is Mac Pro (3.7 GHz quad-core intel xeon E5, 16G memory). The recon-all runtime (Freesurfer version 5.3.0, no parallel) for a single subject is usually 7~8 hours. The specs of VM on GCP as follows, Linux CentOS 6, 16 CPU(Intel(R) Xeon(R) @ 2.50GHz) with 60 G memory I installed Freesurfer v 6.0.0 and run recon-all with -parallel -openmp num flag No matter what number I put (6,8,12,16 after openmp), the recon-all runtime of single subject ranges 6-7 hours. Is this reasonable? So only 1-2 hour shorter than my Mac Pro?? Or is there anything I should pay attention to set up? Thanks~~ -- Yi-Fang Chuang (莊宜芳), M.D., Ph.D. Assistant Professor Institute of Public Health, National Yang-Ming University No. 155, Sec. 2, Linong Street, Taipei, 11221 Taiwan (R.O.C) +886-2-28267000#7981 chuangy(a)ym.edu.tw <chuangy(a)mail.nih.gov> Attending physician Department of Psychiatry, Far Eastern Memorial Hospital No.21, Sec. 2, Nanya S. Rd,. Banqiao Dist., New Taipei City 220, Taiwan (R.O.C) Special Volunteer NIA-Laboratory of Behavioral Neuroscience-Unit of Clinical and Translational Neuroscience BRC-Biomedical Research Center, 04C316 251 Bayview Blvd. Baltimore, MD chuangy(a)mail.nih.gov ᐧ

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Re: [Freesurfer] Trouble Installing FreeSurfer
by fsbuild 28 Jan '19

28 Jan '19

External Email - Use Caution Hello Rodrigo, Did you download the tar file freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz from this page, and attempt to follow the steps below ? https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall If you do not have permission to untar (write files) into /usr/local, you could try using another path. But usually if the tar command has a problem it will echo some error/text to the terminal, e.g., "Permission denied", or say there was an error. If the command simply returns to the prompt than it should have succeeded, e.g., success with "$" bash shell prompt. $ tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz$ Please try and point out the step that does not work for you. - R. On , at 17:47  1/28/2019, Rodrigo Montenegro <rmontenegro11(a)gmail.com> wrote:        External Email - Use Caution        Dear FreeSurfer Team, I’m a Medicine student at Oxford University and I have just registered to FreeSurfer. I just went through the registration process so I'm very new to FreeSurfer but have only run to problems so far and would like to ask for your help: 1.       I have register with FreeSurferWiki but can’t login: it gives me one of the following errors:i.                      “Error 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache serve”.ii.                   Or that it is an “Invalid username or password” (not sure if  2.       More importantly I have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine and I have the “freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz” to install FreeSurfer but the being totally new to Linux I have not had success to install it:i.                     I’m not sure if at all the files are unzipped from the .gz file.ii.                   And I have been unable to create the Bash files to define the environment for it. 3.        Finally, I notice that you do have an installation for Virtual Disk Image but the download for it (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu…) is a gz file not a .vdi file as it should be (see picture below): <image002.jpg> So either way I wasn’t able to get through with the installation and any help is appreciated. Could you please provide some advice? Many thanks, Rodrigo Montenegro+44(0)7503070807 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trouble Installing FreeSurfer
by Rodrigo Montenegro 28 Jan '19

28 Jan '19

External Email - Use Caution Dear FreeSurfer Team, I'm a Medicine student at Oxford University and I have just registered to FreeSurfer. I just went through the registration process so I'm very new to FreeSurfer but have only run to problems so far and would like to ask for your help: 1. I have register with FreeSurferWiki but can't login: it gives me one of the following errors: i. "Error 403 Login/Edit allowed only on https/SSL connections Login/Edit allowed only on https/SSL connections Guru Meditation: XID: 1153030795 Varnish cache serve". ii. Or that it is an "Invalid username or password" (not sure if 2. More importantly I have also tried to install FreeSurfer in Virtual Box (4096 MB Memory; 32 MD Video Memory; Ubuntu 64 Bits) without any success. The Ubuntu system works fine and I have the "freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz" to install FreeSurfer but the being totally new to Linux I have not had success to install it: i. I'm not sure if at all the files are unzipped from the .gz file. ii. And I have been unable to create the Bash files to define the environment for it. 3. Finally, I notice that you do have an installation for Virtual Disk Image but the download for it (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtu albox-linux-x86-stable-pub-v5.3-full.vdi.gz) is a gz file not a .vdi file as it should be (see picture below): So either way I wasn't able to get through with the installation and any help is appreciated. Could you please provide some advice? Many thanks, Rodrigo Montenegro +44(0)7503070807

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mri_vol2vol
by Nasiriavanaki, Zahra 28 Jan '19

28 Jan '19

Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually made, from fsaverage to individual subject's space. I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my command below: mri_vol2vol --mov ./${ROI}/ROI4.mgz --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz --talres 2 --interp nearest --regheader Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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cortical thickness calculation based on hammersmith segmentation
by Boris Rauchmann 28 Jan '19

28 Jan '19

External Email - Use Caution <>Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjects. I tried mri_vol2surf and then mris_seg2annot but without success so far. What commands would you recommend me to run? Thanks, Boris

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Cortical & subcortical cluster size
by Jahan, Bushra 28 Jan '19

28 Jan '19

Hi, I'm wondering which column in the FreeSurfer summary file represents the cluster size for the cortical and subcortical clusters.

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Cannot create template when running longitudinal freesurfer 6.0.0
by Kilian Pohl 28 Jan '19

28 Jan '19

External Email - Use Caution Hi , The following command worked fine under 5.3.0 recon-all -openmp 88 -sd LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer -base template_baseline_1 -tp baseline -tp 1 -all but now it produces there error ERROR: It appears that the -base templateID that you passed: -base template_baseline_1 is an existing regular (cross sectional) run! Please make sure you pass a new name (not one of the time points) for the template with -base. For example, if you are trying to create a -base: \' -base BertTemplate -tp Bert1 -tp Bert2 ... \' There is no existing regular (cross sectional) run. Do you know what the issue is ? The only dirs in LAB_S00308/standard/20161209_2776_12092016/structural/longitudinal/freesurfer are lrwxrwxrwx 1 djk root 100 Jan 28 10:29 1 -> ../../../../20161209_2776_12092016/structural/freesurfer6/LAB_S00308_standard_20161209_2776_12092016 lrwxrwxrwx 1 djk root 100 Jan 28 10:29 baseline -> ../../../../20080725_3594_07252008/structural/freesurfer6/LAB_S00308_standard_20080725_3594_07252008 drwxr-xr-x 3 djk root 23 Jan 28 10:29 template_baseline_1 Thanks Kilian

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Question regarding white substance with Freesurfer
by Erika Portera 28 Jan '19

28 Jan '19

External Email - Use Caution Good evening, I write you to resolve a problem with the program of freesurfer. Also following the tutorial for the corrections, I don't succeed in integrating parts of white substance. The problem concerns the underlying images ( error temporal gyrus sx) I thank you for your help. Erika Portera

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Freesurfer January 2019