Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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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Italian Summer School: Interdisciplinary Research on Brain Network Dynamics
by Jovicich, Jorge 28 Jan '19

28 Jan '19

External Email - Use Caution Dear all, we are organizing an international summer school on interdisciplinary research oriented to the study of brain network dynamics (June 24-28, 2019). More information: https://event.unitn.it/brandyschool2019/ Feel free to disseminate to relevant groups. Regards, Jorge -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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Orientation by direction cosines
by Ritesh Mahajan 26 Jan '19

26 Jan '19

External Email - Use Caution Hello Team, Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines: Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What does this signify ? 0.999377 0 -0.0352819 -0.00916448 0.965676 -0.259588 0.0340709 0.25975 0.965075 Suppose it is Head First Supine. Any help will be really appreciated. Thanks, Ritesh Mahajan

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dispaly retinotopy result
by starxifd 25 Jan '19

25 Jan '19

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FSFAST poor registration
by Keri Woods 25 Jan '19

25 Jan '19

External Email - Use Caution Hi I have a problem very similar to this one: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html I've tried the suggestions given there, but it didn't fix my problem. I'm running the FSFAST preproc-sess stream and the quality of the registration is very poor for most of the subjects. I've tried initializing the registration differently, using bbregister with --init-fsl, --init-spm and init-header, which didn't improve the results at all. I've also tried register-sess with --init-fsl, --init-spm and init-header, as well as spmregister-sess and fslregister-sess. Is there anything else I could try? Using the SPM GUI, the registration was fine, so I thought that spmregister-sess would have been an improvement, but it wasn't. Is there anyway I can import the registration obtained using the SPM GUI? Thanks for your help. Thanks, Keri

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