Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

skull stripping and white matter labelling
by miracle ozzoude 21 Oct '16

21 Oct '16

Hello experts, I did my skull stripping and white matter labelling using an lesion explorer and I want to replace the brainmask.mgz and wm.seg.mgz generated by freesurfer with the brainmask and wm.seg.mz from lesion explorer. Is there a freesurfer script that can do it? Thanks, Paul

3 3

Interpretation of QA tools results
by Matthieu Vanhoutte 21 Oct '16

21 Oct '16

Dear FS experts, Could you explained me how to interpret results from the QA tools. Please find attached the recon_checker summary log. 1) How to know there is a problem according to results below: *checking subcortical label: Left-Cerebral-Exterior, 0 +/-* *checking subcortical label: Left-Cerebral-White-Matter, 0 +/-* *checking subcortical label: Left-Cerebral-Cortex, 0 +/-* *checking subcortical label: Left-Lateral-Ventricle, 1.77932 +/-* *checking subcortical label: Left-Inf-Lat-Vent, 0.115084 +/-* *checking subcortical label: Left-Cerebellum-Exterior, 0 +/-* *checking subcortical label: Left-Cerebellum-White-Matter, 0.768042 +/-* *checking subcortical label: Left-Cerebellum-Cortex, 2.50118 +/-* *checking subcortical label: Left-Thalamus, 0 +/-* *checking subcortical label: Left-Thalamus-Proper, 0.324235 +/-* *checking subcortical label: Left-Caudate, 0.190688 +/-* *checking subcortical label: Left-Putamen, 0.24631 +/-* *checking subcortical label: Left-Pallidum, 0.0782828 +/-* *checking subcortical label: 3rd-Ventricle, 0.127606 +/-* *checking subcortical label: 4th-Ventricle, 0.0697322 +/-* *checking subcortical label: Brain-Stem, 1.2108 +/-* *checking subcortical label: Left-Hippocampus, 0.191568 +/-* *checking subcortical label: Left-Amygdala, 0.0665945 +/-* *checking subcortical label: Left-Insula, 0 +/-* *checking subcortical label: Left-Operculum, 0 +/-* *checking subcortical label: Line-1, 0 +/-* *checking subcortical label: Line-2, 0 +/-* *checking subcortical label: Line-3, 0 +/-* *checking subcortical label: CSF, 0.0903738 +/-* *checking subcortical label: Left-Lesion, 0 +/-* *checking subcortical label: Left-Accumbens-area, 0.0259807 +/-* *checking subcortical label: Left-Substancia-Nigra, 0 +/-* *checking subcortical label: Left-VentralDC, 0.196737 +/-* *checking subcortical label: Left-undetermined, 0 +/-* *checking subcortical label: Left-vessel, 0.0043689 +/-* *checking subcortical label: Left-choroid-plexus, 0.0806885 +/-* 2) When looking at the white matter QA, three colors are used: red (pial surface ?), yellow (white surface ?) and green (?). Does it make sense to verify all colored surfaces or only the white matter surface in this WM QA ? How to decide when rejecting bad preprocessed subject ? Best regards, Matthieu

2 1

Cortical Thickness Zero Values
by Taha Abdullah 21 Oct '16

21 Oct '16

Hello All, Quick question, I ran recon-all with the qcache option and after converting the ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am noticing some vertices have 0mm thickness and it varies, for example, one subject had 53 vertices labeled as zeros while another had over 9,000 vertices. Is there a method I can use to have a thickness value for each of the 163000+ vertices? I am not sure if this is a possible registration issue to mni305. Thanks in advance, Taha -- *Taha Abdullah* *Department of Physiology,* *Northwestern University Feinberg School of Medicine* *MS in Physiology and Biophysics, Georgetown University 2015* *Work Cell: (312)-451-8468*

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cannot find input file
by Marja Caverlé 21 Oct '16

21 Oct '16

Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja

3 15

Re: [Freesurfer] Ubuntu 16.04 solution?
by NIELS JANSSEN . 21 Oct '16

21 Oct '16

This issue has been resolved. The problem was not Ubuntu 16.04. For some bizarre reason I received the wrong license file contents. When using my institutional email on the freesurfer website registration form I receive this file: The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Which is not the contents of the license file. However, when I put in my gmail email address on the registration form I receive an email with the correct license file. I hope the freesurfer support team can look into this issue. Thanks again. On Thu, Oct 20, 2016 at 4:57 PM, NIELS JANSSEN . <njanssen(a)ull.edu.es> wrote: > Hi Burkhard, > > Thanks for the message but this does not solve my problem. I untarred as > root in /usr/local, and as myself in /home. I also requested a new license > file (which appears the same btw), and it does not matter. For all options > I am still getting the same error saying my license is invalid (ERROR: > Invalid FreeSurfer license key found in license file). Note that when I > installed version 5.3 the license file worked fine (but I got the > nu_correct) problem. > > I am lost here as to what is causing this. I feel like going back to 14.04 > may be the only way forward. > > Thanks again. > > > > > > >> Hi Niels, I also downloaded the development version recently. After >> untarring all files >> are mine (my uid & gid). Did you unpack the tar file as root? >> Then, I had to request a new license from the freesurfer team. Freesurfer >> did >> not accept the old license anymore. But that was it - now it runs again. >> And I >> did not see this mri_nu_correct error anymore. >> all the best, >> Burkhard -- >> Dr. Burkhard Maess >> Max Planck Institute for Human Cognitive and Brain Sciences >> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig >> Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess >> 'at' >> cbs.mpg.de, http://www.cbs.mpg.de > > > > > -- > Niels Janssen > Cognitive Neuroscience Laboratory > Institute of Biomedical Technologies > Center for Biomedical Research of the Canary Islands > University of La Laguna > Tenerife, Spain > http://www.neurocog.ull.es/en > -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

1 0

Fw: [mri_cvs_register] error: sLF Undefined variable
by Stefano Zappala' 21 Oct '16

21 Oct '16

Hello FreeSurfer Developers, I am having some problems using the mri_cvs_register toolbox of FS. The error is the following one (it is caused even in the simplest case of registration of the sample data file "$FREESURFER_HOME/subjects/sample-001.mgz" over the CVS template)(the installation folder is /home/zappst/Desktop/freesurfer): zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs Log file is /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz_to_cvs_avg35.mri_cvs_register.1610210944.log: No such file or directory. Then I tried to add the "--nolog" argument, causing another error: zappst@Ubuntu:~$ mri_cvs_register --mov /home/zappst/Desktop/freesurfer/subjects/sample-001.mgz --nolog Using the CVS template as registration target... The outdir: /home/zappst/Desktop/freesurfer/subjects//home/zappst/Desktop/freesurfer/subjects/sample-001.mgz/cvs sLF: Undefined variable. Actually, the same error regarding the undefined variable sLF is caused even when calling mri_cvs_register on other images. I tried in vain to uninstall FS and now I have the version "freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0" on Ubuntu 16.04 LTS. The test reported in http://freesurfer.net/fswiki/DownloadAndInstall for testing the installation completed successfully (so it seems that the problem is related to mri_cvs_register). So, I was wondering what can I do in order to solve the problem. Thanks for the attention. Best, Stefano.

1 0

mris_register question
by Nicholas Heugel 20 Oct '16

20 Oct '16

I am encountering an odd effect when using the Freesurfer maps in Brainstorm. I have Individual activity for multiple subjects where the activity generally seems to look generally well spread across teh gyrus and sulcus in task relevant areas. However, when I map the individual subjects onto the freesurfer average anatomy, and average the activity it's primarily in the sulcus that the activity across subjects is prevalent. Most notably, it becomes heavily present in the Sylvian fissure. I was looking through the mris_register function, and it seems the sulci are used as one of the primary alignment measures, and was wondering if this could be giving rise to this propensity of the group maps to appear predominantly in the sulcus. Looking through the settings I am not 100% clear on what all the settings do. So I was wondering if anyone had encountered this issue before. And what settings for the mris_register I should look at adjusting to try and correct the issue. Thank you for your time and assistance. Nicholas Heugel Biomedical Engineering Ph.D Candidate Marquette University

2 3

FS download for Windows
by John Hettema 20 Oct '16

20 Oct '16

All, Last week I downloaded the Windows installation version (Virtualbox) from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall. After completion ~ 90 minutes later, it was quite confusing what got downloaded and where. There might be 2 potential issues I wanted to check before I do it again: 1. I made the mistake of unzipping the .gz file, leaving me with 12 files with extensions .CUSTOMDESTINATIONS-MS. 2. I already had VB on my PC from the AFNI course OCT 2015. Not sure if that messed anything up. Is there any way for me to run my current version of VB with these files? If not, what should I do when I download the package this time? Thanks, Jack Hettema John M. (Jack) Hettema, M.D., Ph.D. Associate Professor Virginia Institute for Psychiatric and Behavioral Genetics Department of Psychiatry, Virginia Commonwealth University Mailing Address: VCU P.O. Box 980126, Richmond VA 23298-0126 Street Address: 800 East Leigh St. Room 1-116, Richmond, VA 23219 Email address: john.hettema(a)vcuhealth.org Telephone: 804-828-8592 Fax: 804-828-1471 NOTE: The information contained in this message may be privileged and confidential and protected from disclosure. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by replying to the message and deleting it from your computer. ---------- VCU Health System http://www.vcuhealth.org ----

1 0

de-identify DICOM
by John Anderson 20 Oct '16

20 Oct '16

2 1

Re: [Freesurfer] Ubuntu 16.04 solution?
by NIELS JANSSEN . 20 Oct '16

20 Oct '16

Hi Burkhard, Thanks for the message but this does not solve my problem. I untarred as root in /usr/local, and as myself in /home. I also requested a new license file (which appears the same btw), and it does not matter. For all options I am still getting the same error saying my license is invalid (ERROR: Invalid FreeSurfer license key found in license file). Note that when I installed version 5.3 the license file worked fine (but I got the nu_correct) problem. I am lost here as to what is causing this. I feel like going back to 14.04 may be the only way forward. Thanks again. > Hi Niels, I also downloaded the development version recently. After > untarring all files > are mine (my uid & gid). Did you unpack the tar file as root? > Then, I had to request a new license from the freesurfer team. Freesurfer > did > not accept the old license anymore. But that was it - now it runs again. > And I > did not see this mri_nu_correct error anymore. > all the best, > Burkhard -- > Dr. Burkhard Maess > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig > Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess > 'at' > cbs.mpg.de, http://www.cbs.mpg.de -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

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Freesurfer October 2016