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30089 discussions

Negative areas in mris_sphere, dark in freeview
by Chris Adamson 13 Mar '18

13 Mar '18

Freesurfer devs, I have a baffling problem in mris_sphere. I have generated some surfaces using an external tool that uses VTK. After converting the surfaces into freesurfer format using a basic format converter, then adding volume geometry to the surface file using the image used to create it the surface appears dark in freeview. When I do mris_inflate followed by mris_sphere, mris_sphere says nearly all the triangles have negative area at the end and it never finishes. I verified in MATLAB that the surface normals (computed by mris_convert) of the original white surfaces point outwards. The darkness in freeview is not fixed by changing the order of the indices of the faces (which should invert the normal). I'm at a loss to explain this. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

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running -hippo-subfields with both T1 and T2 using FS 6.0
by Alexopoulos, Dimitrios 13 Mar '18

13 Mar '18

I need a clarification with the command to run for generating the hippo subfields on 6.0 using both a T1 mprage and T2 space (both 1mm isotropic). I'd like to run the entire recon-all -all surface and hippo subfields processing stream. Would this be the correct command: recon-all -s subject -i dicom.dcm -hippocampal-subfields-T1T2 T2.nii.gz T1T2 -all Thanks. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix
by Douglas Greve 13 Mar '18

13 Mar '18

Hi Kai, please remember to post to the list. Your FSGD file is not quite right. Gender is a discrete variable and should be represented by two groups not as a covariate. If Sequence is discrete, then you need four groups (Gender by Sequence). doug On 3/9/18 3:20 AM, k.ohmstedt(a)stud.uni-heidelberg.de wrote: > Dear Douglas, > > the fsgd file I used is attached. Thank you for your help! > > > Best regards > > Kai > > Zitat von "Douglas N. Greve" <dgreve(a)mgh.harvard.edu>: > >> can you send your fsgd file so that I have a better idea of what you are >> mentioning? >> >> >> On 03/08/2018 08:39 AM, k.ohmstedt(a)stud.uni-heidelberg.de wrote: >>> Dear all, >>> >>> I am trying to correlate psychometric measurements and the local >>> Gyrification Index. >>> To do so, I use the FreeSurfer pipeline to calculate the lGI and then >>> PALM, following the advice in this thread >>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.ht…) >>> >>> >>> All my subjects are part of the same group, so I used a FSGD with the >>> group "main" to create the design matrix and mask for my data that are >>> required by PALM. >>> Having a closer look at the design matrix that was created, I found >>> that there was a variable for the group that was the same for all my >>> patients. As it is the same for all patients, I thought eliminating it >>> would not be a problem. But after re-running PALM without it, there >>> were huge differences in my results and effects were notably larger >>> and more significant. >>> >>> Do any of you have any experience which option is best in this case? >>> Is it a valid choice to eliminate the variable for the group, as it is >>> the same for each patient anyway? >>> >>> Furthermore, would you recommend centering for the design matrix? I >>> found that this can have an impact, but I am lost on in which cases it >>> should be done and in which it shouldn't. >>> >>> >>> Thank you for your help! >>> >>> >>> Best regards >>> >>> Kai Ohmstedt >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> >> > >

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Re: [Freesurfer] TRACULA -stat coord output file
by Yendiki, Anastasia 12 Mar '18

12 Mar '18

Hi Carissa – These are MNI coordinates. These mean paths are created only for visualizing group results. However the actual FA, etc measures that are used for group analyses are generated in each subject’s native space. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, March 12, 2018 at 12:54 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA -stat coord output file Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all –stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa

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hew hippocampal and amygdala subfields
by Frodl, Thomas 12 Mar '18

12 Mar '18

Dear All, could you pease give me some advice? When I tried to run the new hippocampal subfield analysis on our high Performance System I got the following error (copied below). It seems the it can't find this MEX file. Many thanks and best wishes Thomas #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Sat Mar 10 16:54:52 GMT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//runtime/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//bin/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/os/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/cports/rhel-6.x86_64/gnu/glib/2.46.2/lib:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/opengl/lib/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/cports/rhel-6.x86_64/gnu/glib/2.46.2/lib:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib Invalid MEX-file '/tmp/MCR_500598999/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64': /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/MCR_500598999/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64) 　 Error in kvlClear (line 11) 　　　 Error in segmentSubjectT1_autoEstimateAlveusML (line 115) 　　　 MATLAB:invalidMEXFile

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TRACULA -stat coord output file
by Carissa Nicole Weis 12 Mar '18

12 Mar '18

Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all -stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa

1 0

FreeSurfer Error Edit Sequence
by David S Lee 12 Mar '18

12 Mar '18

Hello Experts, Do you suggest FreeSurfer users to *strictly* follow the *error edit sequence* (Brain Mask --> WM --> GM --> Control Points) listed here (link below)? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData If not, can users follow this sequence instead: Brain Mask --> Control Points --> GM --> WM? The justification here is to minimize the time spent to perform hand edits. Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

2 1

e-mail error {Disarmed}
by 郑凤莲 09 Mar '18

09 Mar '18

Hi FS list, When I sent an e-mail to you, I always recieved a disarmed e-mail, as follows: What' wrong? Is there any way to resolve it? Sincerely, Zheng | | 13181786167 邮箱：13181786167(a)163.com | 签名由网易邮箱大师定制

1 0

Recon-all {Disarmed}
by 郑凤莲 09 Mar '18

09 Mar '18

Hi experts, I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline for cotical thickness and LGI. Is it suitable? Or are the results reliable, such as the LGI value of precental? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Potential ways to overlay perfusion ROIs onto cortical thickness maps
by Arsenije Subotic 09 Mar '18

09 Mar '18

Dear experts, I am trying to figure out the best way to overlay areas of low CVR reactivity and correlate that with cortical thickness measurements in those given regions. I was able to overlay our CVR map onto an inflated cortical surface in 3D and modify the configuration to see areas of low perfusion in blue. Using QDEC, I also know that you can manually trace an ROI and generate cortical thickness measurements within that ROI for a given subject. My question is, is it possible to manually trace an ROI in freeview? I tried doing it but it doesn't allow me to use the 'new ROI' when I use the drop down menu. And additionally, is there some way to accurately generate perfusion values within that ROI and then precisely transfer this ROI outline into QDEC so that the cortical thickness ROI is as close to the ROI in the CVR map as possible? Please let me know what you think. Thanks! Arsenije

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