[Freesurfer] question about freeview in freesurfer 7.4.0 and qt

External Email - Use Caution Dear freesurfer experts, recently I update freesurfer to freesurfer 7.4.0 under Ubuntu 20.04. when I try to launch freeview, I get error message as: freeview This application failed to start because no Qt platform plugin could be initialized.

[Freesurfer] make brainstem surface file and make average brainstem surface

External Email - Use Caution Dear Freesurfer experts, Could I use the brainstem file (brainstemSsLabels.v1x.FSvoxelSpace.mgz) and make it as surface file ? if I have multiple subjects' file, how to make the average surface file for visualization ? Sincerely Jung Lung Hsu

[Freesurfer] matlab 2019b and brainstem substructures analysis

External Email - Use Caution Dear Freesurfer experts, I will analysis brainstem structure and I use Freesurfer 7.2 version and maltab 2019b. I wonder if I need to install Matlab R2014b runtime or how to run hippocampal subfield/brainstem module by matlab2019b Thanks your

[Freesurfer] FLAIR in hippocampus subfield segmentation

Dear Freesurfer experts Under Freesurfer V6 version, could the hippocampus subfield segmentation use high resolution FLAIR image ? if yes, is the command line -hippocampal-subfields-T1T2 ? Thanks JLH ___ Freesurfer mailing list

[Freesurfer] sulcus measurement from aparcstat2table

Dear FS expert I use the aparcstat2table and generate the cortical volume/thickness. I have a question regarding sulcus volume and thickness meaning. For example, it generate lh_S_front_inf volume and thickness, which represents as left inferior frontal sulcus. Did the volume represent as CSF

[Freesurfer] decompression error of CentOS 6.5

Dear freesurfer experts, I download freesurfer CentOS 6 version and my PC is CentOS 6.5 version. When I decompression it, I get error message: gzip: stdin: invalid compressed data--format violated tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable:

[Freesurfer] FW: how do display a particular region for visucalization

From: tulu [mailto:t...@ms36.hinet.net] Sent: Wednesday, December 04, 2013 8:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: how do display a particular region for visucalization Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an example

[Freesurfer] how do display a particular region for visucalization

Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an example. Is there any script or manual descript how to do that ? Sincerely yours JLH ?xml:namespace prefix = v ns = urn:schemas-microsoft-com:vml / ?xml:namespace prefix = o ns =

[Freesurfer] display selected gyrus in specific color

Dear freesurfer experts, I try to combine some selected gyrus and display them all in red color, other brain structures will keep in gray color in freeview. I search for color lookup table page but don't know if I need to change the .annot file or not. How to correctly do that ? sincerely

[Freesurfer] reference of adult normal volume from cortical parcellation

Dear FS experts, Is there any reference about the volume of cortical gyrus after FS cortical parcellation in normal adult people ? I need the reference value of regional volume base on the cortical parcellation made by FS. Please instruct me the reference paper. Thanks help JLH

[Freesurfer] read and write thickness file ?

Dear FS experts, I would like to read cortical thickness data from lh.thickness.fwhm10.fsaverage.mgh file and do some calculation. then save the result as thickness file. which matlab script should I use ? sincerely yours Jung-Lung, Hsu___ Freesurfer

[Freesurfer] how to read lh.avg_thickness data ?

Dear FS experts, is it possible to read cortical thickness data from lh.avg_thickness data into matlab for further process ? which tool I need to use ? sincerely yours Jung Lung Hsu___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] interpretation of qdec results

lt;pgt;Dear FS experts,lt;br /gt;I use qdec to do two group study. in QDEC, it set Normal = 1 and Disease = 2, useamp;nbsp;AGE as covariateamp;nbsp;and apply DODS model, after analyze group cortical thickness, it showed significant negative T value (blue color) in some brain areas. I have two

[Freesurfer] make_average_subject error in T1.mgz and t1.mgz

lt;pgt;Dear FS experts,lt;br /gt;I use FS5.1 and previous data run on other machine. When I try to make_average_subjects program, I get error message that it can not get T1.mgz data from subject folder. When I check my dataset, actually it has t1.mgz rather than T1.mgz. how could I change the

[Freesurfer] white matter volume and qdec

Dear Freesufer experts,I would like to do the group comparison of white matter volume in various white matter regions base on white matter parcellation. I have no idea about how to do that. Is it the same as cortical thickness comparison in qdec ? could any one give some guide about how to do that

[Freesurfer] color scale bar in freeview

Dear Freesurfer experts, I use freeview to display the cortical thickness. Is it possible to change the color map in color scale bar ? how to make the color map such as use jet color ? thanks in advance JLH--- 本郵件來自HiNet WebMail ---___ Freesurfer mailing

Re: [Freesurfer] overlap individual thickness map on average surface

Thank Bruce, sorry for my simple question. I try to display one subject's thickness map on average surface. so I try mri_surf2surf --srcsubject /root/freesurfer/subjects/r00275571 --srcsurfval /root/freesurfer/subjects/r00275571/surf/lh.thickness --trgsubject /root/freesurfer/subjects/fsaverage

[Freesurfer] overlap individual thickness map on average surface

Dear FS expertsI hope to display individual's thickness map on average subjects' surface after I finish all subjects' recon-all step and make_average_subject step. Is anyone can guide me how to do that ? thanks in advancebestJLH--- 本郵件來自HiNet WebMail

[Freesurfer] make_average_subject

Dear FS experts, I read the tutorial and don't know how to perform average all subjects' volume and surface by make_average_subject. I finish all subjects' recon-all steps and try to average them. when I type make_average_subjects --fsgd and it comes out the error message: $Id:

[Freesurfer] only color premotor gyrus use annotation file

Dear Freesurfer experts, I wish to draw a selected gyrus on the whole hemisphere. Could I only color display the selected gyrus and use other color on all others gyrus from annotation file ? if yes, how to do it. Thank help Kl chen ___ Freesurfer

[Freesurfer] freeview and annotation file

Dear freesurfer experts,I would like to use freeview to check the pial surface and label with annotation file. how to do it ?thanks your helpbestJL--- 本郵件來自HiNet WebMail ---___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] CentOS 5.1 and freesurfer and tksurfer

Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen

[Freesurfer] display bilateral pial surface by tksurfer

Dear freesurfer experts, Can I use tksurfer to display two surface volume ? how to display bilateral pial surface from same subject under tksurfer ? Thanks replay Sincerely Kl chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] update patch for freesurfer

Dear freesurfer experts, I wonder if there any update patch I need to download after I install the latest release of dev version of freesurfer ? Thanks replay Kl chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] question about aseg.stat data

Dear freesurfer experts, I use freesurfer and bert data to run recon-all script. It can finish without error. However, when I check the aseg.stats data and find some regions such as inslula or operculum volume are zero. Is it right ? or I should change something other than default setting

[Freesurfer] long time to finish a case by recon-all

Dear Freesurfer experts, First of all, I thanks for your wonderful tool. I run the recon-all autorecon-all script and it can finish my mri data without error. The only problem is it need 3 days (about 72 hours) to finished one mri data. I wonder if anyone have same experience and how to