[Freesurfer] sulcus measurement from aparcstat2table

[tulu]

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
volume in this sulcus ? and what is the thickness of sulcus meaning ?

Thanks

JLH

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[Freesurfer] how do display a particular region for visucalization

[tulu]

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

[tulu]

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. Is there any script or step to do that ?

Sincerely yours

JLH

CombinedNeuroimagingforAD2013.jpg

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[Freesurfer] display selected gyrus in specific color

[tulu]

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
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[Freesurfer] reference of adult normal volume from cortical parcellation

[tulu]

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

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[Freesurfer] FLAIR in hippocampus subfield segmentation

[tulu]

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

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[Freesurfer] decompression error of CentOS 6.5

[tulu]

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: exiting now

 

I wonder why I get this error message and how to correct it ?

Sincerely

JLH

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[Freesurfer] read and write thickness file ?

[tulu]

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___
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[Freesurfer] how to read lh.avg_thickness data ?

[tulu]

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___
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[Freesurfer] freeview and annotation file

[tulu]

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 ---___
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[Freesurfer] CentOS5.3 and freesurfer

[tulu]

Dear FS Experts,

Is it compatible to use CentOS 5.3 for install freesurfer ? both tksurfer
and tkmedit, freeview can run successfully ?

Any suggestion is helpful 

Thanks in advance

Jung lung hsu

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[Freesurfer] only color premotor gyrus use annotation file

[tulu]

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

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[Freesurfer] transform back to origin coordination ?

[tulu]

Dear Freesurfer experts,

I use freesurfer and when I finish recon-all
autorecon1, I would like to transform Brainmask.mgz image back to origin
coordination. How to do it ?

Thank replay

Kl chen






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[Freesurfer] mni305 template large than normalized MRI data ?

[tulu]

Dear Freesurfer experts,

I use fs 3.0.4 stable version on FC4. In recon-all stage 1, I check
tkregister2 for my subject's MRI. I found the MNI305 template is large than
normalized T1. Is it right ?

Thanks replay

KL Chen

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[Freesurfer] display bilateral pial surface by tksurfer

[tulu]

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

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[Freesurfer] CentOS 5.1 and freesurfer and tksurfer

[tulu]

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

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[Freesurfer] make_average_subject

[tulu]

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: make_average_surface,v 1.39.2.2 2009/07/30 23:33:52 nicks Exp $Wed Nov 17 22:35:55 CST 2010/rootsetenv SUBJECTS_DIR /root/freesurfer/subjects/AD8output ddir is /root/freesurfer/subjects/AD8uid=0(root) gid=0(root) groups=0(root),1(bin),2(daemon),3(sys),4(adm),6(disk),10(wheel)make_average_surfaceWed Nov 17 22:35:55 CST 2010/root/root/freesurfer/bin/make_average_surface--fsgd AD8_fsgd.txtinput subjects: 00030096 00275571 04719019 06543135 06574530 07020866 08521537 08975833output subject: averagemri_add_xform_to_header -c auto /root/freesurfer/subjects/AD8/average/mri/mni305.cor.mgz /root/freesurfer/subjects/AD8/average/mri/mni305.cor.mgzINFO: extension is mgz#...@# Making lh registration template -/root/freesurfer/subjects/AD8/averagemris_make_template -norot -annot aparc lh sphere.reg 00030096 00275571 04719019 06543135 06574530 07020866 08521537 08975833 lh.reg.template.tifnot aligning hemispheres before averaging.zeroing medial wall in aparccreating new parameterization...processing subject 00030096 (1 of 8)reading spherical surface /root/freesurfer/subjects/AD8/00030096/surf/lh.sphere.reg...reading colortable from annotation file...colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt)ripping medial wall...computing parameterization for surface /root/freesurfer/subjects/AD8/00030096/surf/lh.inflated.H...curvature mean = -0.011, std = 0.968computing parameterization for surface /root/freesurfer/subjects/AD8/00030096/surf/lh.sulc...computing parameterization for surface /root/freesurfer/subjects/AD8/00030096/surf/lh.smoothwm...processing subject 00275571 (2 of 8)reading spherical surface /root/freesurfer/subjects/AD8/00275571/surf/lh.sphere.reg...f[244302]->v[1] = -1 - out of range!curvature mean = -0.001, std = 0.581curvature mean = -0.068, std = 1.569
which steps should I perprocess before I make average surface ?
thanks
JL
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[Freesurfer] overlap individual thickness map on average surface

[tulu]

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

[tulu]

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 --trgsurfval /root/freesurfer/subjects/fsaverage/surf/mylh.thickness --hemi lh  
but i get error message: ERROR: could not determine type of /root/freesurfer/subjects/fsaverage/surf/mytlh.thickness
how can I correct it ? thank in advance
best
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[Freesurfer] color scale bar in freeview

[tulu]

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
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[Freesurfer] white matter volume and qdec

[tulu]

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 ? thank in advancebestJLH--- 本郵件來自HiNet WebMail ---___
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[Freesurfer] make_average_subject error in T1.mgz and t1.mgz

[tulu]

Dear FS experts,
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 setting from 
T1.mgz to t1.mgz
thanks help
JLH
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[Freesurfer] mri_cvs_register version for CentOS4 and CentOS5

[tulu]

Dear FS experts
I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I 
need to upgrade the mri_cvs_register and applyMorph for correction ?
best
JLH
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[Freesurfer] interpretation of qdec results

[tulu]

Dear FS experts,
I use qdec to do two group study. in QDEC, 
it set Normal = 1 and Disease = 2, use AGE as covariate and 
apply DODS model, after analyze group cortical thickness, it showed significant 
negative T value (blue color) in some brain areas. I have two questions in 
qdec
1. the contrast  set as 1 -1 0 0 but I don't know 
if it represents as Normal - Disease (normal group is thinner than Disease) or 
Disease - Normal (disease group is thinner than normal) ?
2. is this 
results come from correction of multiple comparison ? or I still need to re-set 
FDR level (default is 0.05) and re-run it ?
thanks in advance
JLH
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[Freesurfer] how to set the number of vertex ?

[tulu]

Dear freesurfer expert,

I am a new user of freesurfer. When I use mri_tessellate,
how to set the number of vertex ?

Thanks replay

JLH






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

[tulu]

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 correct it (I use P4 2.8G CPU with 2G RAM, OS is Linux Fedora Core 4).

Thanks replay 

KL chen






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[Freesurfer] question about aseg.stat data

[tulu]

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 ? thanks replay

Sincerely

KL chen






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[Freesurfer] update patch for freesurfer

[tulu]

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






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[Freesurfer] matlab 2019b and brainstem substructures analysis

[tulu]

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 help

Jung Lung Hsu

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

[tulu]

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

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[Freesurfer] question about freeview in freesurfer 7.4.0 and qt

[tulu]

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. Reinstalling the application may fix this problem.
 
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, 
vnc, wayland-egl, wayland, webgl, xcb.
 
Abort (core dumped)

could anyone can direct me how to solve this problem ?
sincerely 
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