Re: [Freesurfer] Choice of ICV estimation

-Suk, Tae Seoul, Korea 2024년 1월 31일 (수) 오전 9:29, Jackson Lee 님이 작성: > External Email - Use Caution > > Hi there, > > > > My question is related to FreeSurfer’s calculations for intracranial > volume (ICV): Given the importance to consider ICV as a potential co

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

External Email - Use Caution Hi Lauren. Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you corrected? best regards Woo-Suk, Tae On Tue, Oct 31, 2023 at 4:29 AM Lauren Stephens wrote: > External Email - Use Caution > > Hi Woo-S

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

nn %s 11 " $ids`) set cmd = ($cmd -o $labdir/anatorig/${segname}+thalnuc.nii.gz) Woo-Suk, Tae Ph.D. Seoul, Korea On Fri, Oct 6, 2023 at 11:42 PM Lauren Stephens wrote: > External Email - Use Caution > > Hi FreeSurfers, > > I am trying to troubleshoot an

[Freesurfer] mri_segstats --sbTIVin

be added to the aseg.stats with the option of mri_segstats --sbTIVin ... But, I can not find "--sbTIVin" option in the mri_segstats command of FreeSurfer 7.4.1 or the recent developer version. How can I add sbTIV to aseg.stats? Sincerely yours Wo

[Freesurfer] trac-all with or without sub-thalamic nuclei segmentation

set usethalnuc = 0 and 1 in the tracula config option. The tracts obtained from the two analyzes were similar in general, but slightly different in detail. Can you elaborate a bit more on what the usethalnuc option does to the results? Sincerely yours. Woo-Suk, Tae Seoul, Korea

Re: [Freesurfer] register to mni space

, to MNI space. But, the transformed fiber bundles were not in MNI 152 space. Would you suggest the other transformation command or correct my mistake to MNI152 space for TRACULA fiber bundles in native space? Sincerely yours Woo-Suk, Tae Seoul, Korea On Fri, Apr 28, 2023 at 10:26 PM Douglas N

[Freesurfer] How to extract TRACULA's fiber bundles in MNI template space

External Email - Use Caution Dear Freesurfer users. I'd like to know how to extract TRACULA's fiber bundles in MNI template space. Are there any command option for trac-all? or commands for already extracted tracks in native space? sincerely Woo-Suk, Tae Seou, Korea

[Freesurfer] TRACULA pathways to MNI space

=func2struct.mat --out=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/warped_fmajor.nii.gz Sincerely Woo-Suk, Tae Seoul, Korea -- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center

[Freesurfer] volume, surface area, and thickness

erts would help me. Sincerely yours Woo-Suk Tae Seoul, Korea I added the reviewer's comments. - 1. Volume/thickness: The authors cite many papers that show volume and thickness differences in MDD. The unresolved part here, however, is the RELATION between cortical thickness an

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Start matlab and just add /usr/local/freesurfer/matlab folder of your linux system to "set path" function (click in matlab's menu) of matlab environment. 2016. 3. 6. 오전 1:07에 "Ankita Chatterjee" 님이 작성: > Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

One possible solution is adding ../freesurfer/matlab to your matlab's set path. Regards Woo-Suk Tae Seoul, Korea Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research

[Freesurfer] TRACULA voxel unit

Dear FreeSurfer and TRACUAL expert I would like to know the volume unit of TRACULA pathes in mm3. It seemed that the result table expressed in volume count. How can I convert it to mm3? Sincerely Woo-Suk, Tae Ph.D. Research

[Freesurfer] TRACULA with Philips par-rec format

Dear TRACULA exports I've successfully processed with Philips DICOM DTI data. But, I have Philips 32 directional DTI data with par-rec format. How can I process par-rec data in TRACUAL? Best regards! Woo-Suk, Tae Ph.D. Research

Re: [Freesurfer] dual boot OS

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } No, you just need multi-core CPU.If you have

[Freesurfer] auto-cropping subcortical structure

of auto-cropping the exported binary files (ex. hippocampus or thalamus) from in aseg.mgz by 'mri_binarize'. The cropped hippocampal image may have about 40 x 40 x 50 voxels dimension.Do you have any idea?Woo-Suk, Tae Ph.D.Chuncheon, Korea ___ Freesurfer

[Freesurfer] volume of Heschl's gyrus

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } HiWhat is the exact term of heschl's gyrus in

Re: Re: Re: [Freesurfer] path error on cluster super-computer

!My error corrected after modifying 'tmpdir in bin/mri_nu_correct.mni'.Best regard!Woo-Suk, Tae Chuncheon, Korea--- Original Message ---From : quot;Pedro Paulo de Magalh?es Oliveira Juniorquot;To : quot;Woo-Suk, Taequot;Date : 2008/07/08 화요일 오전 1:12:44Subject : Re: Re: [Freesurfer] path error

[Freesurfer] path error on cluster super-computer

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer experts!I had a error message

Re: Re: [Freesurfer] path error on cluster super-computer

: [Freesurfer] path error on cluster super-computer I would try: chmod -R 777 /usr/tmp 2008/7/6 Woo-Suk, Tae [EMAIL PROTECTED]: Dear FreeSurfer experts!I had a error message when I ran a subjects on cluter super-computer.It seemed that the error was caused by permission on quot;/usrquot; directory.How

[Freesurfer] how to continue from breaking point of 'recon-all'

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear Freesurfer expertsMy one 'recon-all -all'

Re: Resp.: [Freesurfer] Freesurfer vs. VBM

failed it with Qdec with unkwon error. Maybe this is a problem of my analysis. Best regards!Woo-Suk, Tae Ph.D.Chuncheon, Korea --- Original Message ---From : quot;Pedro Paulo de Magalh?es Oliveira Juniorquot;To : quot;Bruce Fischlquot;Date : 2008/05/15 목요일 오후 10:09:53Subject : Resp.: [Freesurfer

[Freesurfer] displaying the result of group analysis in thickness or p-value

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer experts.I have finished the

[Freesurfer] error: libexpat.so.0

libraries: libexpat.so.0: cannot open shared object file:No such file or directoryquot; was occured.But, quot;libexpat.so.0quot; was already installed.How can I correct it?Woo Suk, Tae Ph.D ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

RE: [Freesurfer] automated parcellation: training set of Freesurfer

atlases. If you provide me the tool for new training set, I'd like to create my own study specific atlas. Really thank for your reply! Sincerely Woo Suk, Tae -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Monday, October 01, 2007 9:03 PM To: Woo Suk, Tae Cc

[Freesurfer] automated parcellation: training set of Freesurfer

training set. I'd like to know more detail, how many training set was used in Freesurfer, and is it possible to define the study specific training set for automated parcellation using Freesurfer? Sincerely Woo Suk, Tae Seoul, Korea ___ Freesurfer

[Freesurfer] TICV references of Freesurfer

Dear Freesurfer developers. I'd like to know the detail process of total intracrainal volume (TICV) measurement by Freesurfer. Would you recommend the directly or indirectly related articles on TICV measurement? Woo Suk, Tae Seoul, Korea

[Freesurfer] changing subject's name

/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not exist ...Loading tal xfm file /usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfmWoo Suk, Tae

[Freesurfer] volumes of aseg, aparc

of aseg, aparc files absolute volumes measured in native space or measured after spatial normalization? Woo Suk, Tae Seoul, Korea ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] some questions about volumes of aseg, .aparc, .aparc.2005s

, .aparc, .aparc.2005s. And they are verified? 3. Are the volumes in lh(or rh).aparc gray matter volumes? 4. What is meaning G_*, and S_* in lh(or rh).aparc.a2005s? 5. How can I separately see the strucures of .aparc, .aparc.2005s in pial surface rendering? Woo Suk, Tae Ph.D Seoul, Korea