[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 Professor, Neuroimaging Lab. Neuroscience Research Institute, Clinical Research Institute, Kangwon National University Hospital Chuncheon, Korea office: 82-33-258-9164 mobile: 82-10-9120-4629 email: ws...@kangwon.ac.kr woos...@gmail.com - ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Default FA threshold value for TRACULA
Dear TRACULA experts Is there any FA threshold value for TRACULA? If yes, what is the FA cutting value and how can I change it? Woo-Suk, Tae Seoul, Korea Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: woosuk@gmail.com, woos...@gmail.com ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] volume, surface area, and thickness
Dear FreeSurfer experts and developers I am confronted with some technical question of a reviewer. I am not sure about "volume = thickness-by-surface area" and the review's opinion (attached below) about volume, surface area, and thickness was correct. Any comments from FreeSurfer's experts 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 and cortical volume: There is no doubt, that both measures are found affected in MDD. This is, because cortical thickess multiplied by the surface area of a gyrus results in its volume, so volumse = thickness-by-surface area. Surface area values themselves are technically more noisy and usually thus less sensitive (due to the problem of false attributions to an area). So, volume is influenced by thickness and surface and is the less specific measure. If a volume effect is detected in a study, it is unclear, if it is driven by thickness, or surface area, or both. In this respect, the study of Schmaal et al. is telling, as it analyzed BOTH measures, finding only thickness effects of MDD, and (practically) no surface area changes except for adolescent MDD. In the adolescent MDD samples gross surface area differences were detected. This means, that the question of "superiority" is rather a question of "specificity": (Cortical) volume findings in adult MDD are mostly driven by thickness differences and are in on way independent from thickness differences. In this respect, the authors should follow the basic geometric principles of morphometry and point out the relatedness of the two. They can simply check this in their FreeSurfer variables (e. g. for total grey matter volume). Not reporting surface area is leaving an interpretational gap as surface area differences could in addition drive volume differences. The authors may want to decide not to present surface area results, but then they should discuss this as limitation to disentangle the origin of volumetric (cortical) effects. This seems important as methylation effects and FKBP5 interact with early life time stress, so effects on surface area as seen in adolescent MDD highlight that surface area effects could play in. ------------ Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: woosuk@gmail.com, woos...@gmail.com ___ Freesurfer mailing list Freesurfer@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.
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 Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: woosuk@gmail.com, woos...@gmail.com On Sun, Mar 6, 2016 at 12:02 AM, Bruce Fischl wrote: > can you send us the recon-all.log file? > > cheers > Bruce > On Sat, 5 Mar 2016, Ankita > Chatterjee wrote: > > > Hello FS experts,I am a bit stuck and was hoping for some advice! > > > > I am using Matlab Student version for my research and was trying to > > determine local gyrification index on some samples that I have processed > via > > the recon-all -all step. > > > > When I run recon-all -lgi on my subject, it starts up, is able to access > > MATLAB, but then gives an error >> Undefined function or variable > > 'make_outer_surface'. Am I missing a package from the MATLAB student > > version? How do I solve this? Any help will be greatly appreciated!!! > > > > Ankita > > > > > ___ > Freesurfer mailing list > Freesurfer@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. > > -- ___ Freesurfer mailing list Freesurfer@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.
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 > on Matlab? I am not very familiar with linux... > > Thanks! > Ankita > > ___ > Freesurfer mailing list > Freesurfer@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. > > ___ Freesurfer mailing list Freesurfer@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.
[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 Professor, Neuroimaging Lab. Neuroscience Research Institute, Clinical Research Institute, Kangwon National University Hospital Chuncheon, Korea office: 82-33-258-9164 mobile: 82-10-9120-4629 email: ws...@kangwon.ac.kr woos...@gmail.com - ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] auto-cropping subcortical structure
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Dear FreeSurfer exports.I need the function 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
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Re: [Freesurfer] dual boot OS
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No, you just need multi-core CPU.If you have quad core CPU, you can run 4 jobs
simultaneously (over 4 jobs possible, but the run time will be needed more) in
the multiple command terminals.Best regard!Woo-Suk, TaeChucheon, Korea---
Original Message ---From : "Ahmed, F, Me "To : "Freesurfer
Mailing List"Date : 2009/10/28 수요일 오후 4:19:02Subject : [Freesurfer] dual
boot OS
Hello,
A quick question, if I wanted to run simultaneous recon-all jobs,
would I have to install Linux as a dual boot operating system as opposed to
what I currently have, which is an emulator?
Thanks,
Fatima
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[Freesurfer] some questions about volumes of aseg, .aparc, .aparc.2005s
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Dear Freesurfer experts.
I have some questions about calculated volumes by freesurfer.
1. Are the volumes in aseg, .aparc, .aparc.2005s absolute volumes measured in
naive space
or volumes measured after spatial normalization.
2. How much accurate the volumes (hippocampus, amygdala, thalamus, insula,
precentral, etc)
in aseg, .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
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[Freesurfer] volumes of aseg, aparc
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Dear Freesurfer experts.
Are the volumes of aseg, aparc files absolute volumes measured in native space
or measured after spatial normalization?
Woo Suk, Tae
Seoul, Korea
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[Freesurfer] changing subject's name
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After recon-all -s tfe10 (subject name) -all, I changed a subject's name
(tfe10) to 001.when I performed group analysis (mris_make_average_surface), I
had the error massage.How can I correct [EMAIL PROTECTED] processing subject
1/42 001... Reading /usr/local/freesurfer/subjects/001/surf/rh.sphere.reg
Talairach transform
/usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not
exist ...Loading tal xfm file
/usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm Read
/usr/local/freesurfer/subjects/001/mri/T1.mgz Surface area: 872.5 cm^2
Applying linear transform Talairach transform
/usr/local/freesurfer/subjects/tfe10/mri/transforms/talairach.xfm does not
exist ...Loading tal xfm file
/usr/local/freesurfer/subjects/001/mri/transforms/talairach.xfm----------------Woo
Suk, Tae
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[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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] automated parcellation: training set of Freesurfer
Dear experts. In the previous technical papers of Freesurfer, the the method of automated parcellation was described, "This procedure automatically assigns a neuroanatomical label to each voxel in an MRI volume based on probabilistic information automatically estimated from manually labeled 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] automated parcellation: training set of Freesurfer
Dear Dr Bruce Fischl. How are you? I preprocessed 41 subjects' MRI to measure the volumes of the cortical and subcortical structures with ver 3.04 Freesurfer. What kind of atlas (Desikan-Killiany atlas or Destrieux atlas?) was used for my data? And how can I choose the atlas between the two 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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] automated parcellation: training set of Freesurfer there are two training sets we use for the two difference parcellation schemes. Once consists of about 40 subjects distributed into 4 groups (young, middle aged, elderly and Alzheimer's for the Desikan-Killiany atlas). The other is 14 young and middle aged subjects in the Destrieux atlas. Defining a new training set is extremely labor intensive, but we distrubute tools for you to do so if you decide to. cheers, Bruce On Mon, 1 Oct 2007, Woo Suk, Tae wrote: > Dear experts. > > In the previous technical papers of Freesurfer, the the method of automated > parcellation was described, > > "This procedure automatically assigns a neuroanatomical label to each voxel > in an MRI volume based on probabilistic information automatically estimated > from manually labeled 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error: libexpat.so.0
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How are you?When I run recon-all -s subjid -all with Fressurfer 4.02,the
process was terminated with the error message of" mris_volmask.bin: error
while loading shared libraries: libexpat.so.0: cannot open shared object file:
No such file or directory"And, when I ran 'qdec' , the same error
"qdec.bin: error while loading shared libraries: libexpat.so.0: cannot
open shared object file:No such file or directory" was occured.But,
"libexpat.so.0" was already installed.How can I correct it?Woo Suk,
Tae Ph.D
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[Freesurfer] displaying the result of group analysis in thickness or p-value
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Dear FreeSurfer experts.I have finished the FreeSurfer analysis using (version
3.04) in the patients with depression.But, the result using qdec was displayed
only in T-value.I'd like to know how can I display the result of group analysis
in thickness (mm) and statistical p value.Best regards.Woo-Suk, Tae
Ph.DChucheon, Korea
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[Freesurfer] FreeSurfer for Redhat 7.3
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Hi!I would like to know the version of Freesurfer for Redhat 7.3.Best
regards.Woo-Suk, TaeChucheon, Korea
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Re: Resp.: [Freesurfer] Freesurfer vs. VBM
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In my case with the patients with chronic major depression, VBM (tissue
concentration) and modulated VBM (volume change) showedmore sensitive findings.
In addition, VBM provide the brain tissue change of subcortical areas.I think
the controlling of TICV (total intracranial cavity volume) is important factor
for FreeSurfer analysis, but I 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 : "Pedro Paulo de Magalh?es Oliveira
Junior"To : "Bruce Fischl"Date : 2008/05/15 목요일 오후
10:09:53Subject : Resp.: [Freesurfer] Freesurfer vs. VBMMartin, I have an still
unpublished work comparing VBM and FS in Alzheimer. I can say to you that FS
provides result much more accurate in this area. Best Regards, Pedro Paulo Jr
2008/5/14, Bruce Fischl : Hi Martin, 1. FS uses geometry to do inter-subject
registration, which in our experience results in a much better matching of
homologous cortical regions than volumetric techniques. 2. FS allows you to
look at the two components of volume separately (thickness and surface area).
We have found that these two do not necessarily track one another, and in the
worst case where one is increasing and the other decreasing the volume change
can be 0. 3. The target we use for registration (the white matter surface
geometry) is completely invariant to gm atrophy, so gm changes won't results
in a different registration. Steve Smith and Morgan Hough at Oxford just did
a pretty comprehensive study of this, so maybe they will chime in. cheers,
Bruce On Wed, 14 May 2008, Martin Kavec wrote: Gentlemen, I am giving a
lecture about aging brain. I only discuss freesurfer, since that's the method
we use for the brain volume and cortical thickness assessment. There are other
methods, such as VBM and SIENA potentially providing similar information. I
would appreciate if you could point me to a reference, which compares
features of Freesurfer and VBM, or if you could provide me your insight on
what are the advantages of FreeSurfer over VBM. I could think of the
following: 1. Freesurfer allowes for the subvoxel precision of the volume
estimation 2. VBM involves strong filtering in order to suppress variations
of individual anatomies 3. 4. 5. Thanks a lot in
advance. Martin ___ Freesurfer
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[Freesurfer] how to continue from breaking point of 'recon-all'
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Dear Freesurfer expertsMy one 'recon-all -all' process was terminated with a
library error.So I'd like to continue the rest process after library update.How
can do it? Woo-Suk, TaeChuncheon, Korea
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[Freesurfer] path error on cluster super-computer
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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
"/usr" directory.How can I correct this problem?Woo-Suk,
TaeChuncheon,
Korea---Iteration
1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber
./tmp.mri_nu_correct.mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create
"/usr/tmp/nu_correct_25115/": Permission [EMAIL
PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 08:51:04]
running: /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify
-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir
/usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct.mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.imp
nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file
or directorymicreate: MINC package entry pointnu_estimate_np_and_em: crashed
while running mincresample (termination status=768)nu_correct: crashed while
running nu_estimate_np_and_em (termination status=768)ERROR: nu_correctLinux
tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008 x86_64 x86_64
x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 7 08:51:05 KST
2008---
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Re: Re: [Freesurfer] path error on cluster super-computer
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The super-user of super-computer did not give me the writing permission for
/usr/tmp,so I should modify the source script of FreeSurfer.How can I do
it?Woo-Suk, TaeChuncheon, Korea--- Original Message ---From : "Pedro Paulo
de Magalh?es Oliveira Junior"To : "Woo-Suk, Tae"Date :
2008/07/07 월요일 오전 9:28:29Subject : Re: [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
"/usr" directory.How can I correct this problem?Woo-Suk,
TaeChuncheon,
Korea---Iteration
1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber
./tmp.mri_nu_correct.mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create
"/usr/tmp/nu_correct_25115/": Permission [EMAIL
PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 08:51:04]
running: /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify
-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir
/usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct..mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.imp
nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file
or directorymicreate: MINC package entry pointnu_estimate_np_and_em: crashed
while running mincresample (termination status=768)nu_correct: crashed while
running nu_estimate_np_and_em (termination status=768)ERROR: nu_correctLinux
tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008 x86_64 x86_64
x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 7 08:51:05 KST
2008---
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Re: Re: Re: [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; }
Thanks Pedro Paulo de Magalh?es Oliveira Junior!My error corrected after
modifying 'tmpdir in bin/mri_nu_correct.mni'.Best regard!Woo-Suk, Tae
Chuncheon, Korea--- Original Message ---From : "Pedro Paulo de Magalh?es
Oliveira Junior"To : "Woo-Suk, Tae"Date : 2008/07/08 화요일 오전
1:12:44Subject : Re: Re: [Freesurfer] path error on cluster super-computer
I think you can change
tmpdir in bin/mri_nu_correct.mni
But first check if you are setting the variables correctly: FREESURFER_HOME and
executing source SetUpFreeSurfer.sh
2008/7/7 Woo-Suk, Tae [EMAIL PROTECTED]:The super-user of super-computer did
not give me the writing permission for /usr/tmp,so I should modify the source
script of FreeSurfer.How can I do it?
Woo-Suk, TaeChuncheon, Korea
--- Original Message ---From : "Pedro Paulo de Magalh?es Oliveira
Junior"[EMAIL PROTECTED] : "Woo-Suk, Tae"[EMAIL PROTECTED] :
2008/07/07 월요일 오전 9:28:29Subject : Re: [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
"/usr" directory.How can I correct this problem?Woo-Suk,
TaeChuncheon,
Korea---Iteration
1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber
./tmp.mri_nu_correct.mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create
"/usr/tmp/nu_correct_25115/": Permission [EMAIL
PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 08:51:04]
running: /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify
-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir
/usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct..mni.25070/nu0.mnc
./tmp.mri_nu_correct.mni.25070/nu1.imp
nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file
or directorymicreate: MINC package entry pointnu_estimate_np_and_em: crashed
while running mincresample (termination status=768)nu_correct: crashed while
running nu_estimate_np_and_em (termination status=768)ERROR: nu_correctLinux
tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008 x86_64 x86_64
x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 7 08:51:05 KST
2008---
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[Freesurfer] volume of Heschl's gyrus
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.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color:
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HiWhat is the exact term of heschl's gyrus in the lists of
rh_lt.aparc.a2005s.stats?Woo-Suk, TaeChuncheon, Korea
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Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
External Email - Use Caution
Hi, Lauren Stephens.
If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
can get an aparc+aseg+thalnuc.nii.gz file without error, and make
subthalamic nuclei related tracks.
#chage codes from
set cmd = mri_binarize
set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)
#to
set cmd = mri_convert
set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
set cmd = ($cmd `printf "--replaceonly-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 error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The
> subregion segmentation prior to trac-all -prep was successful and
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated. In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1mbZ6TiwAjZyXHWt0vWwUF4mmwAlMoO41mwD4m80I0xkM0yxR3a_Z7YeDCGNXtP3wyVlhdxN0ChbZDaAjEuhQoghPYxMAJSteUSqeB7MF4-L0Tf8FsDLFXiWNz-KnU-re_mqlz-AXa2mAnoH8hvKI6IJ23ANyNMGBis5RO1oMhTy5yDaI833kgeGvPVzrc3UXngF13YAI3utqkrkb0ssut4jifFVnS-uAlo1HkadPcWDYYEsre38v2YeJ7XQTOanc719223QJmCY28ugu02PGBxFplISpgGt8DWtq6RSKnosmxtFNVPUXPLSCWLjQ8b1R/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
--
Woo-Suk, Tae Ph.D. Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
wo os...@gmail.com
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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-Suk,
>
> I was able to make the change however, I am still receiving the same
> error.
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
> mri_convert -at
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dmri/xfms/anatorig2diff.bbr.lta
> -rt nearest
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz
>
>
> reading from
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz...
>
> error: niiRead(): error opening file
> /Users/corpuscallosum/Desktop/TRACULA/RRD/R001A/R001A/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz
>
> Darwin PSYC-C02DP05D0833.stanford.edu 22.6.0 Darwin Kernel Version
> 22.6.0: Fri Sep 15 13:39:52 PDT 2023;
> root:xnu-8796.141.3.700.8~1/RELEASE_X86_64 x86_64
>
>
> trac-preproc exited with ERRORS at Mon Oct 30 12:24:56 PDT 2023
>
> Do you have any further suggestions to fix this issue?
>
> Thank you,
>
> Lauren Stephens
>
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Woo-Suk Tae <
> woos...@gmail.com>
> *Sent:* Saturday, October 28, 2023 10:34 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation
> aparc+aseg+thalnuc.nii.gz
>
>
> External Email - Use Caution
>
> Hi, Lauren Stephens.
> If you change some codes in trac-preproc ( in path/freesurfer/bin ), you
> can get an aparc+aseg+thalnuc.nii.gz file without error, and make
> subthalamic nuclei related tracks.
>
> #chage codes from
> set cmd = mri_binarize
> set cmd = ($cmd --i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)
> set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz)
>
> #to
> set cmd = mri_convert
> set cmd = ($cmd -i $fsdir/mri/$segname.mgz)
> set cmd = ($cmd `printf "--replaceonly-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 error during TRACULA preprocessing and the
> issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The
> subregion segmentation prior to trac-all -prep was successful and
> mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz
> and other Thalamic Nuclei files were generated. In the archives I saw two
> others have experienced a similar issue without a resolution in the
> thread.
>
> I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have
> attached the log file, log error, and my configuration file.
>
> Any help would be greatly appreciated!
>
> Thank you,
>
> Lauren Stephens
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
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Re: [Freesurfer] Choice of ICV estimation
External Email - Use Caution Based on my personal experience, if you have T1 and T2 MRIs, use the sbTIV from samseg, and if you only have T1 MRI, use the TIV value from CAT12. Next, use the sbTIV from T1 samseg. I recommend not using the eTIV value for degenerative diseases. Woo-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 covariate > when assessing volumetric differences in ROIs between groups, which ICV > output is recommended? > > > > FreeSurfer’s recon-all generates eTIV (which is widely used by default in > literature, and is a registration-based method). Conversely, the SAMSEG > pipeline generates sbTIV (relatively newer approach which is a > segmentation-based method). While these two would be the most obvious > choice, many papers also consider correcting for supratentorial volume to > be an appropriate approach. > > > > To some degree, the choice of method would be guided by the research > question. However in the most simple of cases (e.g., non-clinical cohorts), > what method is recommended? Why would someone, for example, opt to use > sbTIV over eTIV? > > > > Warm regards, > > Jackson Lee > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1SX4ZEE_h46UB0tE8ncL1b8hMHcfiryNjOHvrdz_ECtYAJTBx4JC6Mkvd9Qco8oNDX_0bOp9izOyQNZU1oZB_I8-jiXL57j2az-EG2suJGI-JONkoCHTQHyDPoEOLrt4ooRxGiiY87qhHkiJJWp-jJoZpOtUBaVLzszxpXist27_IQHBWsVhu4oSTaFrm8DHVUoIcLPhm4iKXZp-r-XWx-3p4NBOn0iHA0ZL0kpKxv33yCS2KXocU9TFaNLNQSLLKHUJLNGVFrsF-2uF-POioewcsU3F0GmrzPrxssPXoe1YRLlrqwg_PHilA06bWgfqpGsbQRF32_ijS0T3Oo6F3Ig/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1zG8aMF9AH3oSP5RVQWJofw5WrdOX3xINPlGSbjadwbM476E2RINCMwDyf8DWiOvWDCMsnig4cCCBuLnEReOFACcaTVdbRCFl1ztV4aVR_nru5rWqJV10keepk0iulCB5bhNcAjD97Fkwv45GsTeoCLsGCtsGl91FDFuyWT6Q8NgbeHqqb4x0YYGDYu9aI0zXFolp7gNDBA9BFstG3TayFKvCYPIHg0IvjHKWW87o9UYkRKEaajagrB1Wt1pwLuH27BS25WKgcHvf7_zbKVT8emw9NcwUon-J1gMLHTPxDc5Z2_NUTrDzPNxN-h7hJH4jQ4zQ3bVoTJjhh9ZzcVgC7A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1zG8aMF9AH3oSP5RVQWJofw5WrdOX3xINPlGSbjadwbM476E2RINCMwDyf8DWiOvWDCMsnig4cCCBuLnEReOFACcaTVdbRCFl1ztV4aVR_nru5rWqJV10keepk0iulCB5bhNcAjD97Fkwv45GsTeoCLsGCtsGl91FDFuyWT6Q8NgbeHqqb4x0YYGDYu9aI0zXFolp7gNDBA9BFstG3TayFKvCYPIHg0IvjHKWW87o9UYkRKEaajagrB1Wt1pwLuH27BS25WKgcHvf7_zbKVT8emw9NcwUon-J1gMLHTPxDc5Z2_NUTrDzPNxN-h7hJH4jQ4zQ3bVoTJjhh9ZzcVgC7A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] atlas for subregional precentral gyrus
External Email - Use Caution Dear FreeSurfer developers, Thank you for developing such an excellent imaging analysis package. Among Freesurfer's parcellation atlases, is there one that divides the precentral gyrus into areas for the tongue (pharynx), face, hand, and arm, etc., or one that separates the superior, middle, and inferior frontal gyri? If not, are there any plans to develop such an atlas in the future?" Woo-Suk Tae Seoul, Korea ------------ Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk@gmail.com, w s...@korea.ac.kr ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] TRACULA pathways to MNI space
External Email - Use Caution
Dear Freesurfer experts
I finished TRACULA's trac-all steps. Then I'd like to transform all DTI
pathways to MNI space.
Are there any commands in freesurfer or any external neuroimaging softwares.
My scripts did not provided no transformation to MNI space.
#bet /Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
/Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz
#flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in
/Users/anal/RH_nml/FS/01/mri/orig/001_betted.nii.gz -omat
/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat
fnirt --in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
--aff=/Users/anal/RH_nml/FS/01/mri/orig/affine_transf.mat
--cout=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--config=T1_2_MNI152_2mm
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm
--in=/Users/anal/RH_nml/FS/01/mri/orig/001.nii.gz
--warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--out=/Users/anal/RH_nml/FS/01/mri/orig/warped_001.nii.gz
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_1mm
--in=/Users/anal/RH_nml/TRA/01/dpath/fmajor_PP_avg33_mni_bbr/path.pd.nii.gz
--warp=/Users/anal/RH_nml/FS/01/mri/orig/nonlinear_transf
--premat=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, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: ws...@korea.ac.kr, woosuk@gmail.com,
wo os...@gmail.com
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[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 -- ------------ Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: ws...@korea.ac.kr, woosuk@gmail.com, wo os...@gmail.com ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] register to mni space
External Email - Use Caution Dear Douglas N. GreveAs you commented, the command, you suggested, transformed well from the aparc+aseg.mgz with native space to MNI 152 space. I also tried the command to transform fiber bundles (the merged_avg33_mni_bbr.mgz), extracted from TRACULA, 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. Greve wrote: > External Email - Use Caution > > you mean you want to map the aparc+aseg.mgz from the subject space to the > cvs/mni152 space using the cvs transform? Try this > mri_convert aparc+aseg.mgz -at cvs.m3z aparc+aseg.from-subject-to-cvs.mgz > where cvs.m3z is the cvs nonlinear registratiopn > > On 4/21/2023 11:12 AM, Carlos Alcocer wrote: > > External Email - Use Caution > I registered a subject to mni space using the mri_cvs_register command > with the --mni flag. However, the output files do not include a new > aparc.a2009s+aseg.mgz. I wanted this atlas overlayed on the mni registered > subject so I could extract one of the labels. Is this possible? > > Thanks, > > Carlos > > > > > ___ > Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1qie6YGV5WOOUaPgTp3nLby4aoCzwUv269sffHyGEcqPJwe3uDYfEGiqcOIBnmKbU_3XYcg04CQUxww_tF-Ldk3-VeAMylc2e1MUJo_5QbNceOPc80ni05XrW3wnjskHR1kZ3FVpfVA5TTGteVExVAMIjAt0cwCYZndXgFIZ0ISIWiawDkbq8YSAI5fn69zfHjAkQdzwouAYbuWV64_ZiD6gPV_Nk7yj-h1QF7r3jb7q-mglJTXHrYvgorDdv8sV3gPBE1pN1V9QfAjSrqTJsNe70dF-ufUPkadDV8Oxei_cnthbQH9xJDCa2VQi7fCnJ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1PAGF-wl6Q5BX1xkQeXUzKFtmGWulSpFsJMnuSyMjKrDXwzejGcaWZ0CyGXTGB2fBWW4jWVHVvnO_sp2g2OtbjiiOg4JVmt7nSmch8nKDtflygTZme81_0fXhujwxuaZuWUNoH3xEB51-Jf_Pa2SxuVXbz8V_XlUrJqkUS42-rCBmz-QdvI529B84DCIDWd4uRdeerGZXSO9AvsWSAgMnORnU2yFdW8911Qz-ksnlarFdpj-_IjSR3-asnjeRuSh0aceQg_y_aeamEZABKqrFGw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1qie6YGV5WOOUaPgTp3nLby4aoCzwUv269sffHyGEcqPJwe3uDYfEGiqcOIBnmKbU_3XYcg04CQUxww_tF-Ldk3-VeAMylc2e1MUJo_5QbNceOPc80ni05XrW3wnjskHR1kZ3FVpfVA5TTGteVExVAMIjAt0cwCYZndXgFIZ0ISIWiawDkbq8YSAI5fn69zfHjAkQdzwouAYbuWV64_ZiD6gPV_Nk7yj-h1QF7r3jb7q-mglJTXHrYvgorDdv8sV3gPBE1pN1V9QfAjSrqTJsNe70dF-ufUPkadDV8Oxei_cnthbQH9xJDCa2VQi7fCnJ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1r65aE8cbo11SK2ln8ACiPDOOt-_ehx8QrAWE_EqApW1Bah546IROUE1oaDnSuSXeHe4my4r9c2VCeyhZQB1sb03ePPZztVeCCQZDXVSzP0XWUP-hMsk4fQwmQ4BtDnRwLsUwDCP1jf_fMQ4STkJTW9cMaYzIkRLtHTGgrnPAxlnJ2Ec4reOhChk1NMkf4lTzg9ItD0tjb_SgO1ngupNhsEUzWCO5RuDW13kB2eQw2wLGNZe4RMY3xY6CpnHGBZCoKsY4pKpB5hd7BSmL84rZntP3-GMh8hSJe6zSVfNiRggKrLhTsGY_QpuamPufHsDS/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1r65aE8cbo11SK2ln8ACiPDOOt-_ehx8QrAWE_EqApW1Bah546IROUE1oaDnSuSXeHe4my4r9c2VCeyhZQB1sb03ePPZztVeCCQZDXVSzP0XWUP-hMsk4fQwmQ4BtDnRwLsUwDCP1jf_fMQ4STkJTW9cMaYzIkRLtHTGgrnPAxlnJ2Ec4reOhChk1NMkf4lTzg9ItD0tjb_SgO1ngupNhsEUzWCO5RuDW13kB2eQw2wLGNZe4RMY3xY6CpnHGBZCoKsY4pKpB5hd7BSmL84rZntP3-GMh8hSJe6zSVfNiRggKrLhTsGY_QpuamPufHsDS/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: ws...@korea.ac.kr, woosuk@gmail.com, wo os...@gmail.com ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine
[Freesurfer] trac-all with or without sub-thalamic nuclei segmentation
External Email - Use Caution Dear FreeSurfer developer. I successfully completed the tracula trac-all analysis using freesurfer 7.4.1. ThalamicNuclei.v13.T1.FSvoxelSpace.mgz images were obtained using segmentThalamicNuclei.sh, and trac-all analyses results were obtained using both 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 Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: ws...@korea.ac.kr, woosuk@gmail.com, wo os...@gmail.com ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] mri_segstats --sbTIVin
External Email - Use Caution Dear Freesurfer developer. According to the explanation in the https://secure-web.cisco.com/1coHbpSG3RMsDJ9eWWcn4zb_ld9qaPCVetqOo5rL5vuLfQQSISVGpVYl8aGgrzcAEShM1ov3Y1kaR3TI9f0riiixXrDWduFbq9YZu7vap8N9ooLrsMvKWnmIS21q5izT5EkhCL70i1Sw_90CUN-1TrF_pR-59FpT3F4Q9wFq-PqMEJ2eu_XExuWxU7lg6O-l_bycvdyEMCDXqh5RGJYHjh0n922PUlRzDFxpXB8bor7XeJEHKpJ7iaaxXxDJo4GuVe1z20CKD41HuVyeQ0zBLLXc6lE6yAoVBRTqJi6XtSiPdd685ICogk8xAkAqtfalRQljoFIba-du8mUaEixFIPA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FsbTIV, it seems that the TIV volume of SAMSEG pipeline could 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 Woo-Suk, Tae -- ------------ Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: ws...@korea.ac.kr, woosuk@gmail.com, wo os...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] NextBrain with 333 labels
External Email - Use Caution Dear FreeSurfer experts I tried to segment my brain MRI using NextBrain.in the most recent FreeSurfer-dev package. I followed the command in https://secure-web.cisco.com/150f92dNZNQHVJBK1fmC5Z4FYOqCYvgP1aIrq7dafQUxfyrR4wSHgPGLPwf0jxqrEBJqs-9YISyUo_u7_Onm0V3w4yaWygtLcx1JF4i9WiTS5ZTKPYLpQ9-Uldh3wQBbbZnRbsvvb1KbOyJKF22HkqyG58bxFrVQFGJXDy_a4M7FZc0gRtGZpqDcgI6QO9YXZPxhk3WjEmkZSigkBreI_rFTBD5mwSU5vIedOcNAPpUHyOikwtFDi3Kw5s7y7Mqm9IfFqXmCnJ9xzSxY-6naJGV0bla9PAJdSX4xLSPaNx8eeO2_FIgx2gjXODXa6uhZ-E0YDfbNW-KE64Udylt4MWQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHistoAtlasSegmentation, but, I got only the volumes of 101 labels How can I got the 333 labels and volumes using NextBrain? my command as follows mri_histo_atlas_segment ../subject/mri/orig.mgz ..subject/mri/histo_atlas_segmentation/ full 1 -1 Best regards Woo-Suk Tae Seoul, Korea Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Korea University College of Medicine, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6077 email: woosuk@gmail.com, w s...@korea.ac.kr woos...@naver.com subject,total intracranial,left cerebral white matter,left cerebral cortex,left lateral ventricle,left inferior lateral ventricle,left cerebellum white matter,left cerebellum cortex,left thalamus,left caudate,left putamen,left pallidum,3rd ventricle,4th ventricle,brain-stem,left hippocampus,left amygdala,csf,left accumbens area,left ventral DC,right cerebral white matter,right cerebral cortex,right lateral ventricle,right inferior lateral ventricle,right cerebellum white matter,right cerebellum cortex,right thalamus,right caudate,right putamen,right pallidum,right hippocampus,right amygdala,right accumbens area,right ventral DC,ctx-lh-bankssts,ctx-lh-caudalanteriorcingulate,ctx-lh-caudalmiddlefrontal,ctx-lh-cuneus,ctx-lh-entorhinal,ctx-lh-fusiform,ctx-lh-inferiorparietal,ctx-lh-inferiortemporal,ctx-lh-isthmuscingulate,ctx-lh-lateraloccipital,ctx-lh-lateralorbitofrontal,ctx-lh-lingual,ctx-lh-medialorbitofrontal,ctx-lh-middletemporal,ctx-lh-parahippocampal,ctx-lh-paracentral,ctx-lh-parsopercularis,ctx-lh-parsorbitalis,ctx-lh-parstriangularis,ctx-lh-pericalcarine,ctx-lh-postcentral,ctx-lh-posteriorcingulate,ctx-lh-precentral,ctx-lh-precuneus,ctx-lh-rostralanteriorcingulate,ctx-lh-rostralmiddlefrontal,ctx-lh-superiorfrontal,ctx-lh-superiorparietal,ctx-lh-superiortemporal,ctx-lh-supramarginal,ctx-lh-frontalpole,ctx-lh-temporalpole,ctx-lh-transversetemporal,ctx-lh-insula,ctx-rh-bankssts,ctx-rh-caudalanteriorcingulate,ctx-rh-caudalmiddlefrontal,ctx-rh-cuneus,ctx-rh-entorhinal,ctx-rh-fusiform,ctx-rh-inferiorparietal,ctx-rh-inferiortemporal,ctx-rh-isthmuscingulate,ctx-rh-lateraloccipital,ctx-rh-lateralorbitofrontal,ctx-rh-lingual,ctx-rh-medialorbitofrontal,ctx-rh-middletemporal,ctx-rh-parahippocampal,ctx-rh-paracentral,ctx-rh-parsopercularis,ctx-rh-parsorbitalis,ctx-rh-parstriangularis,ctx-rh-pericalcarine,ctx-rh-postcentral,ctx-rh-posteriorcingulate,ctx-rh-precentral,ctx-rh-precuneus,ctx-rh-rostralanteriorcingulate,ctx-rh-rostralmiddlefrontal,ctx-rh-superiorfrontal,ctx-rh-superiorparietal,ctx-rh-superiortemporal,ctx-rh-supramarginal,ctx-rh-frontalpole,ctx-rh-temporalpole,ctx-rh-transversetemporal,ctx-rh-insula orig.mgz,1419376.0,220960.44,245143.2,10524.024,587.158,15226.364,52580.062,6486.725,3172.058,4943.819,997.611,1138.142,1562.307,22484.832,3706.669,1661.134,261044.23,728.837,3948.052,214498.89,245845.8,9837.828,718.207,13765.447,51108.062,6712.08,3496.43,5091.322,1375.864,3605.934,1659.212,752.937,4012.216,3250.569,3550.659,7069.224,5283.201,5283.12,11321.66,9482.133,9294.902,2968.696,12740.552,7399.551,9934.023,5933.83,10030.493,3143.083,3958.854,4723.826,2698.144,3607.302,4775.2,8966.294,7736.732,11202.881,8488.257,2193.497,11974.645,18276.135,11847.277,9773.046,10573.724,3902.399,5289.5,2280.618,6189.164,2676.067,4380.078,5957.62,4729.964,4715.353,12645.911,13072.519,11313.838,4713.169,11478.066,6345.908,9426.335,5379.622,8431.767,4249.72,4183.77,4015.33,4713.499,5082.48,3224.371,8941.531,4713.256,11673.148,9511.726,2455.12,11325.822,17844.521,13702.588,8688.552,9427.185,3657.71,3965.856,2597.757,6605.644 ___ Freesurfer mailing list Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted
