Re: [Freesurfer] Thickness vs surface area

Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Monday, January 25, 2021 1:09 PM To: Freesurfer support list Subject: [Freesurfer] Thickness vs surface area External Email - Use Caution Hello, I am performing analyses looking at brain

[Freesurfer] Thickness vs surface area

External Email - Use Caution Hello, I am performing analyses looking at brain measures for a neurodegenerative disorder. I wanted to ask whether the accuracy for surface area is as high as is for thickness? I would appreciate your advice or any references. Thanks

Re: [Freesurfer] Thickness group normalization

?​ ​ *От:* freesurfer-boun...@nmr.mgh.harvard.edu от имени Vyacheslav Yarkin *Отправлено:* 5 февраля 2020 г. 11:47 *Кому:* Freesurfer support list *Тема:* Re: [Freesurfer] Thickness group normalization External Email - Use Caution I got the

Re: [Freesurfer] Thickness group normalization

: Freesurfer support list Тема: Re: [Freesurfer] Thickness group normalization External Email - Use Caution I got the idea but faced an issue with mris_preproc, the command is: mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas thickness --out avg_91_to_lh.mgh

Re: [Freesurfer] Thickness group normalization

: freesurfer@nmr.mgh.harvard.edu Тема: Re: [Freesurfer] Thickness group normalization Do you have a group of subjects that you want to use as an average? If so, you can just map all their thickness maps to your patient subject with mris_preproc --target patientsubjectname [then usual arguments

Re: [Freesurfer] Thickness group normalization

Do you have a group of subjects that you want to use as an average? If so, you can just map all their thickness maps to your patient subject with mris_preproc --target patientsubjectname [then usual arguments] Compute the mean with mri_concat outputofmris_preproc.mgz --mean --o groupmean.mgz Yo

[Freesurfer] Thickness group normalization

External Email - Use Caution Hello Freesurfer Team, Would you be so kind to provide freesurfer steps to implement warping fsaverage mean thickness data on individual subject inflated brains ? I am using expert opts to disable cortical thickness restriction, and set mris_thickne

Re: [Freesurfer] Thickness problem

sig = -log10(p)*sign(contrast), so if p=.01, then sig=2. The sign(contrast) is the direction of the contrast On 12/19/2019 4:14 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your comment. I compared cortical thickness bewteen two groups. I have a que

Re: [Freesurfer] Thickness problem

External Email - Use CautionHi Dr. Greve, Thank you for your comment.I compared cortical thickness bewteen two groups. I have a question. What does the values mean in the "sig.table.dat" file (ex. 0.571)? Good luck,   -

Re: [Freesurfer] Thickness problem

Can you try running the ROI results with mri_glmfit? ie, if you ran aparcstats2table to get the ROI results you input to SPSS, then run mri_glmfit --table table.dat --fsgd g1v4.fsgd --C group.diff.mtx --glmdir table.g1v4.glmdir where table.dat is the result of aparcstats2table Then look at t

[Freesurfer] Thickness problem

External Email - Use CautionHi there, I obtained results for right thickness using aparcstats2table.Then, ANCOVA was used to compared right thickness between two group (age, sex, edu, ICV as covariates)using SPSS. A group showed higher right thickness in the superior fr

Re: [Freesurfer] Thickness measurements.

yes, you can use the binary mris_thickness to compute the thickness cheers Bruce On Wed, 1 Aug 2018, Nillo, Ryan Michael R wrote: External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a

[Freesurfer] Thickness measurements.

External Email - Use Caution Hello FreeSurfer experts, I want to use FreeSurfer to generate thickness files using my own surfaces. Is there a way to use white and pial surfaces not generated from the mris_make_surfaces to create thickness files? Mahalo, Ryan M Nillo Staff

Re: [Freesurfer] thickness measure in basal ganglia

Yes, I mean a cerebellar parcellation. Do you project to distribute them. Thanks Giovanni Envoyé de mon iPhone > Le 26 févr. 2018 à 15:17, Bruce Fischl a écrit : > > Hi Giovanni > > do you mean a cerebellar parcellation? We have several prototypes but haven't > distributed anything yet. >

Re: [Freesurfer] thickness measure in basal ganglia

Hi Giovanni do you mean a cerebellar parcellation? We have several prototypes but haven't distributed anything yet. cheers Bruce On Mon, 26 Feb 2018, Giovanni de Marco wrote: Hello, is there an atlas for the cerebellum using freesurfer ? Many thanks for the information. Best Giovanni 2

Re: [Freesurfer] thickness measure in basal ganglia

Hello, is there an atlas for the cerebellum using freesurfer ? Many thanks for the information. Best Giovanni 2018-01-11 9:15 GMT+01:00 de Marco : > Many thanks Bruce for your rapid and clear response. > Have a nice day > Best > Giovanni > > Envoyé de mon iPhone > > > Le 11 janv. 2018 à 02:27,

Re: [Freesurfer] thickness measure in basal ganglia

Many thanks Best Giovanni Envoyé de mon iPhone > Le 11 janv. 2018 à 15:59, Bruce Fischl a écrit : > > it means the degree to which larger putamen and larger thickness are > correlated >> On Thu, 11 Jan 2018, de Marco wrote: >> >> Just a clarification. I would like to compare two groups of p

Re: [Freesurfer] thickness measure in basal ganglia

it means the degree to which larger putamen and larger thickness are correlated On Thu, 11 Jan 2018, de Marco wrote: Just a clarification. I would like to compare two groups of patients in terms of thickness. If I choose putamen as covariable (VI) in the design, what means the correlation bet

Re: [Freesurfer] thickness measure in basal ganglia

Just a clarification. I would like to compare two groups of patients in terms of thickness. If I choose putamen as covariable (VI) in the design, what means the correlation between putamen and groups for the thickness ? Thanks Giovanni > Le 11 janv. 2018 à 09:15, de Marco a écrit : > > Man

Re: [Freesurfer] thickness measure in basal ganglia

Many thanks Bruce for your rapid and clear response. Have a nice day Best Giovanni Envoyé de mon iPhone > Le 11 janv. 2018 à 02:27, Bruce Fischl a écrit : > > Hi Giovanni​​ > > the basal ganglia are little balls of gray matter, so I'm not sure how one > would measure thickness there. We do

Re: [Freesurfer] thickness measure in basal ganglia

Hi Giovanni​​ the basal ganglia are little balls of gray matter, so I'm not sure how one would measure thickness there. We do supply volume for each nucleus cheers Bruce On Thu, 11 Jan 2018, Giovanni de Marco wrote: Hello,​​ ​​In stats-table,​​ ​​I did'n​​ t find the thickness of

[Freesurfer] thickness measure in basal ganglia

Hello, ​​ ​​ ​​ ​​ ​​ ​​ In stats-table, ​​ ​​ I did'n ​​ t find the thickness of ​​ ​​ ​​ ​​ basal ganglia. ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ ​​ Please, c ​​ an we ​​ get

Re: [Freesurfer] thickness of corpus callosum

people have used the medial axis for this I believe. Not sure we have any code around for it anymore, although we once did. You basically compute the medial axis, then for each point on it you should have the radius of the largest inscribed circle as the thickness cheers Bruce On Tue, 24 Oct

[Freesurfer] thickness of corpus callosum

Respected Sir, How can we measure the thickness of corpus callosum? Thank you With regards Vidhu Agarwal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-

Re: [Freesurfer] Thickness from ROI_mask.label

Hi Stefano mris_anatomical_stats -l ROI_mask.label ... should do the trick cheers Bruce On Tue, 30 May 2017, std...@virgilio.it wrote: > Hi list, > is possible to calculate the thickness of a ROI_mask.label which I have drawn > using tksurf? > Please could you suggest a command line? > Thanks

[Freesurfer] Thickness from ROI_mask.label

Hi list,is possible to calculate the thickness of a ROI_mask.label which I have drawn using tksurf?Please could you suggest a command line?ThanksStefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/li

Re: [Freesurfer] Thickness asymmetry and LH/RH corresponding vertices in fsaverage

Yes, I think so. One hemi will be systematically different than the other, and this can easily be picked up in the stats On 03/23/2017 10:07 AM, Dorian P. wrote: > Thank you Douglas. > > I understand the rigor needed in the analysis and I agree. One more > question for my curiosity. > > My thic

Re: [Freesurfer] thickness from pial and white

resolution data has dimension larger than that. Is it possible to have a wm.mgz larger than 256^3? Or some kind of trick to make it happen? Thanks,Xiaomin Date: Wed, 10 Dec 2014 11:37:29 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from

Re: [Freesurfer] thickness from pial and white

s, Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM To: Freesurfer suppo

Re: [Freesurfer] thickness from pial and white

>> MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not >> open file. >> Thanks, >> Xiaomin >> ________ >> From: yu...@hotmail.com >> To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] thickness from pial and white

>> MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not >> open file. >> Thanks, >> Xiaomin >> ________ >> From: yu...@hotmail.com >> To: freesurfer@nmr.mg

Re: [Freesurfer] thickness from pial and white

aomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks.  I will try mris_fill. Xiaomin From: Bruce Fischl Sent: ‎Tuesday‎, ‎December‎ ‎9‎, ‎2014 ‎4‎:‎31‎ ‎PM To: Freesurfer support

Re: [Freesurfer] thickness from pial and white

MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks,Xiaomin From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 + Thanks. I will try

Re: [Freesurfer] thickness from pial and white

> mris_thickness? I need the wm.mgz to generate the ratio of gray >>> vs. white matter. >>> >>> Xiaomin >>> >>> Date: Tue, 9 Dec 2014 09:55:21 -0500 >>> From: fis...@nmr.mgh.harvard.edu >>> To: freesurfer

Re: [Freesurfer] thickness from pial and white

1:08 PM, Xiaomin Yue wrote: >>> >>> Hi Bruce, >>> >>> Thanks for your response. What's the inputs to the >>> mris_thickness? I need the wm.mgz to generate the ratio of gray >>> vs. white matter. >>> >>> Xiaomin >>

Re: [Freesurfer] thickness from pial and white

ponse. What's the inputs to the >> mris_thickness? I need the wm.mgz to generate the ratio of gray >> vs. white matter. >> >> Xiaomin >> >> Date: Tue, 9 Dec 2014 09:55:21 -0500 >> From: fis...@nmr.mgh.harvard.edu >> T

Re: [Freesurfer] thickness from pial and white

response.  What's the inputs to the mris_thickness?  I need the wm.mgz to generate the ratio of gray vs. white matter.  Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

Re: [Freesurfer] thickness from pial and white

mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: > > Hi All, >

Re: [Freesurfer] thickness from pial and white

o generate the ratio of gray vs. white matter. > > Xiaomin > > Date: Tue, 9 Dec 2014 09:55:21 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] thickness from pial and white > > the thickness you can generate usi

Re: [Freesurfer] thickness from pial and white

Hi Bruce, Thanks for your response. What's the inputs to the mris_thickness? I need the wm.mgz to generate the ratio of gray vs. white matter. Xiaomin Date: Tue, 9 Dec 2014 09:55:21 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

Re: [Freesurfer] thickness from pial and white

the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc On Mon, 8 Dec 2014, Xiaomin Yue wrote: Hi All,   Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfe

[Freesurfer] thickness from pial and white

Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm

Re: [Freesurfer] Thickness measurements on longitudinal data set

Sounds great, will try that! Again, thank you very much for your help! Bastian. On 22 July 2014 01:53, Martin Reuter wrote: > Hi Bastian, > > yes, lta are the (here rigid) transformations (dat files are deprecated). > > you can use mri_convert -at > > or mri_vol2vol for mapping images. > > I thi

Re: [Freesurfer] Thickness measurements on longitudinal data set

Hi Bastian, yes, lta are the (here rigid) transformations (dat files are deprecated). you can use mri_convert -at or mri_vol2vol for mapping images. I think, however, you are not interested in mapping images, but in ROI's on the surface. You can do the following: - draw/create the ROI in the

Re: [Freesurfer] Thickness measurements on longitudinal data set

Thank you for clarification, Martin! Will do so and also try registration of base >> TP1.long etc. Does FS create registration files (.dat) for this purpose automatically? I found some *.lta files in the /mri/transfers folder of the base image but am not sure how to apply them (maybe tkregister2

Re: [Freesurfer] Thickness measurements on longitudinal data set

Hi Bastian, use the longitudinal base for it. Also, once your ROI is in that space you can simply apply it in each long as they are in the same space as the base. The registration of base >> TP1.long etc. probably only changes results very little. Best, Martin On 07/18/2014 10:45 AM, Bastian

[Freesurfer] Thickness measurements on longitudinal data set

Dear Freesurfer-Experts, I am currently trying to measure Cortical Thickness of a Volume-defined ROI in a patient measured at 4 timepoints. Basically, I am interested in a ROI resulting from fMRI activation measured on Timepoint 1. I would then like to get thickness values in the same ROI for all

Re: [Freesurfer] Thickness values to a common space

Can you send the exact command line you are using (no wildcards or substitutions) and the terminal output that you get? On 04/15/2014 11:52 AM, sabin khadka wrote: > Hi Doug, > Thanks for the reply. > Those are the two steps I followed to extract vertexwise surface area, > thickness and pial_lg

Re: [Freesurfer] Thickness values to a common space

Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv

Re: [Freesurfer] Thickness values to a common space

what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: > Hi all, > > Related question to this. > I am trying to extract vertexwise surface area values in an ascii > files. For that I am doing > > mri_surf2surf --hemi ?h --srcsubject area

Re: [Freesurfer] Thickness values to a common space

Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc

[Freesurfer] Thickness values to a common space

I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve

[Freesurfer] Thickness analysis on fetal brain

Hi list, we would like to perform cortical thickness analysis on fetal brain. We have a single shot T2 image (good quality) and T1 image (poor quality). All images are in 2D with overlapping and they are acquired by using 1.5 tesla. We have some questions: 1. Do you know a post-processing way to

Re: [Freesurfer] thickness for "subcortical structures"

Hi Francesco no, they are not cheers Bruce Tue, 25 Mar 2014, Francesco Puccettone wrote: Hi Louis, thanks! I am still not sure whether or not structures such as the hippocampus and the amygdala are considered part of the cortex by freesurfer (they are referred to as `subcortical` but I think

Re: [Freesurfer] thickness for "subcortical structures"

Hi Louis, thanks! I am still not sure whether or not structures such as the hippocampus and the amygdala are considered part of the cortex by freesurfer (they are referred to as `subcortical` but I think an anatomist would say they are in fact part of the cerebral cortex), and whether it makes sens

[Freesurfer] thickness for "subcortical structures"

Hello, I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still te

Re: [Freesurfer] thickness for "subcortical structures"

Hi Francesco, This wiki page has pretty good definitions for the morphometry stats. Let us know if you want to clarify anything though. https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Tue, 25 Mar 2014, Francesco Puccettone wrote: > Hello, > > I've read that cortical thic

Re: [Freesurfer] thickness visualization in SPM

Use mri_surf2vol doug On 2/5/14 11:31 PM, Muhammad Naveed Iqbal Qureshi wrote: Hi, How can I convert freesurfer .thickness files into .nii volume data to analyze in SPM I have already converted the .thickness files into .nii format by using mri_convert command but the converted files

[Freesurfer] thickness visualization in SPM

Hi, How can I convert freesurfer .thickness files into .nii volume data to analyze in SPM I have already converted the .thickness files into .nii format by using mri_convert command but the converted files can not be visualize in spm probably I need to project the thickness on anatomical

Re: [Freesurfer] Thickness values

In the QDEC output folder in each contrast there will be a file named something like cache.th20.abs.y.ocn.dat. This will have a row for each subject and a column for each cluster. The value is the mean thickness for that subject for that cluster. Is this what you need? doug On 02/02/2014 01

[Freesurfer] Thickness values

Hello Freesurfers, Is there anyway (command, anything on QDEC) to get a list of the thickness values in the significant clusters? Specifically, is there anyway to get the actual value of the maximum thickness in the blobs (in millimeters)? Or the mean thickness of the blobs for each subject? Than

[Freesurfer] Processing Freesurfer thickness files in SPM for ANOVA

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Med

Re: [Freesurfer] Thickness vertex by vertex

Thanks all, I did it :) Cheers Giusy Inviato da iPhone Il giorno 28/ago/2013, alle ore 18:40, Avram Holmes ha scritto: > check the .vol values I think they should match those from read_curv. > > Avram > > > On Wed, Aug 28, 2013 at 11:37 AM, Giusy Chinnici > wrote: >> Thanks all, >> >> I

Re: [Freesurfer] Thickness vertex by vertex

you can use read_label and the first column (+1) for the indices Bruce On Wed, 28 Aug 2013, Giusy Chinnici wrote: Thanks all, I opened the file subj/surf/?h.thickness with MATLAB using the function read_curv(subj/surf/lh.thickness). I obtained a vector with dimensions nverticesX1, but I need

Re: [Freesurfer] Thickness vertex by vertex

Giusy, You can access vertex level info in Matlab with MRIread('SUBJECT.FILENAME'). Avram On Wed, Aug 28, 2013 at 8:42 AM, Giusy Chinnici wrote: > Dear all, > > Is there available a function that, given a certain ROI, returns per > vertex thickness (not the average thickness)? > > Thanks > Che

Re: [Freesurfer] Thickness vertex by vertex

you mean only within that ROI? I don't think so, but this would be pretty easy in matlab On Wed, 28 Aug 2013, Giusy Chinnici wrote: > Dear all, > > Is there available a function that, given a certain ROI, returns per vertex > thickness (not the average thickness)? > > Thanks > Cheers > > Giusy C

[Freesurfer] Thickness vertex by vertex

Dear all, Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? Thanks Cheers Giusy Chinnici ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] thickness

On 5/11/13 7:41 PM, Tudor Popescu wrote: Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while fact

[Freesurfer] thickness

Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't qui

Re: [Freesurfer] thickness=0, what that means?

those are probably in non-cortical regions like the midline cheers Bruce On Thu, 24 Jan 2013, jm wrote: > Dears Freesurfer: > > We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we > can see some vertexes with thickness value equal to 0 (thickness=0 mm). > Could you tell me when

Re: [Freesurfer] thickness=0, what that means?

It usually means that it is part of the medial wall where there is no cortex. For technical reasons we need to have the surface be a closed surface (like a sphere). That means that there have to be places that don't have cortex but we still need to represent. In these places thickness is set to

[Freesurfer] thickness=0, what that means?

Dears Freesurfer: We are looking into *lh.thickness.fwhm15.fsaverage**.mgh* file and we can see some vertexes with thickness value equal to 0 (thickness=0 mm). Could you tell me when that value is reported by Freesurfer? what do (thickness=0) means? Thanks in advance !!! <>___

Re: [Freesurfer] Thickness and variable plot in glmfit

You can run tksurfer, something like cd glmfitdir tksurfer fsaverage lh inflated -aparc -overlay contrast/sig.mgh -fsgd y.fsgd doug On 07/30/2012 01:16 AM, Jeni Chen wrote: > Hello again, > > In Qdec we get a plot of the data for a particular vertex showing the > variable and the thickness in

[Freesurfer] Thickness and variable plot in glmfit

Hello again, In Qdec we get a plot of the data for a particular vertex showing the variable and the thickness in the x, y axis respectively. Is there a way to get the same plot when using glmfit? Where do I find the data for the plot? Thank you! Jeni Chen __

Re: [Freesurfer] thickness or volume?

Run mris_preproc with the --meas volume option. Make sure to get an up-to-date version of mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc doug Lindsay Ercole wrote: > What is the current opinion on using cortical volumes rather than > reporting on thickne

Re: [Freesurfer] thickness or volume?

Hi Lindsay they are both biologically relevant measures, it's just a question of what you are investigating. If you are doing volume it's probably worth decommposing it into surface area and thickness though to understand the underlying neurobiology better Bruce On Tue, 13 Dec 2011, Lindsay E

[Freesurfer] thickness or volume?

What is the current opinion on using cortical volumes rather than reporting on thickness? Sincerest thanks, Lindsay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] thickness-age correlation

Antonella Kis wrote: > Dear Freesurfer experts, > > I am doing a thickness-age correlation group difference study (patients > versus controls. I would like to know if: > > 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the > change in thickness with age > Yes. > 2)w

[Freesurfer] thickness-age correlation

Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age 2)what is the best iteration number for the simul

Re: [Freesurfer] thickness measurement workflow & tksurfer sliver

Hi, I found this - http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, just after mailing the group. I hope going through and the tutorial on QDEC this will help my cause. Thanks, Jaichander On Mon, Jul 18, 2011 at 3:45 PM, Jaichander S wrote: > Hi freesurfers, > > 1. I am a new

[Freesurfer] thickness measurement workflow & tksurfer sliver

Hi freesurfers, 1. I am a new user of freesurfer. I want to measure,compare cortical thickness in corresponding regions of the cortex in a group of subjects. Is there a description of steps involved in doing this? >From what I have read till now, I know that I can create ROIs and use the instruct

Re: [Freesurfer] Thickness measurements stats

I can't say whether it's the best way, but it should be relatively unbiased On Tue, 5 Jul 2011, Ignacio Letelier wrote: Then, and finally is this method the best way to determine whether exist any cortical thickness anomaly, I mean, to use a normal  control acquisition as comparisson? Thanks

Re: [Freesurfer] Thickness measurements stats

Then, and finally is this method the best way to determine whether exist any cortical thickness anomaly, I mean, to use a normal control acquisition as comparisson? Thanks in advance Ignacio. 2011/7/5 Bruce Fischl > Hi Ignacio, > > the thickness is definitely affected by factors such as sequenc

Re: [Freesurfer] Thickness measurements stats

Hi Ignacio, the thickness is definitely affected by factors such as sequence type, field strength and acquisition parameters (not to mention age, maybe gender, etc...) so I think you need to acquire your own control(s) on a matched acquisition. cheers. Bruce On Tue, 5 Jul 2011, Ignacio Let

Re: [Freesurfer] Thickness measurements stats

Hi Ignacio, I see. You could do that, but I don't think it will show what you want. There is a big geometric component to the thickness - crowns are thick and fund are thin - so at the very least you might try including mean curvature as a covariate. cheers Bruce On Fri, 1 Jul 2011, Ignacio

Re: [Freesurfer] Thickness measurements stats

Sorry I didn't realize since you have the same domain. Ok, Let's say I do know the mean cortical thickness value of a subject. Then is it possible know what brain areas differ more from that mean value by using a color map visualization (I.e. for example: red = higher deviations, deep blue = low

Re: [Freesurfer] Thickness measurements stats

Hi Ignacio you mean different from the median in that subject? Easy enough to do in matlab, but we don't have anything out of the box to do it cheers Bruce On Fri, 1 Jul 2011, Ignacio Letelier wrote: Hi forum Is it possible to get statistical maps of  cortical thickness differences in th

[Freesurfer] Thickness measurements stats

Hi forum Is it possible to get statistical maps of cortical thickness differences in the same subject? I.e. to know what areas differ most from the median -- Ignacio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harv

Re: [Freesurfer] thickness analyse

wang, i think having the imported roi thickness data in your qdec.table.dat file is confusing you. you should just delete that data from your qdec.table.dat, keeping just 'fsid' and 'addiction' columns. from looking at your analysis (which appears you have done everything right), it is not used a

Re: [Freesurfer] Thickness values for every voxel

If you don't have MatLAB, you can also do: $>mris_calc -out lh.thickness.asc lh.thickness ascii which will convert the 'lh.thickness' into an ascii file (in this case, 'lh.thickness.asc') containing the thickness per vertex per line. Incidentally, this will work with any FreeSurfer curvature fi

Re: [Freesurfer] Thickness values for every voxel

Hi Ana, yes, it's stored in the ?h.thickness file, which you can load into matlab or tksurfer for visualization/analysis. cheers Bruce On Tue, 4 May 2010, Ana Catarino wrote: > Hello, > > Does anyone know if there is a way of getting access to the values of > thickness for each voxel / point i

Re: [Freesurfer] Thickness values for every vertex

*Use the commands:* *mri_surf2surf --s subject --hemi lh --sval-tal-xyz white **--tval-xyz --tval lh.white.tal** * *mris_convert lh.white.tal lh.white.tal.asc* Ref: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011618.html You can make search in previous answers of the ma

[Freesurfer] Thickness values for every vertex

Hello, Does anyone know if there is a way of getting access to the values of thickness for each vertex in the mesh? Thank you, Ana Catarino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] Thickness values for every voxel

Hello, Does anyone know if there is a way of getting access to the values of thickness for each voxel / point in the mesh? Thank you, Ana Catarino ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] thickness of frontal lobe

Hello, I looked at the results from stage 3 and found out it has 1100 regions (we might not use qdec since we have many other variables to control). But it is beyond manageable levels. What we want might two things: The first one might be a general measure of thickness (or volume) of each

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

or cluster-mass method within freesurfer? Thank you so much! Stefan Message: 1 Date: Fri, 29 Jan 2010 14:57:34 -0800 From: Don Hagler Subject: Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results To: Doug Greve Cc: freesurfer maillist Message-ID: Content-Type: text

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

500 > From: gr...@nmr.mgh.harvard.edu > To: dhagle...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - > different results > > Don, why do you say that .05 is too liberal? We use a simulation-based > test

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

FDR is NOT more conservative than cluster-based methods, in general. The smoother the data, the more conservative FDR is. In my experience with surface-based data, FDR has been less sensitive than cluster-based methods -- perhaps because my data was very smooth. > Stefan Brauns wrote: > >> W

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

e multiple comparison > corrected p value, for which you would usually use 0.05. > > > Date: Fri, 29 Jan 2010 10:02:45 -0500 > From: stefan.bra...@googlemail.com > To: Freesurfer@nmr.mgh.harvard.edu > Subject

Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

nd is the multiple comparison corrected p value, for which you would usually use 0.05. Date: Fri, 29 Jan 2010 10:02:45 -0500 From: stefan.bra...@googlemail.com To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results Hi there, we are s

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