Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

. All the files are binary, no? Are you getting an error? cheers Bruce On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:   External Email - Use Caution Dear FS's experts, I am trying to downsample some surface data from fsaverage to fsaverage6 with the following command:  mri_surf2surf

Re: [Freesurfer] Compare vertexwise correlation maps

trast. > > On 9/2/2019 11:14 AM, Matthieu VANHOUTTE wrote: >> External Email - Use Caution >> >> Dear experts, >> >> I would like now to determine if there is statistically difference >> between vertexwise correlation maps (whether one is stati

[Freesurfer] Compare vertexwise correlation maps

External Email - Use Caution Dear experts, I would like now to determine if there is statistically difference between vertexwise correlation maps (whether one is statistically "stronger" than the other). Would there be a way to do this with Freesurfer? (r-to-z Fisher

[Freesurfer] Estimation of surface based smoothing

External Email - Use Caution Dear experts, Knowing the size of the effects on volume-based data, does anyone would know a way to estimate the size of the effects on surface data? Best, Matthieu ___ Freesurfer mailing list

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

Are you also looking to have freeview snap pictures for you? > > On 7/18/19 11:57 AM, Matthieu VANHOUTTE wrote: > > External Email - Use Caution > > Sorry not to be precise on my answer. > > > > I can easily open freeview to load overlay on surface and configure >

[Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

External Email - Use Caution Dear experts, I use tksurfer in command line to generate multiple faces images of overlays on the fsaverage surface. Graphically it is possible via freeview to set the color scale of the overlay with "Color Wheel" setting. I searched into the

Re: [Freesurfer] Within-subject vertexwise correlation

edu> a écrit : > I'm not sure that this is a question we can answer. If you do smooth, then > you should smooth both modalities the same amount. > > On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > Dear FS experts, > > I wou

[Freesurfer] Within-subject vertexwise correlation

External Email - Use Caution Dear FS experts, I would like to compute within-subject correlation between two modalities based on vertexwise maps in fsaverage space. I wonder whether I have to smooth the normalized surface-based maps before computing vertexwise within-subject

[Freesurfer] Error with "recon-all -make all" following multiple manual editing

External Email - Use Caution Dear Freesurfer's experts, Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all". However, during the process, I goth for both subjects the following error

Re: [Freesurfer] Left and right pial surfaces crossing in medial cortex

External Email - Use Caution Dear Experts, Would you have any advice? Best, Matthieu Le mar. 26 mars 2019 à 13:54, Matthieu VANHOUTTE < matthieuvanhou...@gmail.com> a écrit : > Dear FS' experts, > > Using both T1 and FLAIR in recon-all to improve pial surfaces,

[Freesurfer] Recon editing + FLAIRpial

External Email - Use Caution Dear Experts, Having launched recon-all process on one subject with supplemental FLAIR data in order to better define pial surface, I still need to follow some recon editing during the QC of this patient. However, when re-launching recon-all to

Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

ich should > be fine for this. The reason that RBV had to be upsampled is that there > is no way to represent the different tissue types at a single (big) voxel > > On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Dear Douglas

[Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

External Email - Use Caution Dear Douglas, RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to compute PVCorrected images. Would it be beneficial to project this PVCorrected images onto gtmseg space surfaces to keep this upsampled resolution ? Or would it be

Re: [Freesurfer] Recon-all XL defect detected...

External Email - Use Caution Hi Bruce, Did you have time to tale a look at ? Best, Matthieu On 19/02/2019 16:39, Bruce Fischl wrote: will do On Tue, 19 Feb 2019, Matthieu VANHOUTTE wrote: External Email - Use Caution Hi Bruce, I don't see major thing that could

[Freesurfer] PETSurfer: Needs for gtmseg

External Email - Use Caution Dear FS's experts, In the perspective of correcting generated surfaces errors or defects, does the gtmseg command need corrected surfaces or could it be launch independently before having these corrected surfaces ? Best, Matthieu

Re: [Freesurfer] Recon-all XL defect detected...

. Take a look at the inflated.nofix and see if you can identify the XL defect. It is probably near the back of the brain since it is one of the first defects encountered. cheers Bruce  On Mon, 18 Feb 2019, Matthieu VANHOUTTE wrote: External Email - Use Caution Dear Freesurfer's

[Freesurfer] Recon-all XL defect detected...

External Email - Use Caution Dear Freesurfer's experts, I have run recon-all on one subject and it stopped with a "XL defect detected..."  (please see below the log): /#@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019// // // mris_fix_topology -rusage

[Freesurfer] PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"

External Email - Use Caution Dear Douglas, I wanted just to compute rescaled PET image without any PVC but following the same process as if I would have applied PVC. Moreover, I didn’t want to reduce FOV with auto mask generated (to still be in the gtmseg space). So I ran the

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Le jeu. 14 févr. 2019 à 21:36, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > >> Le 14 févr. 2019 à 19

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution > Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: >> >> External Email - Use Caution >> >> >> >> Le jeu. 14 févr

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: > > External Email - Use Caution > > > > Hi Douglas, > >

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

, Greve, Douglas N.,Ph.D. wrote: > The GTM operates on regions, so you can't do trilin interp. The > operations that you describe below are not used in mri_gtmpvc. If  you > are trying to get something close to what the GTM does, then use nearest > neighbor > > On 2/14/19 3:43 AM,

Re: [Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Hi Douglas, Could you help me concerning my previous questions ? Thanks, Matthieu > Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE a > écrit : > > Hi Douglas, > > Thanks for clarification. Why use "nearest neighbo

[Freesurfer] PETSurfer: "mri_gtmpvc --psf 0 --no-tfe" voxel-wise output

External Email - Use Caution Dear Douglas, Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Any advice ? Best. Le jeu. 7 févr. 2019 à 23:12, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Yes that's what I mean. But does this command provide an intensity > normalized voxel-wise image ? > > Co

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

19 à 23:06, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > Do you mean the mean intensity not corrected for PVC? I would just run > mri_gtmpvc with --psf 0 --no-tfe to turn off PVC > > On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote: > > > > External

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hello experts, Anyone would have an advice on my previous questions ? Best, Matthieu Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Hi Douglas, > > In order to apply intensity normaliza

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Could you answer to my previous question ? Best, Matthieu > Le 30 janv. 2019 à 14:48, Matthieu Vanhoutte a > écrit : > > Hi Douglas, > > In order to apply intensity normalization to non-PVC PET images based on mean

[Freesurfer] Combination of multiple PET projection: "mri_vol2surf --projfrac" vs. "mris_expand"

External Email - Use Caution Dear Freesurfer’s experts, I have read the paper from Marcoux, et al. « An Automated Pipeline for the Analysis of PET Data on the Cortical Surface ». Frontiers in Neuroinformatics 12 (10 décembre 2018). https://doi.org/10.3389/fninf.2018.00094

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

aseg structures, then they are the same. > > On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Hi Douglas, >> >> >>> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. >> <mailto:dgr...@mgh.h

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, > Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Dear Dougla

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Please find comments inline below. best, Matthieu > Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote: >> External Email - Use Cau

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

. based on PVE corrected reference region’s mean intensity) ? Many thanks in advance for helping. Best, Matthieu > Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > I'm not sure what you mean. If you are turning off PVC, why are you > computing RBV and MGX? What is your command line? What do you mean that > these options don't seem to work? > > On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

Re: [Freesurfer] Robust PET signal projection

External Email - Use Caution Hi Douglas, Could you answer to my previous request ? Best, Matt > Le 21 déc. 2018 à 20:31, Matthieu Vanhoutte a > écrit : > > Thanks Douglas. > > Is there a way to compute a weighted average in one command with fscalc ? >

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Could you answer to my previous request ? Best, Matt > Le 21 déc. 2018 à 20:22, Matthieu Vanhoutte a > écrit : > > Hi Douglas, > > Thanks for helping. > > To have an only rescaled voxel-wise PET image, th

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Could you answer to my previous request ? Best, Matt > Le 21 déc. 2018 à 20:29, Matthieu Vanhoutte a > écrit : > > Hi Douglas, > > Thanks for these clarifications. I have however one misunderstanding. > > Whe

Re: [Freesurfer] Which T1 volume to use for coregistration with PET volume

On 12/31/18 10:53 AM, Bruce Fischl wrote: >> HI Matt >> >> yes, I would agree, but Doug will give you the definitive answer >> >> cheers >> Bruce >> On Fri, 28 Dec 2018, Matthieu Vanhoutte wrote: >> >>>External Email - Use Caution >

[Freesurfer] Which T1 volume to use for coregistration with PET volume

External Email - Use Caution Dear Freesurfer’s experts, I used mri_coreg command to coregister PET image onto T1 volume. Basically, this command coregister PET image onto orig.mgz volume (default target). However, I wonder if T1.mgz wouldn’t be a better target since it has been

Re: [Freesurfer] Robust PET signal projection

robably will not make a difference. > > On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > Dear experts, > > Is there any advice on this point ? > > Best, > Matthieu > > > Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte <

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

not to use template.reg.lta computed by mri_coreg ? What are the differences between those different files ? Best, Matthieu Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote: > >

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

dgr...@mgh.harvard.edu> a écrit : > You will need to set --psf 0 and --no-tfe to fully turn off PVC. > > On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > Hi Douglas, > > Could you help me on this point ? > > Best, > Matt

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution > > Hi Douglas, > > Could you help me about my previous mail with questions ? > > Thanks, > Matthieu > > > Le ven. 7 déc. 2018 à 14:31, Matthieu Vanhoutte < > matthieuvanhou...@gmail.com> a écrit : > >> H

Re: [Freesurfer] Robust PET signal projection

External Email - Use Caution Dear experts, Is there any advice on this point ? Best, Matthieu Le mer. 12 déc. 2018 à 10:47, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Dear Freesurfer's experts, > > In order to have a robust PET si

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Could you help me on this point ? Best, Matthieu Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Dear Douglas, > > Is it possible to use mri_gtmpvc command in order to inte

[Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Dear Douglas, Is it possible to use mri_gtmpvc command in order to intensity normalize PET images without applying PVE correction by setting --psf to 0 ? Best, Matthieu ___ Freesurfer mailing list

[Freesurfer] Robust PET signal projection

External Email - Use Caution Dear Freesurfer's experts, In order to have a robust PET signal projection, is it possible compute the projected PET signal as a weighted average of the PET signal intersecting with the surfaces ranging from 35 to 65% of the cortical tickness with a

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Could you help me about my previous mail with questions ? Thanks, Matthieu Le ven. 7 déc. 2018 à 14:31, Matthieu Vanhoutte a écrit : > Hi Douglas, > > Thanks for these clarifications. I added some others questions inlin

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, I come back on my previous question concerning survival bias in LME. Do you have an advice ? Best, Matthieu > Le 19 oct. 2018 à 16:30, Matthieu Vanhoutte a > écrit : > > Hi Martin, > > Do you mean that high at

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Thanks for these clarifications. I added some others questions inline below. Best, Matthieu > Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 11/30/2018 07:15 AM, Matthi

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Thanks for these clarifications. I added some others questions inline below. Best, Matthieu > Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. a > écrit : > > > > On 11/30/2018 07:15 AM, Matthi

[Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for

[Freesurfer] [PETSurfer] MGX and RBV Correction

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both

Re: [Freesurfer] Longitudinal stream : LME and limits of model

cally less time points, means more variance > on the slope estimates, but that should be considered in LME). But I am > not a statistician. > > Best, Martin > > > On Wed, 2018-10-17 at 18:46 +0200, Matthieu Vanhoutte wrote: > > External Email - Use Caution >

Re: [Freesurfer] Longitudinal stream : LME and limits of model

gt; Best, Martin > > On Tue, 2018-10-16 at 16:15 +, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > Hi Martin, > > > > It's been a long time since this discussion but I return on this from > > now... The problem is that I followed longitu

Re: [Freesurfer] Longitudinal stream : LME and limits of model

n > the image from the acquisition. We currently don’t use non-linear > registration across time points (only rigid). > > Best, Martin > > > On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte < > matthieuvanhou...@gmail.com> wrote: > > Hi Martin, > > Please

Re: [Freesurfer] Troubles to determine the type of recon editing needed

it : > Yes - if you've used the -bigventricles flag, you should always include it > with the recon-all command. > > > Bram > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf

Re: [Freesurfer] Troubles to determine the type of recon editing needed

. 2018 à 18:03, Bruce Fischl a écrit : > I think it should be ok. It will be a bit slower, but shouldn't reduce > accuracy I don't think. Try it and see > Bruce > On Tue, 18 Sep 2018, Matthieu > Vanhoutte wrote: > > > > > External Email - Use Caution &g

Re: [Freesurfer] Troubles to determine the type of recon editing needed

l of your subjects with it > > cheers > Bruce > On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: > > >> External Email - Use Caution >> >> Dear Bram, >> >> It looks like the -bigventricles flag fixed my problem with my specific >> subject

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM. I

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Dear Bram, Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag. Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and

[Freesurfer] Compare longitudinal evolution of two vertex-wise data

Dear experts, Do you know if there would be a mean to compare longitudinal evolution of two vertex-wise data (i.e. kind of longitudinal correlation) with LME tools or others ? Best regards, Matthieu ___ Freesurfer mailing list

Re: [Freesurfer] Effect of continuous time-varying covariate across time in LME models

Dear Freesurfer's experts, Would anybody have advice concerning my requests in below mail ? Thanks in advance. Best regards, Matthieu 2017-07-01 11:37 GMT+00:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > Dear Freesurfer’s experts, > > I would like to test if neuropsyc

[Freesurfer] Effect of continuous time-varying covariate across time in LME models

Dear Freesurfer’s experts, I would like to test if neuropsychological score across time (continuous time-varying covariate) has an effect on metabolism maps. However, I don’t manage to understand how to define design matrix and contrast associated to assess it with LME models. I picked up

[Freesurfer] Surface area of a define volume projection on cortical surface

Dear Freesurfer's experts, Given the well known size of a voxel I would like to know the equivalent surface area once projected on the white fsaverage cortical surface. Could anyone give me a proper way of computing this ? Best regards, Matthieu ___

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

plain me ? Best, Martin On 05/17/2017 11:12 PM, Matthieu Vanhoutte wrote: Hi Martin, I will read up on interpretation of time varying covariates. If initially I use score as variable fixed across time, and define a variable for 'score x time' interaction: 1) Would putting only 1 to 'scor

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

re as a variable (fixed across time - would probably do this for intial testing anyway) or score as time-varying covariate, but would read up on how to interpret results in the presence of time-varying-covariates. I am not a statistician. Best, Martin On 05/16/2017 08:09 PM, Matthieu Vanhoutte w

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

eraction. Sorry, but I cannot do your design. Ultimately the model is the research question that you are asking and it is important that this is done correctly. Maybe there is a local biostats person that you can talk to? Best, Martin On 05/15/2017 08:20 PM, Matthieu Vanhoutte wrote: Hi Martin,

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

2017 8:08 PM, "Martin Reuter" <mreu...@nmr.mgh.harvard.edu> a écrit : Hi Matthieu, yes, that is possible. Instead of group, you use a variable for your score (and interaction etc). Sometimes it may also makes sense to use score instead of time. Best, Martin > On 12 May 2017,

[Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Dear Freesurfer's experts, I have searched through the mailing list but haven't found any answer to my question. Is it possible with LME model to make correlations between for example cortical thickness surface data and cognition scores along time ? As it is possible to test for interaction of

Re: [Freesurfer] Longitudinal: obtain rigid registration matrix from cross to long subject

.@nmr.mgh.harvard.edu] on behalf of Matthieu Vanhoutte [ > matthieuvanhou...@gmail.com] > *Sent:* Friday, March 24, 2017 10:43 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Longitudinal: obtain rigid registration matrix > from cross to long subject > > Dear Freesu

[Freesurfer] Longitudinal: obtain rigid registration matrix from cross to long subject

Dear Freesurfer's experts, I would like to obtain the rigid registration matrix of the transformation between cross and long subject. Where could I find this (.dat or .lta file) ? Best regards, Matthieu ___ Freesurfer mailing list

[Freesurfer] Recon-all : mri_watershed Error: indices out of bounds

Dear Freesurfer's experts, I ran a classic recon-all and got stucked on a problem I couldn't find in the mailing list: "*mri_watershed Error: indices out of bounds*" *mri_watershed -T1 -brain_atlas /home/global//freesurfer5.3//average/RB_all_withskull_2008-03-26.gca

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

your data after reprocessing. > > Antonin Skoch > > > Dear experts, > > Does anybody could answer my last request ? > Best, > Matthieu > > 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > > > Dear FS's experts, > >

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear experts, Does anybody could answer my last request ? Best, Matthieu 2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > Dear FS's experts, > > I have run all my cross with v5.3 and hesitate to run all longitudinal > process with v6. Do

[Freesurfer] Longitudinal stream with v6 but cross with v5.3

Dear FS's experts, I have run all my cross with v5.3 and hesitate to run all longitudinal process with v6. Does that make sense and will improve the process or would it be risky to do this ? Many thanks for your lights ! Best regards, Matthieu ___

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Dear FS's experts, Could you answer me about questions from below inline precedent mail ? Best regards, Matthieu 2016-11-22 21:31 GMT+01:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > Hi Martin, > > Please see inline below: > > Le 22 nov. 2016 à 17:04

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Martin, Please see inline below: > Le 22 nov. 2016 à 17:04, Martin Reuter <mreu...@nmr.mgh.harvard.edu> a écrit : > > Hi Matthieu, > (also inline) > >> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte >> <matthieuvanhou...@gmail.com <mailto:matthie

Re: [Freesurfer] Longitudinal stream : LME and limits of model

the ones that I will include in the model (three time points / subject ; if existing 6 time points for any subject ?) Best regards, Matthieu > > Best, Martin > >> On Nov 21, 2016, at 7:07 PM, Matthieu Vanhoutte <matthieuvanhou...@gmail.com >> <mailto:matthieuvanhou

[Freesurfer] Longitudinal stream : LME and limits of model

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would

Re: [Freesurfer] Longitudinal surface analysis of PET data

ansforms from base to each time point in the long > mri/transforms directory and probably also in the base/mri/transforms dir. > > Best, Martin > > On Nov 14, 2016, at 5:49 PM, Matthieu Vanhoutte < > matthieuvanhou...@gmail.com> wrote: > > Thank you !

Re: [Freesurfer] Longitudinal surface analysis of PET data

Thank you ! Best regards, Matthieu 2016-11-14 17:48 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Rigid. > > > On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote: > > Still using rigid-body registration on --long subject directory ? > > > > Or

Re: [Freesurfer] Longitudinal surface analysis of PET data

> > On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > > Dear Freesurfer's experts, > > > > I come back to you concerning questions of registrations. > > > > Since during the longitudinal process each --long subject directory > > has been registered o

Re: [Freesurfer] Longitudinal surface analysis of PET data

23:05 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Yes > > > On 09/30/2016 05:05 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Does the surface of the closest MRI time point mean the surface of the > > -long subject time poi

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Is it better to compute mean to weight by number of vertices or surface area ? Best, Matthieu Le 11 nov. 2016 11:33 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> a écrit : > Vertices do not have equal areas and are not equally spaced > > > On 11/11/2016 05:11

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

it on fsaverage, then mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.area.sum --accumulate On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote: > > Dear Douglas, > > Yes I would like to in order to compu

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

with mri_segstats ? Best regards, Matthieu Le 11 nov. 2016 9:21 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> a écrit : > NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you > want area? > > > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote: > &

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

7.6819 1.4396 4.4862 10.9042 6.4180 As my inputs are all surface data could I consider that NVoxels is equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ? Best regards, Matthieu > Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte <matthieuvanhou...@gma

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

9637 > > > On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote: > > Dear Freesurfer's experts, > > > > Could anyone please explain me the difference I got with command line > > in below mail ? > > > > Best regards, > > Matthieu > > > > 2016-08-

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Freesurfer's experts, Could anyone please explain me the difference I got with command line in below mail ? Best regards, Matthieu 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > Dear experts, > > I am in trouble with two ways of computing

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

d of 6 to account for the scaling (voxel size error). > But it is *much* better to get the voxel sizes right and use 6 dof > > > On 10/06/2016 02:50 PM, Matthieu Vanhoutte wrote: > > > > Hi Douglas, > > > > Dis you have time to take a look at ? > > >

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Hi Douglas, Dis you have time to take a look at ? Best regards, Matthieu Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte" <matthieuvanhou...@gmail.com> a écrit : > Hi Douglas, > > I have just sent it to you on Filedrop. > > Best regards, > Matthieu > > 2016

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Hi Douglas, I have just sent it to you on Filedrop. Best regards, Matthieu 2016-10-03 17:45 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to > me on our filedrop? > > On 10/3/16 6:55 AM, Matthi

Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Pet2T1.BS7.register.dof6.mri_coreg.lta --s 207118_M0_2014-01-29 --surfs * *mri_coreg done* Best regards, Matthieu 2016-09-30 21:07 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Can you send the mri_coreg terminal output? > > > On 09/29/2016 11:19 AM, Matthi

Re: [Freesurfer] Longitudinal surface analysis of PET data

.edu> a écrit : > There is no such long process for PET. The idea is that you process the > MRI in a longitudinal way, then sample the PET data onto the surface of > the closest MRI time point. Then proceed in a way similar to the > thickness analysis > > > On 09/29/2016 11:08 A

[Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

Dear Freesurfer's experts, I would like to register PET image onto T1 anatomical. I used bbregister with the following command and it failed : *bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out

Re: [Freesurfer] Longitudinal surface analysis of PET data

than cortical thickness from cross-sectional to -long subject directories ? If this is the case, which commands should I use to mimic cortical thickness longitudinal data ? Many thanks in advance for helping ! Best regards, Matthieu 2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte <matthieuvan

Re: [Freesurfer] Longitudinal surface analysis of PET data

olds you PET information. From that point > on everything should be identical to the thickness analysis. > > So this is really more a question how to get your PET data sampled onto the > surface. If no one else replies, write that into the subject line and repost. > > Best, Marti

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Hello FS's experts, Would anyone have an advice for my problem ? Best regards, Matthieu 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte <matthieuvanhou...@gmail.com>: > Dear experts, > > I am in trouble with two ways of computing mean intensity with > mri_segstats. >

[Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which

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