[Freesurfer] MGH/Harvard: Postdoc in brainstem diffusion and PET imaging in aging/dementia position

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical Schoo

[Freesurfer] MGH/Harvard: Postdoc in brainstem diffusion and PET imaging in aging/dementia

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical Schoo

[Freesurfer] MGH/Harvard: Postdoc position in 7T brainstem fMRI and non-invasive vagus nerve stimulation

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical Schoo

[Freesurfer] MGH/Harvard: Brainstem PET and DTI postdoc position

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School

[Freesurfer] Postdoctoral fellowship at MGH in Brainstem PET and DTI

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School

[Freesurfer] Postdoctoral position at Massachusetts General Hospital / Harvard Medical School

External Email - Use Caution Postdoc Position in the Department of Radiology, Massachusetts General Hospital / Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School

[Freesurfer] Postdoc position at MGH/Harvard

External Email - Use Caution Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts,

Re: [Freesurfer] Smooth surface overlay

ore your analysis On 8/9/2019 2:46 PM, Jacobs, H (NP) wrote: External Email - Use Caution Hi all, I created an overlay surface map of my analyses (with pvalues in log10) using R. Now I would like to smooth this map to extract clusters and I tried to use: mri_surf2surf --prune --s fsa

[Freesurfer] Smooth surface overlay

External Email - Use Caution Hi all, I created an overlay surface map of my analyses (with pvalues in log10) using R. Now I would like to smooth this map to extract clusters and I tried to use: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 3 --sval lh_analyses.mgh --tval

[Freesurfer] Postdoc position at MGH/Harvard Medical School

External Email - Use Caution << I will attend the AAIC2019 conference in Los Angeles. Send me an email if you like to meet and discuss this position >> Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the

[Freesurfer] Cluster-wise multiple comparison correction

External Email - Use Caution Hi all! I would love to use the cluster-wise multiple comparison correction method in FS 6.0 for our PET data (in fsaverage space and smoothed). However, since we have some complex models, I did the statistical analyses in R and then converted this t

[Freesurfer] Research fellow / postdoc position in 7T (f)MRI brainstem imaging

External Email - Use Caution Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusett

[Freesurfer] cannot find subject

External Email - Use Caution Dear FreeSurfer, I just installed FreeSurfer6 on my computer and tried to run a subject (license file is set). I sourced freesurfer and have set the subjects_dir. However, when running the recon-all, I get the following error : ERROR: cannot find /A

[Freesurfer] curvature

Dear FreeSurfer, In the stats files (e.g aparc) there are also statistics for the "integrated rectified mean curvature", "integrated rectified gaussian curvature", "folding index" and "intrinsic curvature index". To what kind of properties do these measures refer and which one is advised to be

[Freesurfer] mammillary bodies

Hello all! I am looking for a automatic or semi-automatic segmentation tool for the mammillary bodies. Any suggestions? Many thanks! Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] methodological questions for manuscript

Great! Thank you Bruce, Heidi On 6/9/17, 9:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >that sounds reasonable to me. > >good luck >Bruce >On Fri, 9 Jun 2017, Jacobs H (NP) wrote: > >> Hi! >> >> For my m

[Freesurfer] methodological questions for manuscript

Hi! For my manuscript, the journal wants me to answer some questions on the methods that I used and I want to make sure I am giving correct information on how FreeSurfer calculates hippocampal volumes. Would it be possible to check my 4 answers and let me know if these are accurate? Question:

Re: [Freesurfer] Tracula: anatomical priors

surfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Jacobs H (NP) [h.jac...@maastrichtuniversity.nl<mailto:h.jac...@maastrichtuniversity.nl>] Sent: Wedne

Re: [Freesurfer] Repost: tracula stats including NAs?

onding p-value accordingly. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Jacobs H (NP) [h.jac...@maastrichtuniversity.nl<

[Freesurfer] Tracula: anatomical priors

Dear FreeSurfers, Where can I find the anatomical ROIs from the aparc/aseg (end and begin points) that are being used to reconstruct the tracts in Tracula? Many thanks Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] Repost: tracula stats including NAs?

Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorte

[Freesurfer] tracula stats

Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines online). In this text file, I saw that on some of these voxels some people have NAs, so their tract is most likely shorter there

Re: [Freesurfer] find surface coordinates in MNI space

se >to MNI152 space). > > > >On 01/27/2017 11:28 AM, Jacobs H (NP) wrote: >> Dear FreeSurfers, >> >> I am trying to locate certain regions from the Desikan atlas on a MNI >> surface (Brainnet-viewer) . >> How can I convert coordinates in surface space

[Freesurfer] find surface coordinates in MNI space

Dear FreeSurfers, I am trying to locate certain regions from the Desikan atlas on a MNI surface (Brainnet-viewer) . How can I convert coordinates in surface space to MNI coordinates and are these the regular coordinates (RAS)? Many thanks. Heidi ___ F

[Freesurfer] Iglesias paper: Hippocampal subfields

Hi! I would like to create a 3D rendering of the hippocampal subfields generated by FreeSurfer (as done in the Iglesias paper). I have tried to do this using Slicer, but the results are not that nice (making a model based on the 1mm mgz file). How were the surfaces in the paper generated? Do you

[Freesurfer] SOLVED: Re: convert FSL atlas label to individual freesurfer T1 space

I figured it out :) From: H Jacobs mailto:h.jac...@maastrichtuniversity.nl>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Saturday, June 4, 2016 at 7:48 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] convert FSL at

[Freesurfer] convert FSL atlas label to individual freesurfer T1 space

Hello! I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following: Flirt -in MNI15_T1_1mm.ni

Re: [Freesurfer] Tracula skip steps

get the tracts in the >first place, you need the images. > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Yes, each nifti contains one volume. I have different nifti’s for the >> different metrics (FA, MD,..) >> Is there a way I can use the trac-all on these

Re: [Freesurfer] Tracula skip steps

only >one volume. Could this be the case? > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 >> gives the same error. Enclosed is the config file. >> Thank you so much >> Heidi >> >>

Re: [Freesurfer] Tracula skip steps

here to find the freesurfer recons of the T1's from >SUBJECTS_DIR (see example config file). Based on your log file, it looks >like you haven't turned off the eddy current compensation, because it's >trying to run it. If you attach your config file, I'll take a look. >

Re: [Freesurfer] Tracula skip steps

hen running everything >without >skipping steps. This will create all the files that are expected to be >there for the registration. > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Dear Anastasia, >> >> Thanks for the feedback. So, does this mean that the

Re: [Freesurfer] Tracula skip steps

on file? Thanks! > >a.y > >On Tue, 31 May 2016, Jacobs H (NP) wrote: > >> Dear FreeSurfers, >> >> The data I have is preprocessed, so I have the all the metrics (FA, MD, >>L1, L2, L3,..) in nifti format. >> On this data I would like to start tracula starti

[Freesurfer] Tracula skip steps

Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in

[Freesurfer] amygdala nuclear subregions

Dear FreeSurfer developers, In the FreeSurferColorLut file I see labels for the subregions of the amygdala. Is it possible to extract the volumes for these regions? And how can I do this? I don't see them in the aseg or aparc stat files. Many thanks! Heidi ___

Re: [Freesurfer] changing the index of labels

This will make the lh labels >different from the rh. You can add a constant to the rh too if you want. > >doug > > >On 10/30/2015 07:12 PM, Jacobs H (NP) wrote: >> Yes, there are different mgz files for left and right (but they have the >> same index numbers and colors

Re: [Freesurfer] changing the index of labels

01:25 PM, Bruce Fischl wrote: >> Hi Heidi >> >> I guess you could do it yourself in matlab using the aseg to figure >> out which hemisphere you are in >> >> cheers >> Bruce >> >> On Fri, 30 Oct 2015, Jacobs H (NP) wrote: >> >>&

[Freesurfer] changing the index of labels

>CA1 has value 206 for left and also for right). >> >>On 10/27/15, 5:01 PM, "Douglas Greve" wrote: >> >>>The color is not important. The question is whether they have a >>>different index. Can you confirm that lh and rh have the same index? >>&g

Re: [Freesurfer] remove label from aseg

I think this one thread might have disappeared (if not, I apologize for my impatience). Heidi On 10/27/15, 5:16 PM, "Jacobs H (NP)" wrote: >I just checked again in freeview and indeed they have the same index (e.g. >CA1 has value 206 for left and also for right). > &g

Re: [Freesurfer] remove label from aseg

rh have the same index? > >On 10/27/15 11:53 AM, Jacobs H (NP) wrote: >> Hi Doug, >> >> Yes, for the aseg they are. But not for the hippocampal subfields: left >> and right have the same color coding. >> I am creating one segmentation, including left and right hi

Re: [Freesurfer] remove label from aseg

; >On 10/24/15 9:29 PM, Jacobs H (NP) wrote: >> Hi. >> >> Just one another related question: now that I was able to combine left >>and >> right hippocampal subfields with the aparc-aseg correctly, I noticed >>that >> the left and right hippocampal subfie

Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg

On 10/25/15, 3:29 AM, "Jacobs H (NP)" wrote: >Hi. > >Just one another related question: now that I was able to combine left and >right hippocampal subfields with the aparc-aseg correctly, I noticed that >the left and right hippocampal subfields have the same color labe

Re: [Freesurfer] remove label from aseg

understand that the left and right subfields (e.g. Left and right CA1) are different areas? Thanks! Heidi On 10/21/15, 11:01 PM, "Jacobs H (NP)" wrote: >Thanks! Works wonderful! >Heidi > >On 10/21/15, 10:50 PM, "Douglas N Greve" >wrote: > >>If you want to re

Re: [Freesurfer] remove label from aseg

Thanks! Works wonderful! Heidi On 10/21/15, 10:50 PM, "Douglas N Greve" wrote: >If you want to remove them, you can use mri_binarize with the --replace >option, replacing them with whatever you want. > >On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >> Hi, >

[Freesurfer] remove label from aseg

Hi, I am trying to generate a segmentation file containing the aseg+aparc but replacing the hippocampus with the hippocampal subfields. With mergeseg I was able to merge the segmentations, but unfortunately parts of the “old” hippocampus (labeled as 17 and 53) are still in there (as the area co

Re: [Freesurfer] warping surface label to volume space

e is an old version that output volume >that is not getting overwritten. Can you name the output file >differently and make sure that it does not exist prior to running the >command? > >On 09/30/2015 04:37 PM, Jacobs H (NP) wrote: >> Hi Doug, >> >> Just as a rem

Re: [Freesurfer] warping surface label to volume space

lt;mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] warping surface label to volume space filedrop2 url at the end of this email On 9/29/15 10:34 AM, Jacobs H (NP) wrote: Sure, where should I upload it to? Thanks! Hei

Re: [Freesurfer] warping surface label to volume space

@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] warping surface label to volume space Can you upload the subject so I can look at it? On 9/29/15 9:05 AM, Jacobs H (NP) wrote: Hi Doug, The label looks actually ok and the surface as well. I attac

[Freesurfer] warping surface label to volume space

Hi, Bringing this to the FS list: I am trying to warp the entorhinal cortex label (ex vivo) to volume space, so that I can see and use the full ROI. Using the command stated below doesn’t seem to work, as it is not in the right location of the subject’s brain. Any thoughts? I used this command

[Freesurfer] PhD-position Research Centre Juelich

With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz Association – is one of the largest interdisciplinary research centres in Europe. Work with us on the grand challenges in the fields of health, energy & environment, and information technology, as well as on the many and

[Freesurfer] PhD-position Research Centre Juelich

With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz Association – is one of the largest interdisciplinary research centres in Europe. Work with us on the grand challenges in the fields of health, energy & environment, and information technology, as well as on the many and

[Freesurfer] 4 groups non-linear effect

Dear FreeSurfer team, We have processed our T1 data of 4 groups of subjects: controls and patients of varying degrees illness. Now we want to perform : - a F-test to compare the 4 groups (we have one covariate that we want to take into account) - a F test to investigate a differential effect o

[Freesurfer] comparing left and right cortical thickness

Dear FreeSurfers, Is it possible to compare left and right cortical thickness patterns, vertex-wise? Thanks Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Divisi

[Freesurfer] DODS slope information

Hi Freesurfers, I just looked at my cortical thickness results, in which I performed an interaction between group (2 groups) and cognition (continuous). I see regions popping up, which is great! Especially since they are related to the task. Now, I made a scatterplot of some of these vertices to

[Freesurfer] complex repeated measure model

Dear FreeSurfers, I am struggling with how to set the fsgd-file and contrast file for a probably complex model. I have two groups: old and young participants. For each participant, I have one T1-weighted image, on which I would like to perform the cortical thickness analyses. This T1 image was

Re: [Freesurfer] matrix ill-conditioned....

Netherlands T +31 43 38 84 090 F +31 43 38 84 092 Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: dinsdag 27 augustus 2013 18:27 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: matrix

Re: [Freesurfer] matrix ill-conditioned....

: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: maandag 26 augustus 2013 23:53 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: matrix ill-conditioned Can you send me the design matrix (Xg.dat) and fsgd file? On 08/26/2013 04:35 PM, Jacobs H (NP) wrote: > Dear D

Re: [Freesurfer] matrix ill-conditioned....

4 092 Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: maandag 26 augustus 2013 21:47 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: matrix ill-conditioned You can try with this version of mri_glmfit which will do the rescaling fo

[Freesurfer] matrix ill-conditioned....

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: vrijdag 23 augustus 2013 17:31 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test The values in the interaction column are probably much larger than the

Re: [Freesurfer] FW: FW: Contrast and F-test

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: vrijdag 23 augustus 2013 17:31 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test The values in the interaction column are probably much larger than the

Re: [Freesurfer] FW: FW: Contrast and F-test

:12 AM, Jacobs H (NP) wrote: > Hi again! > > I am trying to run these contrasts but FreeSurfer tells me that "ERROR: > matrix is ill-conditioned or badly scaled, condno = 101380 > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of

Re: [Freesurfer] FW: FW: Contrast and F-test

On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: > Arrghh, again wrong email, sorry > > Thanks. I think I understand the rational behind it. > Just to be sure, would this be correct: > > For each group separately > 0 0 0 1 0 0 (group - cognition - education - cognition x educat

Re: [Freesurfer] FW: FW: Contrast and F-test

correct doug On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: > Arrghh, again wrong email, sorry > > Thanks. I think I understand the rational behind it. > Just to be sure, would this be correct: > > For each group separately > 0 0 0 1 0 0 (group - cognition - education - cognit

[Freesurfer] FW: FW: Contrast and F-test

@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] FW: Contrast and F-test you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: > Dear D

[Freesurfer] FW: Contrast and F-test

: [Freesurfer] Contrast and F-test If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: > Hi all, > > I my manuscript, I examined the as

[Freesurfer] Contrast and F-test

Hi all, I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). Would this be the corr

[Freesurfer] Postdoc position at the Research Centre Juelich

The Cognitive Neuroscience group of the Research Centre Juelich has an open position for a postdoctoral researcher on mapping an modulation networks in Alzheimer's disease. See enclosed document for more information or contact Dr. Heidi Jacobs: h.jac...@fz-juelich.de Best Heidi __

Re: [Freesurfer] Contrast of three groups

mei 2013 17:30 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Contrast of three groups Hi Heidi, That will test the effect of the continuous variable averaged over the 3 groups. doug On 05/29/2013 10:40 AM, Jacobs H (NP) wrote: > Hi FreeSurfers, > > I have a more st

[Freesurfer] Contrast of three groups

Hi FreeSurfers, I have a more statistical question: I have three groups of subjects and I want to examine the effect of a continuous variable (cognition). Is it possible to examine three groups? Or should I do pairwise comparisons? What would the contrast than look like? Something like this: 0

[Freesurfer] warping results on surface

Hi FreeSurfer! A colleague has retinotopic results that he would like to overlay on the FS surface (most likely fsaverage). The retinotopic data is in 2mm isotropic resolution. What would be the best way to be able to overlay this data correctly? Should he first warp the volume to the volume of f

Re: [Freesurfer] basic comparison

rvard.edu] Verzonden: donderdag 11 oktober 2012 17:57 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] basic comparison can you send the full terminal output? On 10/11/2012 11:56 AM, Jacobs H (NP) wrote: > Hi Doug, > > This is from the log file: > >

Re: [Freesurfer] basic comparison

Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Verzonden: donderdag 11 oktober 2012 17:52 Aan: Jacobs H (NP

Re: [Freesurfer] basic comparison

f not enough DOF. doug On 10/11/2012 08:31 AM, Jacobs H (NP) wrote: > Hi FreeSurfers, > > I am preparing a simple presentation, to show some basic stuff in my lab and > therefore I would like to compare the cortical thickness of two subjects. > Is there a way to do this? For the GLM,

[Freesurfer] basic comparison

Hi FreeSurfers, I am preparing a simple presentation, to show some basic stuff in my lab and therefore I would like to compare the cortical thickness of two subjects. Is there a way to do this? For the GLM, I probably have not enough degrees of freedom? Is there a way that I could subtract the t

Re: [Freesurfer] Repost: fsgd file

cortical variable vs a continuous variable. If you want to look at a scatter plot of your continuous variables, why not just do it in matlab or excel? doug On 07/16/2012 04:47 AM, Jacobs H (NP) wrote: > Dear FreeSurfers, > > I hope you can help me out with a problem in coding my fsgd

[Freesurfer] Repost: fsgd file

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the spatial difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cogni

[Freesurfer] fsgd file

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scor

[Freesurfer] Repost: question regarding my contrast

Dear FreeSurfers, I have been doing some basic cortical thickness analyses, which all went good. Now I want to analyze some additional things, and I want to make sure that my contrast files are ok. Could you help me out or give me advice? So, I have three groups (control - MCI - Alzheimer) and

[Freesurfer] question regarding my contrast

Dear FreeSurfers, I have been doing some basic cortical thickness analyses, which all went good. Now I want to analyze some additional things, and I want to make sure that my contrast files are ok. Could you help me out or give me advice? So, I have three groups (control - MCI - Alzheimer) and

[Freesurfer] visualization after cluster correction

Hi FreeSurfers, This is more a visualization question. I did the cortical thickness analyses on my data and compared my two groups statistically. After that I ran the mri_glmfit-sim to correct for multiple comparisons using the cluster correction. When I visualize the results, each cluster has i

[Freesurfer] question regarding the comparison of two methods: repost

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothe

[Freesurfer] question regarding the comparison of two methods

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothed

[Freesurfer] question regarding the comparison of two methods

Dear FreeSurfers, We are comparing two methods to measure the volume of a subcortical structure (our method and FreeSurfer). We want to compare them spatially, by doing a voxel-based analyses. We thought to isolate the structure from the aseg.mgh as well as our own structure. Then we smoothed b

Re: [Freesurfer] Defining cluster threshold

-Oorspronkelijk bericht- Van: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Verzonden: 06 October 2010 20:40 Aan: Jacobs H (NP) CC: 'freesurfer@nmr.mgh.harvard.edu' Onderwerp: Re: [Freesurfer] Defining cluster threshold Hi Heidi, I'm not sure what you are asking for. Do you want to

[Freesurfer] Defining cluster threshold

Hi FreeSurfers, I have done my DTI analyses (dt_recon with TBSS) and the statistical analyses in FreeSurfer. Now I have defined the clustersize with mri_volcluster, but I find this rather arbitrary. Is there a way to calculate a minimum size cluster threshold (by using for example a Monte Carlo

[Freesurfer] question regarding minimum p-values in cortical thickness

Hi, Last year, I have been working for four months with David Salat and so, I have learnt a lot, including the dt_recon command. >From David, I also learnt to use mri_segstats command in order to get minimum >p-values for each label in my volume. However, now I have performed cortical thickness