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
@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
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
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
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
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
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.
>
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
>>
>>
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
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
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
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
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
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
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
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
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
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,
>
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
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
;
>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
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
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
>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
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:
>>
>>&
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
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
___
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
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
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
__
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] 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
@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
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
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
: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
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
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
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
: 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
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
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
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
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
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
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,
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
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:
>
>
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
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
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
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
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
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.
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<
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
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:
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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,
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
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
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
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
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
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
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
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
-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
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
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
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
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
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