Yes, that worked Thank you.
> Have you tried rebooting your computer?
>
> Best,
> Ruopeng
>
>> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>
>> Hello FS Community,
>> Lately, whenever I am trying to use freeview I get the following error
>> message:
>>
>> freeview.bin: err
Hello FS Community,
Lately, whenever I am trying to use freeview I get the following error
message:
freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
cannot open shared object file: No such file or directory
Exit 127
The error started showing up after the cluster went down
I'm actually curious about this as well!
Best,
Panos
> Hi Doug, still wondering about this - thanks!
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara
> Johanna [smakar...@mgh.harvard.
Sorry for the follow up email, but I realized my mistake. When running the
mri_robust_register command even though I used the lta flag for the output
register file, I gave the extension .dat to the file. It seems like this
is what caused the problem.
Panos
> Dear FS community,
>
> I used mri_rob
Dear FS community,
I used mri_robust_register to register a volume to the fsaverage space,
and then tried to use the resulting .lta file to register another vol on
the same space as the original volume, to fsaverage, using mri_vol2vol.
The structure of the command I used is:
mri_vol2vol --mov --t
Hi Doug,
Thanks for your response!
Panos
> I would recon the mni152 (or whatever space the AAL atlas is in), map
> the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to
> transfer them to the individual.
>
> On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS commun
Hi FS community,
I have recon-ed a set of subjects and I was interested in also obtaining
structural info (cortical thickness, gray matter volume, surface area
etc.) based on a different atlas than the ones FS is using, and in
particular the AAL atlas.
I was wondering whether my approach would be
Hi Bruce and Doug,
Both methods sound great. Thank you both for your help!
Best,
Panos
> I don't think there is a single command line to do it, but if you can
> get the centroid voxel from somewhere else (eg, fsl), then you can run
> mri_volsynth --template template.nii.gz --pdf delta -delta-crs
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file
of just the centroid of a binary volume (represented maybe as a dot of
1x1x1 mm^3 voxel size).
I know how to find the coordinates of the centroid (through either the
fslstats command or MATLAB), but I didn
Dear FS Community,
I was wondering whether there is a way to create a binary volumetric file
of just the centroid of a binary volume (represented maybe as a dot of
1x1x1 mm^3 voxel size).
I know how to find the coordinates of the centroid (through either the
fslstats command or MATLAB), but I didn
Thanks a lot Doug!
Additionally, I've been trying to calculate the curvature of an ROI
extracted from a CT scan. Is there a way to do that in Freesurfer even
though this ROI is not part of an MRI? (I was playing with
mris_anatomical_stats and mris_curvature_stats but have been unsuccessful
so far s
Hi FS experts,
I was wondering whether there is a tool to measure the kurtosis and
skewness of an ROI. (For instance would the mri_kurtosis.m script under
the FS home directory be the best option for the measurement of kurtosis?)
Thanks in advance,
Panos
__
Hello,
I am interested in performing some statistical analysis in the
Supplementary motor area, but I think that none of the current Freesurfer
atlases have it defined as an ROI (for instance in the parcellation of the
cortex).
Therefore, I was wondering whether there is a way to come up with an R
Hi Doug,
I see, making wm masks and converting them to mni space sounds like a
great idea for what I had in mind. Thanks for your help!
Best,
Panos
>
> We are not properly set up for doing VBM. I suppose you could make
> binary WM masks and map them into mni305 space or CVS space, but we
> don't
Hi Doug,
Yes, doing a VBM analysis would be precisely what I had in mind.
Thanks,
Panos
>
> I'm not sure what you mean. Do you want to do something like a VBM
> analysis on WM?
> doug
>
> On 11/13/2014 04:31 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Experts,
>>
>> I am interested in doing
Hi FS Experts,
I am interested in doing a group analysis between different cohorts using
the white matter volume as the variable of interest. Would the best way to
do that be to follow the group analysis pipeline described in the wiki for
cortical thickness (but replace the --meas thickness with -
Hi Marie,
Thank you for your reply. I wanted to compare the LGI and Surface Area
between two cohorts, from which one has a significantly higher
intracranial volume than the other. I was wondering about the correction
because the results, especially in the case of SA, are the opposite before
and af
Hi FS Community,
I was wondering whether LGI and Surface Area need to be corrected for
total Intracranial Volume.
Thanks in advance,
Panos
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I see, thanks!
> 1. No, just add up all the ventricle measures.
> 2. I think FSL might do this, but you would probably have to mask out the
> ventricles as I doubt they label sulcal csf separately
>
>
> On Tue, 17 Jun 2014,
> pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Thanks for your
Hi Bruce,
Thanks for your reply! I had a couple follow up questions:
1) In order to calculate the total ventricular CSF, should I add the CSF
volume reported in the aseg.stats file to the other ventricular volumes or
no?
2) Would there be a way to segment the sulcal CSF based on the T2 image?
T
Hi FS community,
I was wondering whether there is a way to calculate accurately the CSF
volume with FreeSurfer (I have both T1 and T2 images). Should I just add
the ventricular structures and the CSF volume reported in aseg.stats or is
there another way to account for the sulcal CSF based on the T
Hi Bruce,
I see. Thanks for letting me know, I'll definitely check it out!
Best,
Panos
> Hi Panos
>
> that binary is as old as the hills and there are way, way newer and
> better things to use (you might check out RvoxM)
>
> cheers
> Bruce
> On Thu, 22 May 2014,
> pfot...@nmr.mgh.harvard.edu wro
Hi Bruce,
I had a few questions concerning the mris_classify_thickness algorithm
that you wrote:
1) Are there any other options (i.e. other flags) that can be specified in
the
mris_classify_thickness -o [options]
... :
...
commandline? Because in the description of th
Hi Bruce,
Thanks again for your help so far. I had a few follow up questions:
1) As far as mapping the average thickness to fsaverage coords, when I was
constructing the average thickness map I used mris_preproc with --target
fsaverage (and then mri_concat), so it's already in fsaverage coordinat
Hi Bruce,
I was having issues with the part after that, that is how to calculate the
average thickness of those bins, after I create them. Thanks again
Best,
Panos
> Hi Panos
>
> no, mris_anatomical_stats won't do it. I would map the average thickness
> to fsaverage coords, then load that into ma
Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting
bins will be in the fsaverage space, and hence I wouldn't be able to use
mris_anatomical_stats to calculate the average thickness of the bins,
since the fsaverage "subject" does not have a wm.mgz file. Did you hav
Hi Bruce,
I see, that's really helpful, thank you!
Best,
Panos
> Hi Panos
>
> I would make an average thickness map in fsaverage space, then in matlab
> divvy up the a-p direction into bins (say 100 of them) and compute the
> average in each bin based on the a/p coordinate
>
> cheers
> Bruce
>
Hi Bruce,
Just to clarify, when you say "average the thickness along each A/P
coordinate" do you mean by looking up at the average cortical thickness of
each parcellation and then calculating their average from P->A, or is
there another way to find the average thickness of each slice and then see
Hi Bruce,
Thank you for your reply. I was interested in looking how the thickness
changes from the posterior to the anterior side of the brain and vice
versa (the thickness gradient).
Thank you again for your time!
Panos
> Hi Panos
>
> it would certainly be possible to make that measurement, bu
Hi FS experts,
I was wondering whether it would be possible to measure the average
cortical thickness at a specific slice (either axial, coronal, or
sagittal). I read in Bruce's paper: "Measuring the thickness of the human
cerebral cortex from magnetic resonance images" that "Measuring the
thickne
Hi Doug,
That sounds great! I'll go ahead and do that. I would just be interested
in coming up with the binary maps of the lobes, not their associated
stats. Should I still go ahead and use mri_segstats or should I use
mri_binarize with the --match flag and the new color map instead?
Thanks for al
Hi Doug,
Thanks for your help, the mri_aparc2aseg command worked fine. In addition,
is there a way to get a binary volume for each of the lobes based on the
result of the mri_aparc2aseg command?
In other parcellation volumes, I would use mri_binarize and the
FreeSurferColorLUT.txt table but here I
Hi FS Community,
I created a lobes annotation file with the --lobesStrict flag of the
mri_annotation2label and then converted it to a volume with the
mri_label2vol command and the --annot flag. However, the resulting volume
is just overlapping on top of the white surface, and not on the whole
cort
Hi Bruce,
That's actually great, thanks for your help!
Best,
Panos
> Hi Panos
>
> the first two are basic differential geometric measures (H and K are the
> typical symbols for them). The second two come from a David Van Essen
> paper
> I think in the late 90s. Sorry, I don't remember the exact
Hi FS Comminity,
I was wondering whether there is a reference that gives the exact
definition of the measures reported in the *h.aparc.stats file (i.e. for
the measures Integrated Rectified Mean Curvature, Integrated Rectified
Gaussian Curvature, Folding Index and Intrinsic Curvature Index).
Than
Hi Bruce,
Yes, that's exactly what I needed, thanks a lot!
Best,
Panos
> Hi Panos
>
> so you want an intensity volume that is zero everywhere except in a
> label? If so, try mri_mask
>
> cheers
> Bruce
>
> On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was w
Hi FS experts,
I was wondering what the best way to extract an ROI from an anatomical
volume would be. For instance, I would like to create a volume of only the
wm-lh-precentral based on the orig.mgz volume and on the segmentation map
wmparc.mgz. I know that something similar can be done with the
>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is
Hi Doug,
Thanks again for your help. I had two questions that came up from doing
some preliminary analysis with the mri_segstats:
1) When running the mri_segstats command with --seg
aparc+aseg_nocortex.mgz (which is the result of the matlab code you
provided below) and with --seg wmparc.mgz, even
That is great,
Thanks a lot, Doug!
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I m
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume in
the --s
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or is
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include the
intensity of the skull, just everything inside, right?
2) Just to be clear on the purpose of including the segmentations in the
command line: The segmentations only specify
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
2) In case I would like to measure the mean intensity of the orig file as
outlined in the second example in
https://surfer.nmr.mgh.harvard.
Hi Martin,
That sounds great. Thanks for your time!
Panos
> Hi Panos
> Yes, except you would not pass the -all flag as you don't want to rerun
> everything:
>
> recon-all -base -tp -tp ... -tp
> -autorecon2-cp -autorecon3
>
> Best, Martin
>
> On 04/01/2014 01:41 PM, pfot...@nmr.mgh.harvard.
Hi Martin,
Thanks for your reply! Yes, that definitely makes sense. I had an
additional probably elementary question: I tried to reconstruct the base
after I added some control points to it, using the command
recon-all -autorecon2-cp -autorecon3 -subjid
but the following error pops up:
ERROR: I
Hi FS community,
I am using FS 5.3 to do a longitudinal analysis on some data of mine. I
have manually edited some of the reconstructed scans (i.e. addition of
control points and white voxels) where the reconstruction was not as
precise:
1) Is the base template created from the recon-all -base co
Hi Doug,
Thanks for your reply. Just to be clear, I need to ask some trivial
questions:
1) I need to do that subtraction in the fsgd file right? (In which case
there will be negative numbers as well)
2) I ran the analysis and the resulting significant clusters when looking
at the results of [1 -
Hi Doug,
Thanks for your reply. Yes there were areas of significant difference
reported in the age slopes maps, after the mri_glmfit command was run.
However, I haven't checked to see yet whether there are surviving clusters
after correction for multiple comparisons. I see, yes that definitely
mak
Hi Doug,
I ran a group analysis comparing a trait between two groups (Diseased vs
Controls) with one continuous variable (age), with the following design
matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map and
the descriptor file, the age slope of the trait in Controls was posit
I see. Thank you
> no, that is only for plotting
>
> On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I was wondering about something. If I have an fsgd file that has no
>> variable set (just the 2 groups: Diseased and Control) do I need to
>> include the DefaultVariabl
Hi Doug,
I was wondering about something. If I have an fsgd file that has no
variable set (just the 2 groups: Diseased and Control) do I need to
include the DefaultVariable line at the end of the file?
Thanks,
Panos
> That's great. Thanks a lot for your help, Doug!
>
>
>>
>> Those are the same t
That's great. Thanks a lot for your help, Doug!
>
> Those are the same things. The way you control for age is to compute a
> value for both groups at the same age (eg, age=0). If you demean the
> age, then the difference will be at age=meanage. With DOSS, the
> difference is always the same regar
Hi Doug,
Thank you for your response.
Concerning scenario 2, I believe I have some hard time understanding the
term intercept. If I'm not mistaken the intercept represents the cortical
thickness at "age 0." The resulting clusters by using a design matrix of
[1 -1 0 0] will give me the areas where
Hi FS community,
I had a few questions regarding my understanding of the group analysis in FS:
1) If I use an fsgd file with Two Groups (One Factor/Two Levels), No
Covariates, and my contrast matrix is [1 -1], do the resulting clusters
(if any) show the regional significant differences between th
I see. Thanks for your input!
Panos
>
> This kind of thing can happen, especially when there is not much
> activity in the map
> doug
>
> On 02/11/2014 12:02 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug and Martin,
>>
>> Thanks both for your replies!
>>
>> Doug, I would normally set the FDR t
Hi Doug and Martin,
Thanks both for your replies!
Doug, I would normally set the FDR to something close to .05 but when this
value didn't give me any significant clusters for my analysis, I was
trying to find which value was the min one that gave significant clusters
just out of curiosity, and th
Hi FS community,
I was wondering if anyone had a chance to give this a look.
Thanks in advance,
Panos
> Hi FS community,
>
> I am doing a cortical thickness comparison between a diseased and a
> healthy group. After running the mri_glmfit command for both hemispheres,
> I project the uncorrecte
Hi FS community,
After I open QDEC, when I try to load my qdec data table, QDEC crashes for
some reason. The error message that comes out at the terminal is:
Returned Error on line 1:
missing close-brace
Stack trace:
missing close-brace
while executing
".vtkKWLoadSaveDialog5.vtkKWFileBrowserW
Hi FS community,
I am doing a cortical thickness comparison between a diseased and a
healthy group. After running the mri_glmfit command for both hemispheres,
I project the uncorrected significance map and there are a number of
significant clusters showing (if you consider the p value to be at mos
Great, thanks Bruce!
Panos
> yes, they should be
> On Tue, 3 Dec 2013, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Yes, I have already resampled my images into 1mm isometric voxel size,
>> so
>> all of the three reported coordinates must be in mm right?
>>
>> Thanks,
>> Panos
>>
>>> t
Hi Bruce,
Yes, I have already resampled my images into 1mm isometric voxel size, so
all of the three reported coordinates must be in mm right?
Thanks,
Panos
> the RAS and TkRegRAS are mm, the voxel coords are not (unless your
> acquisition is 1mm isotropic)
>
> cheers
> Bruce
>
>
> On Tue, 3 Dec
Hi FS experts,
When I open a file with freeview, are the coordinates reported in the
third row under Cursor (right under RAS and TkReg RAS) in mm?
Thank you for your time,
Panos
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Great, thanks Doug!
Panos
>
> yes
>
>
> On 11/12/2013 03:21 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks for your response. In addition, as it it mentioned in the wiki
>> page
>> the total white matter volume is volume inside the white surface minus
>> anything that is not WM.
Hi Doug,
Thanks for your response. In addition, as it it mentioned in the wiki page
the total white matter volume is volume inside the white surface minus
anything that is not WM. Would it be correct to say that even though the
total white matter volume calculation is based on a surface-based volu
Hi,
I am using FS v5.3 and I had two questions regarding the calculation of
cortical thickness in the stats files:
1) Is the average cortical thickness of each structure (i.e. precuneus)
calculated by averaging the cortical thickness values of each location in
that structure?
2) Is the mean thic
Hi FS Community,
I have a binary mask and have used the mri_volcluster command to come up
with different clusters and their volumes based on that binary mask.
However, I was wondering if it would be possible to come up with the sum
of the sizes (in mm3) of all the different clusters that come out
Hi FS Community,
I was wondering whether there is a way to get a binary mask of the pons.
Thanks in advance,
Panos
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The information
I see, thanks Doug!
> It is --sum, not --sumfile
> doug
>
>
> On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Community,
>>
>> I am using the mri_volcluster command but for some reason the --sumfile
>> shows up as an unknown flag. Is there another way to get a summary text
>> f
Hi FS Community,
I was wondering whether there is a way to convert a FLOAT type niftii file
to an INT type niftii file.
Thanks in advance!
Best,
Panos
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Thanks Bruce!
Panos
> Hi Panos
>
> that means that you reran one of the surfaces but not the other. Try
> running recon-all -make all, which should check to see if the
> surfaces/volumes are up-to-date and rebuild them if needed. Note that
> having an euler number of 2 doesn't mean the surfaces m
Hi FS Community,
I have been using control points and adding wm voxels in the wm.mgz volume
of a subject, in order to fix the reconstruction, and after doing so for a
number of times, when I tried to run the command:
tkmedit brainmask.mgz -aux wm.mgz -surfs
the following message popped up:
Rea
Hi FS Community,
I am using the mri_volcluster command but for some reason the --sumfile
shows up as an unknown flag. Is there another way to get a summary text
file?
(I am using FS 5.3 stable.)
Thank you for your time!
Best,
Panos
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echo
limit >>
Hi Doug,
The same error message comes up.
Panos
> try this instead
>
> recon-all -all -subjid CAA_022_struc
>
> On 08/27/2013 11:23 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS Commuity,
>>
>> I am using the stable version 5.3 of FS to recon-all a subject of mine,
>> but the job is aborted an
1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
User: pfotiad Machine: eesmith Platform: Linux PlatformVersion:
2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
Hi FS Community,
Is there a way to create a binary mask of everything that is inside the
cortical ribbon of a subject (including the cortical ribbon)?
I ran:
mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me
a binary mask of the cerebral cortex, but I was wondering whether
I see, thanks Bruce!
> Hi Panos,
>
> not unless you want to restrict the registration to be rigid (6 dofs)
>
> cheers
> Bruce
> On
> Mon,
> 5 Aug 2013, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS Community,
>>
>> Is there a way to control for the size and shape of a ROI when applying
>> co-regis
Hi FS Community,
Is there a way to control for the size and shape of a ROI when applying
co-registration? For instance, I drew a ROI in a scan through freesurfer,
and then when I coregistered that ROI to another scan, the resulting ROI
had a different shape and number of voxels compared to the ori
Hi Bruce,
I'm sorry, I didn't phrase the question correctly. I do know why the
orig.mgz comes out like that, however, I don't now why does the inflated
surface in tksurfer look as if a chunk is missing out of it.
Thanks again,
Panos
> Hi Panos,
>
> you probably want to get a neuroradiologist to
Hi,
I ran tksurfer (with the inflated surface option) on a couple of my
subjects that had a major deformation in their orig.mgz file and the
inflated surface of tksurfer looked as if a chunk was missing off of it at
the position where the deformation is located. Is that normal?
I have attached tw
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