Hello,
This is regarding the registration of functional data to freesurfer
parcellations
(http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace).
The rsfMRI is sampled at 2x2x2.
After running reg-feat2anat and aseg2feat
>> a = MRIread('aparc+aseg'); %Original aparc+aseg ou
On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:
Hi, This is a new issue as it used to run well before.. I run recon-all ... ...
-autorecon1 - force and it completes without error but I don't have all the
files..
Attached is a screenshot. On the right is the output from a file that w
uis
>
> On Tue, 7 May 2013, Sudhin A. Shah wrote:
>
>> On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:
>>
>> Hi, This is a new issue as it used to run well before.. I run
>> recon-all ... ... -autorecon1 - force and it completes without
>>
Louis Nicholas Vinke
[vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 07, 2013 12:05 PM
To: Sudhin A. Shah
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all completes without all the info..
Yes, the -all flag will run autorecon1, autorecon2, and autorecon3.
recon-all -all -i -s
Hi,
I got the following error:
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
vertex 88778 has 0 face
No such file or directory
Thanks,
S
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Freesurfer maili
v5.0.0
On May 16, 2013, at 2:18 PM, Bruce Fischl wrote:
> Hi Sudhin
>
> what FS version are you running?
> Bruce
>
>
> On Thu, 16 May 2013, Sudhin A. Shah wrote:
>
>> Hi,
>>
>> I got the following error:
>>
>> CORRECTING DEFEC
1) BEST FITNESS (M) is 984.24263
mri =0.000 curv = 4.318 unmri = -1001.515
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
63 patches have been generated - 38 self-intersected
max face = 36973(40653) - loop = 46 (73) - ntries
1) BEST FITNESS (M) is 984.24263
mri =0.000 curv = 4.318 unmri = -1001.515
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
63 patches have been generated - 38 self-intersected
max face = 36973(40653) - loop = 46 (73) - ntrie
BEST FITNESS (M) is 984.24263
mri =0.000 curv = 4.318 unmri = -1001.515
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )
63 patches have been generated - 38 self-intersected
max face = 36973(40653) - loop = 46 (73) - ntries =
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
vertex 88778 has 0 face
No such file or directory
Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar
5 19:39:49 UTC 2012 x86_64
===
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if an
CORRECTING DEFECT 1 (vertices=33, convex hull=57)
After retessellation of defect 1, euler #=-41 (88676,260208,171491) :
difference with theory (-61) = -20
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal vector of length zero at vertex 88778 with 0 faces
v
Hi! Can you please send this to me?
On May 28, 2013, at 4:24 PM, Bruce Fischl wrote:
> the new topo fixer will correct this problem
> Bruce
> On Tue, 28 May 2013, Sudhin A. Shah wrote:
>
>> BEST FITNESS (M) is 984.24263
>> mri =0.000 curv = 4.318 unmri = -
On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:
CORRECTING DEFECT 1 (vertices=33, convex hull=57)
After retessellation of defect 1, euler #=-41 (88676,260208,171491) :
difference with theory (-61) = -20
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
Hi,
recon-all was successful.
But when I try
reg-feat2anat --feat '/home//func/2_reg' --subject xyz
I get an error with
MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): could not
open file
Loading mov
Projecting LH Surfs
Loading lh.white surf
No such file or directory
Th
Hi
ERROR: MRIthickenThinWMStrands: invalid x,y,z!
Numerical result out of range
Any tips?
S
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The information in this e-mail is int
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat & aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer) against
every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/pr
Hello,
I have been running Freesurfer parcellations on my raw MRI. Is it better to
first reset the origin (Step 5
herehttp://www.mccauslandcenter.sc.edu/CRNL/sw/tutorial/html/eventspm.html)
BEFORE parcellating?
Thanks,
S
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F
fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2
On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
& aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have
Hello,
I am remotely logged in to my Ubuntu system(from Mac). I have previously run
tkregister2 but am now having trouble;
Opening window subj
Window type not found
register: tkoinitwindow(name) failed.
Is there a solution to this?
Thanks,
S
___
Fre
On Feb 21, 2013, at 2:16 PM, Sudhin A. Shah wrote:
> Hello,
>
> I am remotely logged in to my Ubuntu system(from Mac). I have previously run
> tkregister2 but am now having trouble;
>
> Opening window subj
> Window type not found
> register: tkoinitwindow(name)
fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2
Hello,
I manually checked the registration of my free surfer parcellations to the
rsfMRI data after reg-feat2anat and aseg2feat.
Problem is that I had to scale (stretch) the functional to make a good fit in
several cases. Is this recommended? How can I avoid this?
Thanks,
S
___
On Feb 22, 2013, at 5:14 PM, Sudhin A. Shah wrote:
> Hello,
>
> I manually checked the registration of my free surfer parcellations to the
> rsfMRI data after reg-feat2anat and aseg2feat.
>
> Problem is that I had to scale (stretch) the functional to make a good fit in
&
Also, if Analyze
> formatted files were used in any step of the workflow, there is a good
> chance that left and right were reversed (although that would not entail
> scaling changes to an attempt to correct).
>
> Nick
>
>>
>> On Feb 22, 2013, at 5:14 PM, Sudhin A.
...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 11:39 AM
To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration & segmentation with FSL -
obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
somethin
Sorry - this doesn't look bad. Still I cannot extract values for the ROI label
2013..
On Feb 25, 2013, at 12:43 PM, "Douglas N Greve"
wrote:
>
> It does not look bad to me. Why do you think it looks wrong?
>
>
> On 02/25/2013 12:29 PM, Sudhin A. Shah wrote
Here is the last subject - coronal view.. This is where I started
scaling/stretching :(
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah
[sut2...@med.cornell.edu]
Sent: Monday, February 25
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 3:28 PM
To: Sudhin A. Shah
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration & segmentation with FSL -
obtaining correlation matrix..
It
Hello,
Is there a lookup table I can use to convert free surfer labels to lobes?
Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I
have 86 labels and want an easy way to differentiate them into the
corresponding lobes.
Thanks,
S
__
Also, is there a way to associate these labels with motor/auditory/visual
cortices? Or do I have to use the specific parcellations?
On Feb 28, 2013, at 9:25 AM, "Sudhin A. Shah" wrote:
> Hello,
>
> Is there a lookup table I can use to convert free surfer labels to lob
;, you would
>
> $>mri_annotation2label --subject sub1 --hemi lh --lobesStrict
> lh.lobesStrict.annot
> $>mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict
> --outdir sub1/label
>
> HTH
> -=R
>
>
> On Thu Feb 28 09:24:58 2013, Sudhin A. Shah
;, you would
>
> $>mri_annotation2label --subject sub1 --hemi lh --lobesStrict
> lh.lobesStrict.annot
> $>mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict
> --outdir sub1/label
>
> HTH
> -=R
>
>
> On Thu Feb 28 09:24:58 2013, Sudhin A. Shah
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote:
> It looks like you might be running a too-old version of
> mri_annotation2label. What FS build/version are you running?
>
>
> On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wro
Hello,
Is there a link to the
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011?
Its not apparent on the page and the link doesn't seem to be working..
Thanks,
S
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Hello,
I am a beginner so please bear with me. I want to obtain binary masks for every
region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not
sure what the labels would be.
I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do
not know which labels t
)Cortex: 1002- 1034, 2002- 2034
I am asking if there is an established list of whole brain parcellations before
I rely on label names to choose the ROIS
On 06/13/11, Douglas N Greve wrote:
>
> Anything that is non-0 will cover the whole brain.
> doug
>
> Sudhin A. Shah wrote:
&g
Hi,
Is there anyway to know all the label #s that are in aparc+aseg-inhighres.mgz.
Thank you,
S
On 06/13/11, "Sudhin A. Shah" wrote:
>
>
> Hi Sorry for bothering you again, but I am not sure I understand.
>
> I was running whole brain correlation analysis
Hi,
I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the
default aparc
mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this
works
But how do I specify aparc+aseg-in-highres.mgz
I tried --aparc+aseg-in-highres but it was not recognised..
Than
volume then use mri_cor2label.
> doug
>
> Sudhin A. Shah wrote:
> >Hi,
> >
> >I am trying to use this for the aparc+aseg-in-highres.mgz file instead of
> >the default aparc
> >
> >mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/lab
> fine. For subcortical, you can use what is in
> $FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
> which can be ignored.
>
> doug
>
> Sudhin A. Shah wrote:
> > Hi,
> >
> > Is there anyway to know all the label #s that are in
> &g
Hi,
Can somebody please help me figure out how to correct this issue?
1 subject - 2 functional scans
1) run recon-all on subject anatomical.
2) process functional series (using AFNI/FSL) - each individually.
3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html)
@ROI_Co
On Jun 17, 2011, at 6:25 PM, "Sudhin A. Shah" wrote:
> Hi,
>
> Can somebody please help me figure out how to correct this issue?
>
> 1 subject - 2 functional scans
>
> 1) run recon-all on subject anatomical.
>
> 2) process functional series (using
functional space?
Thanks,
S
On 06/21/11, Douglas N Greve wrote:
>
> Hi Sudhin, this looks like an AFNI question. Have you tried posting to
> the AFNI list?
> doug
>
> Sudhin A. Shah wrote:
> >
> >
> >
> >
> > On Jun 17, 2011, at 6:25 PM, &qu
Got it :
aseg2feat --feat featdir --seg aparc+aseg
On 06/22/11, "Sudhin A. Shah" wrote:
>
>
> Hi,
>
> So I think I found the solution -
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical)
>
> reg-feat2anat
> aseg2feat
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