[Freesurfer] Problem with preproc-sess per-session and question about registration

[Wiegand, Katrin]

Hi,

I have two short questions concerning motion correction using preproc-sess and 
registration files

1) Running preproc-sess using per-session as e.g. like this
preproc-sess -per-session -fwhm 0 -sliceorder siemens -surface vpID lhrh -s 
vpID -fsd bold -mni305
should result in a "fmc" output stem, doesn't it? This however, this is not the 
the case (I received "fmcpr"), so I'm wondering whether the error occured 
(only) at the labeling stage or whether motion correction was indeed computed 
for each run separately (I also received register files for each run, i.e. in 
each bold/run directory, rather than "global ones" within the bold directory). 
Is this a known issue?

2) Furthermore I'd be very glad if someone could shed some light on the 
registration process (using fslregister-sess) for -per-run mc and the various 
register-files that are produced. In particular,  I do not understand how the 
output of the statistical analysis of the functional data (averaged over all 
runs) is mapped onto the high resolution anatomical data, when every run is 
registered seperately. Which register file is needed in order the visualize the 
results? And what about checking the accuracy of the registration, do I have to 
check this for every run?

I am using freesurfer Version 5.1.0  
(freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) on ubuntu 11.10 (64b).

Thanks a lot in advance,

Katrin


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Re: [Freesurfer] fsaverage error - too many levels of symbolic links

[Gibbard, Clare]

Hi,

Thank you for your suggestions Doug and Dan.  Moving my subjects directory 
outside of the freesurfer tree and deleting the symbolic link and then 
recreating it as per the instructions at www.freesurfer.net/fswiki/FsAverage 
seem to have sorted the problem.

Best wishes,
Clare


From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: 21 February 2012 18:03
To: Gibbard, Clare
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsaverage error - too many levels of symbolic links

Hi Clare, try moving your SUBJECTS_DIR outside of the freesurfer tree.
doug

Gibbard, Clare wrote:
> Hi,
>
> I am running recon-all on several scans, but it is exiting with an
> error.  I think the error is occurring because my symbolic link to
> fsaverage is self-referential.  However, the symbolic link is
> generated automatically during recon-all so I cannot see how to
> correct it.  I have tried deleting the fsaverage from my subjects
> directory and re-running recon-all, but this did not work.
>
> I can see that others have had this error before, but I can't see the
> solution.  Are you able to help?  I have previously run recon-all
> without getting this error.  Thank you.
>
> ls -l /home/clare/freesurfer/freesurfer/subjects/fsaverage gives this:
> lrwxrwxrwx 1 clare clare 52 2012-02-17 08:27
> /home/clare/freesurfer/freesurfer/subjects/fsaverage ->
> /home/clare/freesurfer/freesurfer/subjects/fsaverage
>
> Here is the error:
> #@# BA Labels lh Fri Feb 17 08:27:35 GMT 2012
> INFO: fsaverage subject does not exist in SUBJECTS_DIR
> INFO: Creating symlink to fsaverage subject...
>
>  cd /home/clare/freesurfer/freesurfer/subjects; ln -s
> /home/clare/freesurfer/freesurfer/subjects/fsaverage; cd -
>
>
>  mri_label2label --srcsubject fsaverage --srclabel
> /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label
> --trgsubject subject_001 --trglabel ./lh.BA1.label --hemi lh
> --regmethod surface
>
> Too many levels of symbolic links
> mri_label2label: could not open label file
> /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label
>
> srclabel =
> /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label
> srcsubject = fsaverage
> trgsubject = subject_001
> trglabel = ./lh.BA1.label
> regmethod = surface
>
> srchemi = lh
> trghemi = lh
> trgsurface = white
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR/home/clare/freesurfer/freesurfer/subjects
> FREESURFER_HOME /home/clare/freesurfer/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading
> /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label
> Linux clare-OptiPlex-990 2.6.35-32-generic #64-Ubuntu SMP Tue Jan 3
> 00:47:07 UTC 2012 x86_64 GNU/Linux
>
> recon-all -s subject_001 exited with ERRORS at Fri Feb 17 08:27:35 GMT
> 2012
>
> Best wishes,
> Clare
> 
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Problem with covariates in design for surface based analysis

[MCLAREN, Donald]

Charlotte,

There is no difference, from a statistical perspective, of nuisance
factors and covariates.

The key questions are:
(1) Do any of these covariates have a differential effect on thickness
between groups?
(2) Do you want to compare the actual group means or the
covariate-adjusted group means (e.g. test the means for subjects as if
the subjects all had the same covariate values)?
(3) Do you have enough subjects to add 5 covariates?
(4) Do you have a valid reason for why all the covariates would have
an effect on thickness? One can always add more covariates to reduce
the error, but its not always a good thing to add covariates just to
reduce the error of the model.

On 2/23/12, Charlotte Bernard  wrote:
>
> Dear Freesurfur users,
>
> I have a question about the design for a surface based analysis! I want to
> compare controls and patients. I have 5 covariates. One is a continous
> variable. The others are categorial variables (4 with 2 levels and 1 with 5
> levels). I want to ajust my result with all of thoses variables. I am
> interested in the difference in thickness between patients and controls.
> Is it possible to construct such design?
> Can I put some of my variables in the "nuisance factors" ? I don't really
> understand the difference between "nuisance factor" and covariabes.
> I really hope somebody can help me.
> Thanks for all!
> All the best,
> Charlotte
>   


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=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
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Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.

[Long]

Thank you Allison, however, I checked the website and it is said that
FreeSurfer transform the orig volume to the MNI305 atlas, so the spatial
normalization in FreeSurfer is still done in volume space but not in
surface space, right?

Best,
Xiangyu

On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player <
astev...@nmr.mgh.harvard.edu> wrote:

> Maybe you can apply the transform using mri_convert or mri_vol2vol created
> during autorecon1. Is that what you are looking for?
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
>
>
> On Feb 22, 2012, at 11:26 AM, Long  wrote:
>
> > Dear all,
> >
> > I had EPI images and T1 image and the EPI images are already
> co-registered to T1 image in their native space. I also run 'recon' on T1
> image. I'd like to try surface-based spatial normalization in FreeSurfer,
> so how can I only do the spatial normalization of EPI images in FreeSurfer,
> i.e., transform EPI images from native space to mni152 space, then I could
> have surface-based normalized EPI images.
> >
> > Best,
> > Xiangyu
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] Question regarding sig.mgh

[Antonella Kis]

Dear All,



1)I would like to know what is the best way in catching the uncorrected 
clusters results from the sig.mgh for a structural study:

Should I use the:

 mri_glmfit-sim \
--glmdir lh.GroupAnalysis_Thickness_15.glmdir \
--cache 2 pos \
--cwpvalthresh .99 \
--overwrite


But in this case I am not getting all the clusters regarding their significance 
after correction by multiple comparison? I don't want the clusters from 
multiple comparisons just the uncorrected one.
 I am not sure why when I look to my clusters in QDEC I get a different p value 
for the uncorrected results sig.mgh that the one cached with the --cwpvalthresh 
.999 for example from QDEC for one cluster rostralmiddlefrontal in sig.mgh I 
got p =0.00338 while with the catche option and --cwpvalthresh .999 I got cwp 
0.75890.
I am doing something wrong?



2) If I know the MNI coordinates how I can get the location I mean the 
segmentation or annotation location of my clusters to the nears cortical label?


  

Many thanks.
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Re: [Freesurfer] mri_convert

[Douglas N Greve]

  Hi Jimmy, I think the problem, if you can call it that, is with
  fslview. Below is from our FAQ. See if that makes sense.

doug




  Q. Why would the orientation of my scans look wrong after
  processing my DICOM files with 'mri_convert'?

A: It can be misleading to check orientation using FSLVIEW because it 
orients volumes based on the way they are on disk so you often get 
things looking pretty strange (e.g., upside-down). FSLVIEW does display 
little letters along the side of the image to indicate what it thinks 
the orientation is, so if you stick to those, then you can properly 
judge whether the orientation is correct.





Jimmy Ghaziri wrote:
> Dear FreeSurfer community,
>
> I'm using the mri_label2vol, the output is in .mgz. I then use 
> mri_convert to convert it to .nii.gz.
> When I do so, the output is corrupted (see attached images). Some 
> colleagues told me that it was because my FreeSurfer had a bug so I 
> uninstalled and installed it back again but nothing changed. I then 
> tried to run it on some other colleague's machine and it worked fine 
> (on one subject just to test).
>
> Any ideas what could be the problem ? I tried to flip the image 90 
> degrees but it won't flip, nothing changes.
>
> Here are the commands I'm launching :
>
> mri_label2vol --seg 
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp 
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o 
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz 
> --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
>
> mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
>
>
> The data looks fine when I open it with tkmedit but it's inverted and 
> cut when opened with fslview.
>
> I cannot continue my analyses even if the data looks fine on tkmedit. 
> When I apply a flirt transformation on the data I get the same cut and 
> inverted brain than on fslview (see flirt attached image).
>
> Is it a problem with my FreeSurfer or a command I'm running the wrong 
> way ? Is there another software to convert .mgz to .nii.gz ?
>
>
> Thank you very much !
>
>
> Jimmy
>
> 
>
>
> 
>
>
> 
>
> 
>
> ___
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_convert

[Jimmy Ghaziri]

Yes, since it appears fine when I open it with tkmedit. But once I apply a
flirt transformation I get the same image on tkmedit than the one on
fslview. I tried to flip the image but it won't change anything since the
brain is cut.
Also, I followed the same steps on my colleagues machine and it worked fine
on his...

Thank you

Jimmy

On Fri, Feb 24, 2012 at 14:27, Douglas N Greve wrote:

>
> Hi Jimmy, I think the problem, if you can call it that, is with
> fslview. Below is from our FAQ. See if that makes sense.
>
> doug
>
>
>
>
> Q. Why would the orientation of my scans look wrong after
> processing my DICOM files with 'mri_convert'?
>
> A: It can be misleading to check orientation using FSLVIEW because it
> orients volumes based on the way they are on disk so you often get things
> looking pretty strange (e.g., upside-down). FSLVIEW does display little
> letters along the side of the image to indicate what it thinks the
> orientation is, so if you stick to those, then you can properly judge
> whether the orientation is correct.
>
>
>
>
>
> Jimmy Ghaziri wrote:
>
>> Dear FreeSurfer community,
>>
>> I'm using the mri_label2vol, the output is in .mgz. I then use
>> mri_convert to convert it to .nii.gz.
>> When I do so, the output is corrupted (see attached images). Some
>> colleagues told me that it was because my FreeSurfer had a bug so I
>> uninstalled and installed it back again but nothing changed. I then tried
>> to run it on some other colleague's machine and it worked fine (on one
>> subject just to test).
>>
>> Any ideas what could be the problem ? I tried to flip the image 90
>> degrees but it won't flip, nothing changes.
>>
>> Here are the commands I'm launching :
>>
>> mri_label2vol --seg ~/Documents/freesurfer/**
>> subjects/pre_al_t1/mri/aparc+**aseg.mgz --temp ~/Documents/freesurfer/**
>> subjects/pre_al_t1/mri/rawavg.**mgz --o ~/Documents/freesurfer/**
>> subjects/pre_al_t1/mri/aparc+**aseg_t1ref.mgz --regheader
>> ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg.mgz
>>
>> mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
>>
>>
>> The data looks fine when I open it with tkmedit but it's inverted and cut
>> when opened with fslview.
>>
>> I cannot continue my analyses even if the data looks fine on tkmedit.
>> When I apply a flirt transformation on the data I get the same cut and
>> inverted brain than on fslview (see flirt attached image).
>>
>> Is it a problem with my FreeSurfer or a command I'm running the wrong way
>> ? Is there another software to convert .mgz to .nii.gz ?
>>
>>
>> Thank you very much !
>>
>>
>> Jimmy
>>
>> --**--**
>> 
>>
>>
>> --**--**
>> 
>>
>>
>> --**--**
>> 
>>
>> --**--**
>> 
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] treatment of missing values in mri_glmfit

[Kristine Beate Walhovd]

 Hi,

 we´re running FS 5.1 and have a data set with a lot of missing values. 
 There are different subsets of persons missing different values of 
 interest, and we´re running analyses on concat files. mri_glmfit not 
 qdec). Is there anyway we can run analyses w/ missings in the fsgd file?

 Best,

 Kristine


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[Freesurfer] REPOST: MNI coordinates

[Antonella Kis]

Hi,

I am trying to find a way to get the segmentation/cortical label (to determine 
corresponding brain structures) in MNI space for a cluster for which I know the 
MNI coordinates. How can I do this?


Many thanks.
Antonella___
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Re: [Freesurfer] REPOST: MNI coordinates

[Martijn Steenwijk]

You could register T1.mgz to MNI 1mm, invert the transformation and then map 
the cluster in MNI to Freesurfer space. 

Best,
Martijn

Verstuurd vanaf mijn iPhone

Op 24 feb. 2012 om 22:19 heeft Antonella Kis  het volgende 
geschreven:

> 
> Hi,
> 
> I am trying to find a way to get the segmentation/cortical label (to 
> determine corresponding brain structures) in MNI space for a cluster for 
> which I know the MNI coordinates. How can I do this?
> 
> 
> Many thanks.
> Antonella
> 
> 
> ___
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> 
> 
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> at
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> properly
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Re: [Freesurfer] mri_convert

[Douglas N Greve]

Oh, the problem may be in your label2vol cmd. Try this one

mri_label2vol --seg 
~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp  
~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --o 
~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz 
--regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz



Jimmy Ghaziri wrote:
> Yes, since it appears fine when I open it with tkmedit. But once I 
> apply a flirt transformation I get the same image on tkmedit than the 
> one on fslview. I tried to flip the image but it won't change anything 
> since the brain is cut.
> Also, I followed the same steps on my colleagues machine and it worked 
> fine on his...
>
> Thank you
>
> Jimmy
>
> On Fri, Feb 24, 2012 at 14:27, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Hi Jimmy, I think the problem, if you can call it that, is with
> fslview. Below is from our FAQ. See if that makes sense.
>
> doug
>
>
>
>
> Q. Why would the orientation of my scans look wrong after
> processing my DICOM files with 'mri_convert'?
>
> A: It can be misleading to check orientation using FSLVIEW because
> it orients volumes based on the way they are on disk so you often
> get things looking pretty strange (e.g., upside-down). FSLVIEW
> does display little letters along the side of the image to
> indicate what it thinks the orientation is, so if you stick to
> those, then you can properly judge whether the orientation is correct.
>
>
>
>
>
> Jimmy Ghaziri wrote:
>
> Dear FreeSurfer community,
>
> I'm using the mri_label2vol, the output is in .mgz. I then use
> mri_convert to convert it to .nii.gz.
> When I do so, the output is corrupted (see attached images).
> Some colleagues told me that it was because my FreeSurfer had
> a bug so I uninstalled and installed it back again but nothing
> changed. I then tried to run it on some other colleague's
> machine and it worked fine (on one subject just to test).
>
> Any ideas what could be the problem ? I tried to flip the
> image 90 degrees but it won't flip, nothing changes.
>
> Here are the commands I'm launching :
>
> mri_label2vol --seg
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
> --temp
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz
> --regheader
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
>
> mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
>
>
> The data looks fine when I open it with tkmedit but it's
> inverted and cut when opened with fslview.
>
> I cannot continue my analyses even if the data looks fine on
> tkmedit. When I apply a flirt transformation on the data I get
> the same cut and inverted brain than on fslview (see flirt
> attached image).
>
> Is it a problem with my FreeSurfer or a command I'm running
> the wrong way ? Is there another software to convert .mgz to
> .nii.gz ?
>
>
> Thank you very much !
>
>
> Jimmy
>
> 
> 
>
>
> 
> 
>
>
> 
> 
>
> 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358  Fax: 617-726-7422
> 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
> 
>
> ___
> Freesurfe

Re: [Freesurfer] Frontal signal drop out

[Mahinda Yogarajah]

Dear Freesurfer Experts,

Would it be easier to upload a typical example of the data I am trying to
salvage, in order to get some hints on how I might proceed with this
problem of loss of frontal signal drop off ?

Thanks in advance.

Mahinda


On Thu, Feb 23, 2012 at 2:06 AM, Mahinda Yogarajah wrote:

> Hi Bruce and Freesurfer Experts,
>
> I tried the suggestions below in these images but without complete
> resolution of the problem - there is an improvement but there is still
> stuff missing right at the front (last 3 to 4 slices).  Is there anything
> else I can try in order to salvage these images ?  As mentioned previously
> there is data there if I alter windowing parameters ...
>
> Would be grateful for any help offered,
>
> Thanks.
>
> Mahinda
>
>
>
>
> On Tue, Jan 24, 2012 at 12:04 AM, Bruce Fischl  > wrote:
>
>> hmmm, could also be a low sensitivity region if the region around the
>> eyes doesn't have coil coverage. I would try putting a line of control
>> points in the white matter going from anterior and moving posteriorly until
>> the drop-off is not that big (i.e. until the T1.mgz has voxels==110 in the
>> white matter)
>>
>>
>> On Tue, 24 Jan 2012, Mahinda Yogarajah wrote:
>>
>>  Hi,
>>>
>>> No problem - thanks for coming back to me.
>>>
>>> Imaging was carried out with a GE Excite II 3-T scanner using an eight-
>>> channel phased array coil. We acquired coronal 3D-T1 weighted fast
>>> spoiled
>>> gradient echo (FSPGR) (0.94 × 0.94 × 1.1 mm) which is what I am plugging
>>> into Freesurfer.
>>>
>>> There is actual data present - changing the windowing settings
>>> (brightness
>>> and contrast) at the front it is possible to make out both grey and white
>>> matter.  It is at a low intensity compared with the rest of the brain.
>>> The
>>> data was acquired some time ago, and I am not sure what the source of
>>> drop
>>> off is.  Thanks for your advice in advance.
>>>
>>> Thanks.
>>>
>>> M
>>>
>>>
>>>
>>> On Mon, Jan 23, 2012 at 11:07 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>  Hi Mahinda,
>>>
>>>  sorry, I meant to respond to this. It's hard to tell from the
>>>  image - is there actually data in the frontal regions? What is
>>>  the source of the drop-off? Is it a slab selective acquisition
>>>  and is anterior/posterior the slab direction?
>>>
>>>  cheers
>>>  Bruce
>>>
>>>
>>>  On Mon, 23 Jan 2012, Mahinda Yogarajah wrote:
>>>
>>>Dear Experts,
>>>
>>>Sorry if this is a repost, but I was not sure it got
>>>posted.
>>>
>>>I have a few subjects that I want to salvage and use
>>>where there appears to
>>>be significant signal inhomogeniety in the last few
>>>frontal slices (see
>>>T1.mgz in attached figure 1).  Despite the use of
>>>control points (placed
>>>with careful adjustments of windowing parameters), I
>>>still can't encompass
>>>all of the the gyri right at the front (see
>>>brainmask.mgz coronal slice in
>>>figure 2).  I would really appreciate some advice on
>>>how to proceed from
>>>here.  Is placing white matter voxels in wm.mgz a
>>>possible solution ? Or is
>>>there another solution ?
>>>
>>>Thanks.
>>>
>>>M
>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/**complianceline.
>>>  If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Frontal signal drop out

[Sita Kakunoori]

Hi Mahinda,

I can take a look if you want to upload a dataset. Please find 
the instructions to upload in this wiki.


http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

Thanks,
Sita.


On Sat, 25 Feb 2012, Mahinda Yogarajah wrote:


Dear Freesurfer Experts,

Would it be easier to upload a typical example of the data I am trying to
salvage, in order to get some hints on how I might proceed with this
problem of loss of frontal signal drop off ?

Thanks in advance.

Mahinda


On Thu, Feb 23, 2012 at 2:06 AM, Mahinda Yogarajah wrote:


Hi Bruce and Freesurfer Experts,

I tried the suggestions below in these images but without complete
resolution of the problem - there is an improvement but there is still
stuff missing right at the front (last 3 to 4 slices).  Is there anything
else I can try in order to salvage these images ?  As mentioned previously
there is data there if I alter windowing parameters ...

Would be grateful for any help offered,

Thanks.

Mahinda




On Tue, Jan 24, 2012 at 12:04 AM, Bruce Fischl 
wrote:



hmmm, could also be a low sensitivity region if the region around the
eyes doesn't have coil coverage. I would try putting a line of control
points in the white matter going from anterior and moving posteriorly until
the drop-off is not that big (i.e. until the T1.mgz has voxels==110 in the
white matter)


On Tue, 24 Jan 2012, Mahinda Yogarajah wrote:

 Hi,


No problem - thanks for coming back to me.

Imaging was carried out with a GE Excite II 3-T scanner using an eight-
channel phased array coil. We acquired coronal 3D-T1 weighted fast
spoiled
gradient echo (FSPGR) (0.94 × 0.94 × 1.1 mm) which is what I am plugging
into Freesurfer.

There is actual data present - changing the windowing settings
(brightness
and contrast) at the front it is possible to make out both grey and white
matter.  It is at a low intensity compared with the rest of the brain.
The
data was acquired some time ago, and I am not sure what the source of
drop
off is.  Thanks for your advice in advance.

Thanks.

M



On Mon, Jan 23, 2012 at 11:07 PM, Bruce Fischl <
fis...@nmr.mgh.harvard.edu>
wrote:
 Hi Mahinda,

 sorry, I meant to respond to this. It's hard to tell from the
 image - is there actually data in the frontal regions? What is
 the source of the drop-off? Is it a slab selective acquisition
 and is anterior/posterior the slab direction?

 cheers
 Bruce


 On Mon, 23 Jan 2012, Mahinda Yogarajah wrote:

   Dear Experts,

   Sorry if this is a repost, but I was not sure it got
   posted.

   I have a few subjects that I want to salvage and use
   where there appears to
   be significant signal inhomogeniety in the last few
   frontal slices (see
   T1.mgz in attached figure 1).  Despite the use of
   control points (placed
   with careful adjustments of windowing parameters), I
   still can't encompass
   all of the the gyri right at the front (see
   brainmask.mgz coronal slice in
   figure 2).  I would really appreciate some advice on
   how to proceed from
   here.  Is placing white matter voxels in wm.mgz a
   possible solution ? Or is
   there another solution ?

   Thanks.

   M



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e-mail
contains patient information, please contact the Partners Compliance
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[Freesurfer] last index missing when using mri_label2vol

[David Grayson]

Hi,

I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the 
final label from the color table file. I tried using the --thresh 1 option, but 
that didn't work either. i.e...
 
mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o 
custom_lh.nii.gz --subject FREESURFER --hemi lh --identity

The last index is no where to be found in the custom_lh.nii.gz. But the other 
indices look OK.

Has anyone encountered this before, and know what to do? Thanks very much!

David
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[Freesurfer] volume size

[Colin Reveley]

Hi -

I would really like to use a volume size greater than 256^3.

I know of all the options and reasons.

what I want is a white matter surface than has fairly evenly spaced nodes
that are in approximate match to the voxels they enclose.

the reason is to seed, track and target using FSL surface tractography. the
brain is a 250um macaque, and it's 320 voxels long unfortunately. the
structural and DWI are the same resolution and in register and acpc
aligned. such a shame to waste.

the freesurfer surfaces are imported into CARET and cross-registered to
F99. but they keep their mesh if I want.

work with another sample showed that node numbers and even coverage over
the WM/GM boundary had a signifiant effect on the FSL metrics, with the
original FS WM surface and derivatives yielding the best results over other
meshes like F99's or anything made with surefit directly from a downsampled
version of the data. that data I could fit into 256^3.

I doubt that the nodes and voxels need to match perfectly, just ballpark
and fairly even spacing.

if I used a downsampled volume at 500um to make surfaces in freesurfer,
maybe I could upsmaple the surfaces afterwards? but then the pial and white
would have to be resampled independently and that's probably no good.

If I have to resample the volume or apply a scaling transform the world
won't end. In fact it will take less time to do probably. But it would be
nice to use a larger size than 256^3 to take advantage of what I've got.

best,

Colin, Sussex
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Re: [Freesurfer] volume size

[Colin Reveley]

sorry - re this:

in principle, is freesurfer particularly sensitive to the orientation of
the brain? It might fit in 256^3 if I rotated it. then I could rotate the
surfaces back when I import to CARET.

It was, actually, rather hard to get a good surface last time. it seemed
that freesurfer needed it really well aligned or there were issues.

But the issue was medio-lateral alignment probably. since it's symmetic LR,
could it's nose be pushed up?

On 25 February 2012 06:11, Colin Reveley  wrote:

> Hi -
>
> I would really like to use a volume size greater than 256^3.
>
> I know of all the options and reasons.
>
> what I want is a white matter surface than has fairly evenly spaced nodes
> that are in approximate match to the voxels they enclose.
>
> the reason is to seed, track and target using FSL surface tractography.
> the brain is a 250um macaque, and it's 320 voxels long unfortunately. the
> structural and DWI are the same resolution and in register and acpc
> aligned. such a shame to waste.
>
> the freesurfer surfaces are imported into CARET and cross-registered to
> F99. but they keep their mesh if I want.
>
> work with another sample showed that node numbers and even coverage over
> the WM/GM boundary had a signifiant effect on the FSL metrics, with the
> original FS WM surface and derivatives yielding the best results over other
> meshes like F99's or anything made with surefit directly from a downsampled
> version of the data. that data I could fit into 256^3.
>
> I doubt that the nodes and voxels need to match perfectly, just ballpark
> and fairly even spacing.
>
> if I used a downsampled volume at 500um to make surfaces in freesurfer,
> maybe I could upsmaple the surfaces afterwards? but then the pial and white
> would have to be resampled independently and that's probably no good.
>
> If I have to resample the volume or apply a scaling transform the world
> won't end. In fact it will take less time to do probably. But it would be
> nice to use a larger size than 256^3 to take advantage of what I've got.
>
> best,
>
> Colin, Sussex
>
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