Re: [Freesurfer] mri_surcluster and centroid option

[Joerg Pfannmoeller]

On Mon, 07 Apr 2014 12:02:24 -0400
Douglas N Greve  wrote:


> Is this group data? Or otherwise on fsaverage? Or on the subject's 
> surface? 

It is on a single subject on its on anatomy (self). 

> How are you determining that the centroid is outside of the 
> cluster?

The coordinates are outside the cluster, there is nothing to worry about that.
 
> It should give you a vertex number for the centroid (I think). 

As you told in your last mail it gives Tal-coordinates and not vertices.

> I opted not to use the centroid by default for this reason. This can 
> happen because the centroid is irregular.

I don not understand this: What do you mean by irregular?

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Re: [Freesurfer] mri_vol2surf --projopt

[Joerg Pfannmoeller]

Sorry for this question, but now I am confused. Do you mean that I should not 
use projopt and just use the interpolation? If so why should I not use projfrac?


On Tue, 08 Apr 2014 15:02:36 -0400
Douglas N Greve  wrote:

> 
> You'll have to do without it for now and just do the interpolation
> 
> On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote:
> > Well, I need to use that option. In this case I will just interpolate to 
> > the 1 mm grid and proceed this way.
> >
> >
> > On Mon, 07 Apr 2014 12:14:47 -0400
> > Douglas N Greve  wrote:
> >
> >> Sorry, I don't understand. You mean it still segfaults without --projopt
> >> or that you have to use projopt?
> >>
> >> On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote:
> >>> Unfortunately that is no option for me.
> >>>
> >>>
> >>>
> >>> On Fri, 04 Apr 2014 15:33:47 -0400
> >>> Douglas N Greve  wrote:
> >>>
>  Don't use --projopt and it won't segfault
> 
>  On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote:
> > The command is:
> >
> > mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> > --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh 
> > --o /.../f001_surf.nii --noreshape --cortex
> >
> > The output is the follwoing:
> >
> >
> > srcvol = /.../f001.nii
> > srcreg = /.../register.f001.dof6.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = subjid
> > surfreg = sphere.reg
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > INFO: changing type to float
> > Done loading volume
> > Loading label /.../label/rh.cortex.label
> > Reading surface /.../surf/rh.white
> > Done reading source surface
> > Reading thickness /.../surf/rh.thickness
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > reading gm volume fraction from /.../map001.gm.mgz
> > reading wm volume fraction from /.../map001.wm.mgz
> > reading csf volume fraction from /.../map001.csf.mgz
> > mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> > --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh 
> > --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault
> > 
> > Do you have an idea about the cause of the error?
> >
> >
> >
> >
> >
> > On Wed, 02 Apr 2014 17:28:14 -0400
> > Douglas N Greve  wrote:
> >
> >> what is your command line that is seg faulting? What is the terminal 
> >> output?
> >>
> >> On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
> >>> Please help me with this issue:
> >>>
> >>> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it
> >>> results in a segmentation fault. It works if I apply mri_vol2vol for
> >>> registration of epi and anatomy, but than an interpolation is
> >>> involved. I would like to avoid the interpolation and apply
> >>> mri_surf2vol directly to the unprocessed data in order to minimize the
> >>> number of interpolations.
> >>>
> >>>
> >>> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
> >>>
> >>>This is something BF added Sept 1 2009:
> >>>
> >>>added --projopt  switch to do optimal linear estimation of 
> >>> gray matter
> >>>values given a set of precomputed gray matter densities.
> >>>
> >>>I don't know what it would mean beyond that
> >>>
> >>>doug
> >>>
> >>>
> >>>On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> >>>> Hello,
> >>>>
> >>>> I found an option in mri_vol2surf for which I could not find 
> >>> a
> >>>documentation. The option is called:
> >>>>
> >>>> --projopt
> >>>>
> >>>> It would be nice if somebody could give a description of this
> >>>option.
> >>>>
> >>>> Respectfully yours
> >>>>
> >>>> pfannmoe
> >>>>
> >>>>
> >>>> ___
> >>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> >>>www.nm

[Freesurfer] Intermediate stages of cortical inflation

[Xuelong Zhao]

Hi, 

I would like to ask whether it is possible to display different levels of 
cortical inflation?

I have been using the command: mris_inflate 

but the -dist and -n flags do not seem to make that much difference. Also, if I 
use fsaverage lh.orig as the input file and using the default options for 
mris_Inflate I don't seem to be able to recover the lh.inflated surface. 

Are there any alternative commands to control the level of inflation? Thanks.


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Re: [Freesurfer] QDEC ANALYSIS

[Douglas Greve]

Try setting the age to be a nuisance variable.
doug


On 4/8/14 7:06 PM, Walton, Matt wrote:

Hello Freesurfer experts.

I am trying to run a QDEC analysis on some MRI data I have. I want to 
see if thickness is correlated with language scores I have for each 
subject, while accounting for differences in age, and gender.


I would like to select the gender as a fixed variable, and both the 
age and language scores as continuous variables, however the QDEC GUI 
will not allow me to select more than one continuous variable at a 
time (from what I've read on the website/mailing list I should be able 
to select up to two.


Any idea of what might be wrong here, and how I can fix it.

Thanks So much,

Matthew Walton


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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

[Douglas Greve]

yep, exactly

On 4/8/14 6:00 PM, Corinna Bauer wrote:

Hi Doug,
After I have the labels then in each subject's T1 space, I will need 
to then put them into diffusion and resting state space.


I already have scripts that put the parcellations into 
subject-specific diffusion/resting state space (using bbregister, 
tkregister2, mri_vol2vol (using the inverse registration from 
bbregister to put the T1 into diffusion space), mri_extract_label 
(extract labels from aparc+aseg.mgz), and then mri_label2vol (register 
each of the extracted labels into diffusion space). Would a similar 
approach work for the new labels?


Corinna


On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Exactly what you have described won't work very well because it
would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)

doug

On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> Hello all,
>
> I am planning to use mris_divide_parcellation to split the Desikan
> atlas into smaller ROIs, but will need the new ROIs to be consistent
> between subjects.
>
> Can I achieve this if I register each subject to fsaverage space and
> then apply the inverse transform to the divided parcellations (which
> are currently done on the fsaverage brain)?
>
> If so, for extracting each label, what would be used for the label
> number?
> (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
> ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>
>
> Thanks
>
> Corinna
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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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

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Re: [Freesurfer] Export freesurfer data

[ye tian]

Dear Doug,

Thank you!

Sincerely,
Ye


On Tue, Apr 8, 2014 at 4:47 PM, Douglas N Greve
wrote:

>
> On 04/05/2014 09:49 PM, ye tian wrote:
>
>> Dear Bruce and Doug,
>>
>> Would you please shine some light on what the freesurfer files mean?
>>
>> For example, rh.orig, once mris_converted, starts with
>>
>> 115750 231496
>> 21.097221 -65.951393 -18.834326 0
>> 20.621031 -66.165680 -18.995041 0
>> .
>>
>> I thought that this file gives all unidentified regions, since 0=unknown,
>> but it doesn't make sense.
>>
>> Furthermore,
>> 1) What do the first two numbers mean?
>>
> I think the first is the number of vertices and the 2nd the number of faces
>
>> 2) Not all files can be fed into mris_convert. Do you recommend using
>> read_surf.m instead?
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>>
>> On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl 
>> > fis...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Ye
>>
>> it is both that, and volumes of label indices (e.g. 17=Left
>> Hippocampus) and surface models (triangles, edges, points) and
>> scalar and vector fields over them.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Mon, 3 Mar 2014, ye tian wrote:
>>
>> Dear Bruce and Doug,
>> Thank you very much!
>>
>> Would you please tell me more about what "freesurfer data"
>> actually is? Is
>> it composed of pixel positions and intensities? If that's the
>> case, how do
>> you calculate cortical thickness?
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>>
>> On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>>
>>
>> wrote:
>>
>>   Can you be more specific about what you mean by "freesurfer
>>   data"? Each
>>   subject has 300MB of "data"
>>   doug
>>
>>   On 02/27/2014 10:48 PM, ye tian wrote:
>>   > Dear Freesurfers,
>>   >
>>   > I would like to do some customized model fitting for
>> cortical
>>   > thickness. Is there a way to export freesurfer data
>> into R or
>>   simply
>>   > as a text?
>>   >
>>   > Thank you very much!
>>   >
>>   > Sincerely,
>>   > Ye
>>   >
>>   >
>> > ___
>> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> 
>>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> 
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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
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>> sent to you
>> in error
>> but does not contain patient information, please contact the
>> sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
>>
> --
> 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
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>
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[Freesurfer] restrain range when calculating subcortical volumes, such as hippocampus

[余]

Hi,

I am wondering how can I get the volume of hippocampus within a certain
range? Given that the most anterior and posterior part of hippocampus may
be more susceptible to errors because of other structures like amygdala and
fornix, so I am wondering if the measurement would be more reliable if the
most anterior and posterior parts of it are excluded. For example,
calculate the volume of hippocampus without the most anterior and posterior
4 slices?

I guess I could calculate manually, by summing the product of area of
hippocampus on every specific slice and the distance between slices. But
where can I get the information about the area on every slice? And what is
the distance between the two slices (if for the coronal view)? Does it
depend on the original DICOM files, or does Freesurfer do some re-slicing
during the reconstruction?

Thank you very much! Best,
QJ
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[Freesurfer] QDEC ANALYSIS

[Walton, Matt]

Hello Freesurfer experts.

I am trying to run a QDEC analysis on some MRI data I have. I want to see if 
thickness is correlated with language scores I have for each subject, while 
accounting for differences in age, and gender.

I would like to select the gender as a fixed variable, and both the age and 
language scores as continuous variables, however the QDEC GUI will not allow me 
to select more than one continuous variable at a time (from what I've read on 
the website/mailing list I should be able to select up to two.

Any idea of what might be wrong here, and how I can fix it.

Thanks So much,

Matthew Walton
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Re: [Freesurfer] Rat cortex Parcellation

[Bruce Fischl]

Hi Mike

there may be people who have done it, but we (at MGH) haven't as far as I 
know.

cheers
Bruce
On Tue, 8 Apr 2014, Craig, Michael wrote:

> Hello,
> I have a question regarding the parcellation of the rat cortex. I am
> interested in parcellating the cortex into distinct regions using an atlas
> and then finding grey matter volumes for each region. I realize that
> Freesurfer is primarily meant to be used on human subjects, but is it
> possible to replace the MNI atlas with a rat atlas (like the LONI rat atlas)
> during the parcellation step? Thanks for your time and help.
> 
> best wishes,
> 
> Mike
> 
>
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

[Corinna Bauer]

Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.

I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the inverse registration from bbregister to put the T1 into
diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
and then mri_label2vol (register each of the extracted labels into
diffusion space). Would a similar approach work for the new labels?

Corinna


On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
wrote:

>
> Exactly what you have described won't work very well because it would be
> in the volume. I would divide up the parcellations in fsaverage space
> like you've done, then map the parcellation to each subject using
> mri_surf2surf (--sval-annot, see example 6)
>
> doug
>
> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> > Hello all,
> >
> > I am planning to use mris_divide_parcellation to split the Desikan
> > atlas into smaller ROIs, but will need the new ROIs to be consistent
> > between subjects.
> >
> > Can I achieve this if I register each subject to fsaverage space and
> > then apply the inverse transform to the divided parcellations (which
> > are currently done on the fsaverage brain)?
> >
> > If so, for extracting each label, what would be used for the label
> > number?
> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
> >
> >
> > Thanks
> >
> > Corinna
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
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Re: [Freesurfer] Extract seed from resting state networks mask (Yeo and Buckner maps)

[Douglas N Greve]

Hi Celine, I would probably map the annot to each individual subject 
using mri_surf2surf (see example 6). Then use mri_aparc2aseg to map it 
into the volume space (see subject/scripts/recon-all.log for the command 
used to generate aparc+aseg.mgz and then change the annot and the output 
filename).

You'll need to know the segmentation number for configuring the seed. To 
get this load the output into tkmedit, something like

tkmedit subject nu.mgz -opacity 1 -seg yournewseg.mgz -aux yournewseg.mgz

All the names will be messed up, but that is ok. Find the seg that you 
are interested in it. When you click on it, see the value presented for 
the aux in the control window. Pass this as -segid when you run 
fcseed-config and spec -seg yournewseg.mgz

doug

On 04/07/2014 03:15 PM, Celine Louapre wrote:
> Hi Freesurfer team
> I am running a functional connectivity analysis on resting state data, and
> I would like to use as seed the precuneus/posterior cingulate region as
> seen on fsaverage/label/${hemi}.Yeo2011_17Networks_N1000.annot.
> However, this region is part of the label 17Networks_16 comprising other
> regions. Is it possible to isolate this specific portion of the label to
> create a seed region for the connectivity analysis ? I tried to do it on
> tksurfer, drawing a path around the region but then I could not figure out
> how to extract this part of the label.
> Thank you very much for your help
> Best
> Celine
>

-- 
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
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Re: [Freesurfer] Export freesurfer data

[Douglas N Greve]

On 04/05/2014 09:49 PM, ye tian wrote:
> Dear Bruce and Doug,
>
> Would you please shine some light on what the freesurfer files mean?
>
> For example, rh.orig, once mris_converted, starts with
>
> 115750 231496
> 21.097221 -65.951393 -18.834326 0
> 20.621031 -66.165680 -18.995041 0
> .
>
> I thought that this file gives all unidentified regions, since 
> 0=unknown, but it doesn't make sense.
>
> Furthermore,
> 1) What do the first two numbers mean?
I think the first is the number of vertices and the 2nd the number of faces
> 2) Not all files can be fed into mris_convert. Do you recommend using 
> read_surf.m instead?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
>
>
> On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Ye
>
> it is both that, and volumes of label indices (e.g. 17=Left
> Hippocampus) and surface models (triangles, edges, points) and
> scalar and vector fields over them.
>
> cheers
> Bruce
>
>
>
> On Mon, 3 Mar 2014, ye tian wrote:
>
> Dear Bruce and Doug,
> Thank you very much!
>
> Would you please tell me more about what "freesurfer data"
> actually is? Is
> it composed of pixel positions and intensities? If that's the
> case, how do
> you calculate cortical thickness?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
>
>
> On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
>
>   Can you be more specific about what you mean by "freesurfer
>   data"? Each
>   subject has 300MB of "data"
>   doug
>
>   On 02/27/2014 10:48 PM, ye tian wrote:
>   > Dear Freesurfers,
>   >
>   > I would like to do some customized model fitting for
> cortical
>   > thickness. Is there a way to export freesurfer data
> into R or
>   simply
>   > as a text?
>   >
>   > Thank you very much!
>   >
>   > Sincerely,
>   > Ye
>   >
>   >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
>
>
>

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects

[Douglas N Greve]

Exactly what you have described won't work very well because it would be 
in the volume. I would divide up the parcellations in fsaverage space 
like you've done, then map the parcellation to each subject using 
mri_surf2surf (--sval-annot, see example 6)

doug

On 04/08/2014 04:54 PM, Corinna Bauer wrote:
> Hello all,
>
> I am planning to use mris_divide_parcellation to split the Desikan 
> atlas into smaller ROIs, but will need the new ROIs to be consistent 
> between subjects.
>
> Can I achieve this if I register each subject to fsaverage space and 
> then apply the inverse transform to the divided parcellations (which 
> are currently done on the fsaverage brain)?
>
> If so, for extracting each label, what would be used for the label 
> number?
> (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035* 
> ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>
>
> Thanks
>
> Corinna
>
>
> ___
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-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Rat cortex Parcellation

[Craig, Michael]

Hello,

I have a question regarding the parcellation of the rat cortex. I am interested 
in parcellating the cortex into distinct regions using an atlas and then 
finding grey matter volumes for each region. I realize that Freesurfer is 
primarily meant to be used on human subjects, but is it possible to replace the 
MNI atlas with a rat atlas (like the LONI rat atlas) during the parcellation 
step? Thanks for your time and help.

best wishes,

Mike
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[Freesurfer] mris_divide_parcellation same divisions between subjects

[Corinna Bauer]

Hello all,

I am planning to use mris_divide_parcellation to split the Desikan atlas
into smaller ROIs, but will need the new ROIs to be consistent between
subjects.

Can I achieve this if I register each subject to fsaverage space and then
apply the inverse transform to the divided parcellations (which are
currently done on the fsaverage brain)?

If so, for extracting each label, what would be used for the label number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*${subj_dir}/hardi_labels/ctx-rh-insula.nii)


Thanks

Corinna
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Re: [Freesurfer] Longitudinal Analysis Questions

[pfotiad]

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.edu wrote:
>> 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: It appears that this subject ID is an existing
>> base/template from longitudinal processing (-base).
>> Please make sure you pass all necessary flags.
>> For example, if you are trying to re-run a -base:
>>
>> \' -base  -tp  ... \'
>>
>> Exit 1
>>
>>
>> In order to reconstruct the base do I need to run again the command that
>> created the base in the first place and then add the flag -autorecon2-cp
>> -autorecon3 that is:
>>
>> recon-all -autorecon2-cp -autorecon3 -base  -tp
>> 
>> -tp  ... -tp  -all ?
>>
>> Thanks in advance,
>> Panos
>>
>>> Hi Panos,
>>>
>>> 1. you need to edit the base. That is actually more important than
>>> editing the individual (cross) time points from the first stage,
>>> especially when the edits are supposed to improve the surface. The
>>> reason is that the surface is taken from the base to initialize all
>>> time
>>> points in the -long step. So accurate surfaces, brainmasks and
>>> talairach
>>> transforms are very important in the base.
>>>
>>> 2. Yes, that is generally OK.  It would be bad if one group has only 3
>>> time points the other 5 though, but if that is relatively balanced
>>> across your groups, you'll be fine.
>>>
>>> Best, Martin
>>>
>>>
>>> On 03/28/2014 03:43 PM, pfot...@nmr.mgh.harvard.edu wrote:
 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 command in
 the
 wiki preserving those edits or do I need to reapply them in the base
 template? I know that this has been answered for previous versions of
 FS
 but I was wondering whether anything has changed in more recent
 versions.

 2) Is it ok to run the longitudinal analysis described in the wiki
 when
 my
 subjects have an unequal number of timepoints (i.e. one person has 3
 different timepoints, whereas another one has five) or should they all
 have the same number of timepoints?
 Thanks in advance!

 Best,
 Panos
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>>> --
>>> Martin Reuter, Ph.D.
>>>
>>> Instructor in Neurology
>>> Harvard Medical School
>>> Assistant in Neuroscience
>>> Dept. of Radiology, Massachusetts General Hospital
>>> Dept. of Neurology, Massachusetts General Hospital
>>> Research Affiliate
>>> Computer Science and Artificial Intelligence Lab,
>>> Dept. of Electrical Engineering and Computer Science,
>>> Massachusetts Institute of Technology
>>>
>>> A.A.Martinos Center for Biomedical Imaging
>>> 149 Thirteenth Street, Suite 2301
>>> Charlestown, MA 02129
>>>
>>> Phone: +1-617-724-5652
>>> Email:
>>>  mreu...@nmr.mgh.harvard.edu
>>>  reu...@mit.edu
>>> Web  : http://reuter.mit.edu
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Martin Reuter, Ph.D.
>
> Instructor in Neurology
>Harvard Medical School
> Assistant in Neuroscience
>Dept. of Radiology, Massachusetts General Hospital
>Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>Computer Science and Artificial Intelligence Lab,
>Dept. of Electrical Engineering and Computer Science,
>Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
> mreu...@nmr.mgh.harvard.edu
> reu...@mit.edu
> Web  : http://reuter.mit.edu
>
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>
>
>

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Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Eiran Harel]

Thank you Zeke and Markus!

From: Z K [zkauf...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 08, 2014 10:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Markus Gschwind; Eiran Harel
Subject: Re: [Freesurfer] Mac OSX installations incomplete? What to do?

Markus,

Thanks for pointing that out. I have added those files to the ftp link.

-Zeke

On 04/04/2014 04:16 PM, Markus Gschwind wrote:
> Thank you Zeke,
>
> What about these?
>
> /usr/local/freesurfer/bin/bet.fsl
> /usr/local/freesurfer/bin/flirt.fsl
> /usr/local/freesurfer/bin/slicetimer.fsl
>
> They are not there neither compared to the ubuntu install.
>
> Best,
> Markus
>
>
>
>
> 2014-04-04 19:05 GMT+02:00 Z K  >:
>
> There are 3 missing fsl files from the OSX snow leopard installation.
> They can be downloaded from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl
>
> Copy them into your "$FREESURFER_HOME/bin" directory.
>
> -Zeke
>
>
>
> On 04/04/2014 12:32 PM, Markus Gschwind wrote:
>  > Dear Freesurfers,
>  >
>  > As discovered here,
>  >
>  >
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
>  >
>  > it seams that some Mac OSX installations suffered from incomplete
> files.
>  >
>  > I just veryfied that I had downloaded the complete image and wget
> says yes:
>  >
>  > Logging in as anonymous ... Logged in!
>  > ==> SYST ... done.==> PWD ... done.
>  > ==> TYPE I ... done.  ==> CWD (1) /pub/dist/freesurfer/5.3.0
> ... done.
>  > ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
>  > ... 3394499614
>  > File has already been retrieved.
>  > 2014-04-04 18:24:26 (0.00 B/s) -
>  > ‘freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg’ saved
>  > [3394499614]
>  >
>  >
>  > So this is what I installed recently and it seems that there are some
>  > files missing (at least some of the fsl-functions in bin).
>  >
>  > Doug, you said that you suspected that it could be a problem of the
>  > installer script?
>  >
>  > What should we do (also Eiran) in order to complete the installation?
>  >
>  > Thanks for you work!
>  > Markus
>  >
>  >
>  > ___
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> 
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>  >
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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>
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Re: [Freesurfer] Longitudinal Analysis Questions

[Martin Reuter]

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.edu wrote:
> 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: It appears that this subject ID is an existing
> base/template from longitudinal processing (-base).
> Please make sure you pass all necessary flags.
> For example, if you are trying to re-run a -base:
>
> \' -base  -tp  ... \'
>
> Exit 1
>
>
> In order to reconstruct the base do I need to run again the command that
> created the base in the first place and then add the flag -autorecon2-cp
> -autorecon3 that is:
>
> recon-all -autorecon2-cp -autorecon3 -base  -tp 
> -tp  ... -tp  -all ?
>
> Thanks in advance,
> Panos
>
>> Hi Panos,
>>
>> 1. you need to edit the base. That is actually more important than
>> editing the individual (cross) time points from the first stage,
>> especially when the edits are supposed to improve the surface. The
>> reason is that the surface is taken from the base to initialize all time
>> points in the -long step. So accurate surfaces, brainmasks and talairach
>> transforms are very important in the base.
>>
>> 2. Yes, that is generally OK.  It would be bad if one group has only 3
>> time points the other 5 though, but if that is relatively balanced
>> across your groups, you'll be fine.
>>
>> Best, Martin
>>
>>
>> On 03/28/2014 03:43 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>> 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 command in the
>>> wiki preserving those edits or do I need to reapply them in the base
>>> template? I know that this has been answered for previous versions of FS
>>> but I was wondering whether anything has changed in more recent
>>> versions.
>>>
>>> 2) Is it ok to run the longitudinal analysis described in the wiki when
>>> my
>>> subjects have an unequal number of timepoints (i.e. one person has 3
>>> different timepoints, whereas another one has five) or should they all
>>> have the same number of timepoints?
>>> Thanks in advance!
>>>
>>> Best,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Martin Reuter, Ph.D.
>>
>> Instructor in Neurology
>> Harvard Medical School
>> Assistant in Neuroscience
>> Dept. of Radiology, Massachusetts General Hospital
>> Dept. of Neurology, Massachusetts General Hospital
>> Research Affiliate
>> Computer Science and Artificial Intelligence Lab,
>> Dept. of Electrical Engineering and Computer Science,
>> Massachusetts Institute of Technology
>>
>> A.A.Martinos Center for Biomedical Imaging
>> 149 Thirteenth Street, Suite 2301
>> Charlestown, MA 02129
>>
>> Phone: +1-617-724-5652
>> Email:
>>  mreu...@nmr.mgh.harvard.edu
>>  reu...@mit.edu
>> Web  : http://reuter.mit.edu
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, Ph.D.

Instructor in Neurology
   Harvard Medical School
Assistant in Neuroscience
   Dept. of Radiology, Massachusetts General Hospital
   Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
   Computer Science and Artificial Intelligence Lab,
   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] failed templates from longitudinal base step

[Martin Reuter]

Hi Laura,

this should not happen. Probably something got mixed up (e.g. creating a 
template from 2 time points that are from different subjects could cause 
these problems).
For testing, you could select one subject from the middle of your data 
set , copy the 2 cross sectionally processed time points into a new 
directory and create the base for this subject there.


Best, Martin


On 04/02/2014 09:10 AM, L. Koenders wrote:


Dear FreeSurfer people,

I have a question regarding the longitudinal pipeline, because 
something goes very wrong with my output.


A short summary of my project: I have 3Tesla data from two timepoints, 
consisting of 50 people, so 100 scans in total. I have two groups, a 
control and an experimental group (cannabis users).


In FS v5.3.0, I ran all scans through the Cross pipeline, and made 
brainmask.mgz pial edits where necessary. So far so good. 
Subsequently, I ran all the scans (all the edited scans) through the 
Base pipeline. This is when I ran into troubles, because only 2 
templates (out of the whole group) turned out all right. The surfaces 
of all other scans are skipping gyri (for an example see attachment 
template_surfs). The scans that turned out allright were the very 
first and very last one of my subjects, which i find suspicous.


I could of course try editing all the templates using control points, 
however I have this feeling that something else is going wrong with 
the registration of baseline and follow up scan. Do you know if this 
is a common error, and if I can do anything to fix it?


I hope you can help me!

Thanks & best regards,
Laura Koenders




AMC Disclaimer : http://www.amc.nl/disclaimer





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--
Martin Reuter, Ph.D.

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
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   reu...@mit.edu
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Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Z K]

Markus,

Thanks for pointing that out. I have added those files to the ftp link.

-Zeke

On 04/04/2014 04:16 PM, Markus Gschwind wrote:
> Thank you Zeke,
>
> What about these?
>
> /usr/local/freesurfer/bin/bet.fsl
> /usr/local/freesurfer/bin/flirt.fsl
> /usr/local/freesurfer/bin/slicetimer.fsl
>
> They are not there neither compared to the ubuntu install.
>
> Best,
> Markus
>
>
>
>
> 2014-04-04 19:05 GMT+02:00 Z K  >:
>
> There are 3 missing fsl files from the OSX snow leopard installation.
> They can be downloaded from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl
>
> Copy them into your "$FREESURFER_HOME/bin" directory.
>
> -Zeke
>
>
>
> On 04/04/2014 12:32 PM, Markus Gschwind wrote:
>  > Dear Freesurfers,
>  >
>  > As discovered here,
>  >
>  >
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
>  >
>  > it seams that some Mac OSX installations suffered from incomplete
> files.
>  >
>  > I just veryfied that I had downloaded the complete image and wget
> says yes:
>  >
>  > Logging in as anonymous ... Logged in!
>  > ==> SYST ... done.==> PWD ... done.
>  > ==> TYPE I ... done.  ==> CWD (1) /pub/dist/freesurfer/5.3.0
> ... done.
>  > ==> SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
>  > ... 3394499614
>  > File has already been retrieved.
>  > 2014-04-04 18:24:26 (0.00 B/s) -
>  > ‘freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg’ saved
>  > [3394499614]
>  >
>  >
>  > So this is what I installed recently and it seems that there are some
>  > files missing (at least some of the fsl-functions in bin).
>  >
>  > Doug, you said that you suspected that it could be a problem of the
>  > installer script?
>  >
>  > What should we do (also Eiran) in order to complete the installation?
>  >
>  > Thanks for you work!
>  > Markus
>  >
>  >
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> 
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>  >
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>
>
> 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
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> but does not contain patient information, please contact the sender
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Re: [Freesurfer] mri_vol2surf --projopt

[Douglas N Greve]

You'll have to do without it for now and just do the interpolation

On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote:
> Well, I need to use that option. In this case I will just interpolate to the 
> 1 mm grid and proceed this way.
>
>
> On Mon, 07 Apr 2014 12:14:47 -0400
> Douglas N Greve  wrote:
>
>> Sorry, I don't understand. You mean it still segfaults without --projopt
>> or that you have to use projopt?
>>
>> On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote:
>>> Unfortunately that is no option for me.
>>>
>>>
>>>
>>> On Fri, 04 Apr 2014 15:33:47 -0400
>>> Douglas N Greve  wrote:
>>>
 Don't use --projopt and it won't segfault

 On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote:
> The command is:
>
> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> /.../f001_surf.nii --noreshape --cortex
>
> The output is the follwoing:
>
>
> srcvol = /.../f001.nii
> srcreg = /.../register.f001.dof6.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = subjid
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Loading label /.../label/rh.cortex.label
> Reading surface /.../surf/rh.white
> Done reading source surface
> Reading thickness /.../surf/rh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
> reading gm volume fraction from /.../map001.gm.mgz
> reading wm volume fraction from /.../map001.wm.mgz
> reading csf volume fraction from /.../map001.csf.mgz
> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> /.../f001_surf.nii --noreshape --cortex: Segmentation fault
> 
> Do you have an idea about the cause of the error?
>
>
>
>
>
> On Wed, 02 Apr 2014 17:28:14 -0400
> Douglas N Greve  wrote:
>
>> what is your command line that is seg faulting? What is the terminal 
>> output?
>>
>> On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
>>> Please help me with this issue:
>>>
>>> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it
>>> results in a segmentation fault. It works if I apply mri_vol2vol for
>>> registration of epi and anatomy, but than an interpolation is
>>> involved. I would like to avoid the interpolation and apply
>>> mri_surf2vol directly to the unprocessed data in order to minimize the
>>> number of interpolations.
>>>
>>>
>>> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
>>>
>>>This is something BF added Sept 1 2009:
>>>
>>>added --projopt  switch to do optimal linear estimation of gray 
>>> matter
>>>values given a set of precomputed gray matter densities.
>>>
>>>I don't know what it would mean beyond that
>>>
>>>doug
>>>
>>>
>>>On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
>>>> Hello,
>>>>
>>>> I found an option in mri_vol2surf for which I could not find a
>>>documentation. The option is called:
>>>>
>>>> --projopt
>>>>
>>>> It would be nice if somebody could give a description of this
>>>option.
>>>>
>>>> Respectfully yours
>>>>
>>>> pfannmoe
>>>>
>>>>
>>>> ___
>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>Outgoing:
>>>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>>___
>>>Freesurfer mailing list
>>>Freesurfer@nmr.mgh.harvard.edu 
>>> 
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>The information in this e-mail is i

Re: [Freesurfer] how to convert fsaverage space mask into other subject original space

[Bruce Fischl]

what kind of a mask? If a label you can use mri_label2label
cheers
Bruce
On Tue, 8 Apr 
2014, Rujing Zha wrote:

> Hi FS experts and others, I try to check my group analysis result by seeing 
> the subjects' original space corresponding area. So
> I need to know how to convert my mask from fsaverage space into specific 
> subject's space.
> Thanks
> All the best.
> RujingZha
> 
> 
> 
>
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[Freesurfer] how to convert fsaverage space mask into other subject original space

[Rujing Zha]

Hi FS experts and others,
I try to check my group analysis result by seeing the subjects' original space 
corresponding area. So I need to know how to convert my mask from fsaverage 
space into specific subject's space.
Thanks
All the best.
RujingZha___
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Re: [Freesurfer] NHP surface reconstruction in FS5.3

[S.V.Shepherd [work]]

I believe ventricles and callosum are correctly labeled. I've been viewing
with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''.  I've
uploaded ( as per the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file
contents of my Otis's mri/ directory, as
SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be
enough?

Ares of concern are
* ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow
grey from CC?
* OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too
bright.
* Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual
overpaint.

stephen

Hi Stephen

Are the ventricles and callosum correctly labeled? If you upload a subject
I'll
try to take a look
Cheers
Bruce


> On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]"
>  wrote:
>
> Greetings,
>
> I've been reconstructing a surface in an NHP using a Kolster T1 scan and
> FS5.3.  It went very well, at first, but I've hit a wall.  I have trouble
in
> occipital (due to poor signal strength/constrast) and some
typical-with-NHP
> problems in ACC and OFC.  I think there are three related questions.
>
> 1) I lose parts of the ACC near the genu of the corpus callosum.  I have
> attached a screen shot -- the white matter and gray matter both look
decent.
> I wondered if the corpus callosum might be handled specially, and if
> differences between human and nhp callosi might prevent the ACC from
growing
> normally?
>
> 2) In trying to deal with this, I greyed out the ACA, which was bright
and
> potentially confounding. I wasn't sure how to do this in
> brain.finalsurfs.manedit, since my understanding is that only 1s
(nonbrain)
> and 255s (wm) were preserved. I tried brain, which got overwritten, but
> ultimately succeeded by editing brainmask and rerunning -autorecon2-wm.
Is
> there a way to repain gray matter in brain.finalsurfs.manedit?
Alternately,
> if I continue editing brainmask (or equivalent) directly, should I be
> darkening or lightening the gray matter in the excluded section of the
ACC?
> I would assume lighten -- but in the OFC, some gray matter (not shown)
> appears to be excluded for being too bright.
>
> 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't
> stuck. I assume this is because autorecon isn't convinced by the wm
> specification after looking at brain.finalsurfs -- how might I (gently!)
> override this?
>
> Thanks very much for your time and patience.
>
> stephen
>
> 
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[Freesurfer] Fw:Re: Re: questions about ROI analysis

[Rujing Zha]

Hi FS experts and others,
I completed the mri_annotation2label and mri_label2label(which used mask 
created from the mri_binarize), but the result is the same as that without 
mask.Here are my codes:

mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh
mri_annotation2label --subject fsaverage --hemi rh --outdir 
$SUBJECTS_DIR/fsaverage/label
mri_label2label --srclabel 
$SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage 
--trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat

Last step used the mask, but its result is just tha same as that without mask. 
I also checked the mask file which doesnot have any problem.
Thanks.
All the best.
Rujing Zha







 转发邮件信息 
发件人：charujing123 
发送日期：2014-02-27 09:46:23
收件人："freesurfer@nmr.mgh.harvard.edu" 
主题：Re:  Re: [Freesurfer] questions about ROI analysis

Thanks doug,
All the best.
Rujing Zha
 
2014-02-27
charujing123
发件人：Douglas N Greve 
发送时间：2014-02-27 01:49
主题：Re: [Freesurfer] questions about ROI analysis
收件人："freesurfer"
抄送：
 
 
On 02/25/2014 08:34 PM, charujing123 wrote: 
> Hidoug, 
> Thanks doug. 
> For 1st question,I want to reduce the search space of vertex-wise  
> analysis to a cluster. 
Extract the cluster that you want from the ocn to create a mask, eg, to  
get cluster2 
mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh 
The run mri_glmfit with --mask cluster2.mgh 
Then run mri_glmfit-sim with simulation 
 
> For 2nd question, i try freeview as tksurfer cannot work. However this  
> website cannot be logged  
> in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit.
>  
try 
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide 
> Thanks. 
> All the best. 
> Rujing Zha 
> 2014-02-26 
>  
> charujing123 
>  
> *发件人：*Douglas Greve  
> *发送时间：*2014-02-25 23:46 
> *主题：*Re: [Freesurfer] questions about ROI analysis 
> *收件人：*"freesurfer" 
> *抄送：* 
> 
> On 2/25/14 10:09 AM, Rujing Zha wrote: 
>> Hi FS experts and others, 
>> I have done two group thickness difference analysis based on whole  
>> brain. Now I want to do correlation analysis between specific ROI  
>> thickness and behavior score. I searched roi in the FS website, but I  
>> cannot distinguish the volume ROI and surface ROI very clearly. So I  
>> have some questions as below: 
>> 1,As I get some clusters in the two group t-test,I want to use one of  
>> these clusters to correlate thickness with behavior score. How to  
>> generate this mask and how to use this mask in the mri_glmfit and  
>> mri_glmfit-sim? 
> Do you mean you want to reduce the search space of a vertex-wise  
> analysis to a cluster or that you want to compute the mean thickness  
> within the cluster and correlate with your behavioral score? 
>> 2,If I want to draw ROI manually or set ROI according previous  
>> studies, how to create this ROI mask. 
> tksurfer can draw a label (as can freeview I think) 
> 
>> Any detailed information will be highly appreaciated. 
>> Thanks. 
>> All the best. 
>> Rujing Zha 
>> 
>> 
>> 
>> 
>> ___ 
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
> 
> 
> ___ 
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> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 
www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
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Re: [Freesurfer] mri_vol2surf --projopt

[Joerg Pfannmoeller]

Well, I need to use that option. In this case I will just interpolate to the 1 
mm grid and proceed this way. 


On Mon, 07 Apr 2014 12:14:47 -0400
Douglas N Greve  wrote:

> 
> Sorry, I don't understand. You mean it still segfaults without --projopt 
> or that you have to use projopt?
> 
> On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote:
> > Unfortunately that is no option for me.
> >
> >
> >
> > On Fri, 04 Apr 2014 15:33:47 -0400
> > Douglas N Greve  wrote:
> >
> >> Don't use --projopt and it won't segfault
> >>
> >> On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote:
> >>> The command is:
> >>>
> >>> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> >>> --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> >>> /.../f001_surf.nii --noreshape --cortex
> >>>
> >>> The output is the follwoing:
> >>>
> >>>
> >>> srcvol = /.../f001.nii
> >>> srcreg = /.../register.f001.dof6.dat
> >>> srcregold = 0
> >>> srcwarp unspecified
> >>> surf = white
> >>> hemi = rh
> >>> trgsubject = subjid
> >>> surfreg = sphere.reg
> >>> reshape = 0
> >>> interp = nearest
> >>> float2int = round
> >>> GetProjMax = 0
> >>> INFO: float2int code = 0
> >>> INFO: changing type to float
> >>> Done loading volume
> >>> Loading label /.../label/rh.cortex.label
> >>> Reading surface /.../surf/rh.white
> >>> Done reading source surface
> >>> Reading thickness /.../surf/rh.thickness
> >>> Done
> >>> Mapping Source Volume onto Source Subject Surface
> >>> reading gm volume fraction from /.../map001.gm.mgz
> >>> reading wm volume fraction from /.../map001.wm.mgz
> >>> reading csf volume fraction from /.../map001.csf.mgz
> >>> mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat 
> >>> --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o 
> >>> /.../f001_surf.nii --noreshape --cortex: Segmentation fault
> >>>
> >>> Do you have an idea about the cause of the error?
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, 02 Apr 2014 17:28:14 -0400
> >>> Douglas N Greve  wrote:
> >>>
>  what is your command line that is seg faulting? What is the terminal 
>  output?
> 
>  On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
> > Please help me with this issue:
> >
> > If I apply mri_surf2vol to a single volume of unprocessed epi-data, it
> > results in a segmentation fault. It works if I apply mri_vol2vol for
> > registration of epi and anatomy, but than an interpolation is
> > involved. I would like to avoid the interpolation and apply
> > mri_surf2vol directly to the unprocessed data in order to minimize the
> > number of interpolations.
> >
> >
> > At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
> >
> >   This is something BF added Sept 1 2009:
> >
> >   added --projopt  switch to do optimal linear estimation of gray 
> > matter
> >   values given a set of precomputed gray matter densities.
> >
> >   I don't know what it would mean beyond that
> >
> >   doug
> >
> >
> >   On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> >   > Hello,
> >   >
> >   > I found an option in mri_vol2surf for which I could not find a
> >   documentation. The option is called:
> >   >
> >   > --projopt
> >   >
> >   > It would be nice if somebody could give a description of this
> >   option.
> >   >
> >   > Respectfully yours
> >   >
> >   > pfannmoe
> >   >
> >   >
> >   > ___
> >   > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> >   www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >   Outgoing:
> >   ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> >   ___
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> > 
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> >
> >
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