Re: [Freesurfer] reg-feat2anat failure

[Douglas N Greve]

This file is created when you run reg-feat2anat and should be the one 
that gets changed with --manxfm func2anat. You can handle this 
differently if you

1. Manually edit the anat2exf.register.dat so that it is relatively 
close (no need to be perfect)
cd feat/reg/freesurfer
tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat 
--surfs

2. Run bbregister:
cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup
bbregister --mov ../../example_func.nii.gz --init-reg 
anat2exf.register.dat --reg anat2exf.register.dat --bold

this second step will fine-tune your hand-edited version. Then go back 
and run aparc2feat, etc.

doug



Michelle Umali wrote:
> Hi Doug,
> The file that changed was exf2std.register.dat.   How do I specify 
> that I wanted that anat2exf.register.dat is supposed to be edited? At 
> what point in the processing stream does this occur?
>
> Did editing exf2std.register.dat do anything?
>
> Thanks.
> Michelle
>
>
>
> On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> The registration that should be used for all of these is
> anat2exf.register.dat found in feat/reg/freesurfer. Can you verify
> that that was the one that you manually changed? Look at the time
> stamp as compared to the other files in that folder.
> doug
>
> Michelle Umali wrote:
>
> Hi Doug,
> I am using reg-feat2anat  on the feat directory of each run.
> reg-feat2anat --feat feadir.feat --subject XX
> Then I checked and adjusted the registration with:
> reg-feat2anat --feat featdir.feat --manual
> Next I checked and adjusted the registration to the standard with:
> reg-feat2anat --feat featdir.feat --manxfm func2std
>
> To generate cortical binary masks I used:
> aparc2feat --feat featdir.feat --annot BA
> fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10
> -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz
>
> To generate subcortical binary masks I did:
> aseg2feat --feat featdir.feat --aseg aparc+aseg
> fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz
> -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz
>
> When I looked at the masks in FSLview and checked the masks
> against the other atlases, everything was off even after
> painstakingly editing the registrations.
> Is there something I am doing wrong?
>
> Thanks.
> Michelle
>
>On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>How are you generating the masks?
>doug
>
>Michelle Umali wrote:
>
>Hi Freesurfers,
>I've run reg-feat2anat on several subjects in order to
>generate binary masks to use in an FSL ppi.
>For 3 subjects, this completely failed.
>
>When I looked at the fsl's own registration of fsl feat 2
>standard (via tkregister2), the registration is fine, but
>after running reg-feat2anat, the registration of the
> feat to
>the freesurfer anatomical and the feat to standard are
>completely off.
>
>I manually fixed and saved the registration edits via
>reg-feat2anat --manual, but when I generated the masks
> again,
>they were totally wrong still.
>When looking at freesurfer's feat to standard
> registration, it
>looks like all the brains weren't tall enough in the
> saggital
>view.  Am I supposed to stretch the feat brain to fit?
>
>How can I fix this so that the masks are accurate?
>
>Thanks.
>Michelle
>  
>  
> 
>
>___
>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
> 

[Freesurfer] problem with generating cesvar.nii

[SHAHIN NASR]

Hi,

 I have generated two different functional connectivity maps for two
different ROI-based seeds. These maps are based on group-average of the same
subjects (generated by using separate isxconcat-sess commands ), and now I
want to see the difference map. To do so, I used mris_calc as below.

> mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub   map2/rh.ces.nii

Also, to generate the rh.cesvar.nii file I used this command:

> mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii   sub
map2/rh.cesvar.nii

But then when I used the glmfit with WLS option as below:

> mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask
../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf
fsaverage rh --wls rh.cesvar.nii

 I faced an error saying: "Error: MRInormWeights: values less than or eq to
0" which I assumed is related to an error in rh.cesvar.nii file (am I
right?). Would you tell me how can I fix this problem?

P.S.: please note that sequence of subjects and all MRI parameters are
exactly the same between the two maps.

-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
___
Freesurfer mailing list
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
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.

Re: [Freesurfer] problem with generating cesvar.nii

[Douglas N Greve]

Hi Shahin, it is not as simple as doing a subtraction of the cesvar 
files. What you are trying to get is the expected variance of your 
difference between the ces files (as a variance, it must be positive). 
To get this you need

cesvardiff = (cesvar1+cesvar2)/(2^2)

The 2^2 is the number of inputs (2) squared.

doug

SHAHIN NASR wrote:
> Hi,
>
>  I have generated two different functional connectivity maps for two 
> different ROI-based seeds. These maps are based on group-average of 
> the same subjects (generated by using separate isxconcat-sess commands 
> ), and now I want to see the difference map. To do so, I used 
> mris_calc as below. 
>
> > mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub   
> map2/rh.ces.nii
>
> Also, to generate the rh.cesvar.nii file I used this command:
>  
> > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii   sub   
> map2/rh.cesvar.nii
>
> But then when I used the glmfit with WLS option as below:
>
> > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii 
> --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat 
> ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii
>
>  I faced an error saying: "Error: MRInormWeights: values less than or 
> eq to 0" which I assumed is related to an error in rh.cesvar.nii file 
> (am I right?). Would you tell me how can I fix this problem?
>
> P.S.: please note that sequence of subjects and all MRI parameters are 
> exactly the same between the two maps.
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>

-- 
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

___
Freesurfer mailing list
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
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.

Re: [Freesurfer] trac-all results

[Anastasia Yendiki]

Hi Ping - Do the corresponding brain masks in diffusion space 
(dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) 
now cover the entire brain well, after the aparc+aseg fixes?


a.y

On Tue, 18 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
problematic data and re-ran the trac-all following your suggestions.
However, the segmented forceps major using "FLIRT" still not getting
good result (see flt.png) though "BBR" one is OK (see bbr.png).
Similarly the segmented L CST using BBR looks weird, but the ones
using FLIRT seem OK.
It appear  the problems are not simply due to the poor segmentation
from the T1 recon-all.

Any further suggestions?

BR,
Ping

On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki
 wrote:


Hi Ping-Hong,

Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
will be extracted from the DWI data by the bet tool, instead of using the
aparc+aseg.

But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
tractography solutions, i.e. the aparc+aseg is where the UnderLying Anatomy
in TRACULA comes from. So the quality of the trac-all results depend on the
quality of the aparc+aseg regardless of where your mask came from.

a.y

On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

Can trac-all just use the mask in diffusion native space (by setting
"usemaskanat = 0"?  ) so I get around the T1 segmentation problem from
FS recon?

It seems that there is no quick answer on fixing the aparc+aseg?

Thank you,
p




On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki
 wrote:


I'll have to refer you back to the freesurfer list for that one. There
are
people with much more expertise than me on troubleshooting the recon-all
stream.

Once you get your recons fixed, you'll have to rerun all trac-all steps
except 1.1 (image corrections).

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


The original aparc+aseg are not good, at least for these two cases. So
which parameters in recon-all should be tweaked?

On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
 wrote:


Is the original aparc+aseg from the freesurfer recon not good either
(from
mri/aparc+aseg.mgz)? Or is it messed up only after registration into
diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the
freesurfer
recon needs to be fixed or if the registration needs to fixed.

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


yeap, the aparc+aseg_masks are not good.
Any way to fix this? Thanks.

On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
 wrote:


I see, the mask may be the answer to the initialization failures! It
seems
like the fmajor you sent me also has its endings masked out? That'd
cause
it
to fail. I wish I'd thought of this earlier!

With usemaskanat = 1, the mask that's used is a slightly dilated
version
of
the aparc+aseg from the FS recon, mapped to diffusion space. So if
the
aparc+aseg has those parts missing, or if the diffusion-anatomical
registration is not good, parts will be masked out that shouldn't.
The
anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if
you've
run
both flirt and bbregister registrations, there'll be 2 of them). Does
this
mask look like something went wrong?

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


I used the default, i.e. set usemaskanat =1, but it looks that
tracts
were not reconstructed at the place where it was masked out (see the
cross-bar at L_unc.png).

I still have no luck in fixing the initialization issue (see
fmajor.png for example).

Thanks.


On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
 wrote:


Hi Ping - If you're using the anatomical brain as a mask (set
usemaskanat
=
1, which is the default), then the diffusion-based mask won't have
an
effect
on your outputs.

BTW, have you had any luck with your initialization issues? Sorry I
haven't
had another chance to look at your data since we last emailed, I
got
bogged
down with some other stuff.

a.y

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I'd like to lower the bet threshold value by "set thrbet = 0.01"
for
skull-stripping because some of the brains have been cut, but it
does
not seem to  make any changes (see attached).

Any suggestion? Thank you,

Ping

On Fri, Sep 30, 2011 at 12:09 PM, Anastasia Yendiki
 wrote:


Yes! Please add the "set reinit = 1" to the file that you pass
with
-c.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


so I should pass with the -c argument instead?

On Fri, Sep 30, 2011 at 12:04 PM, Anastasia Yendiki
 wrote:


That file gets overwritten by whatever is in the file that you
pass
with
the
-c argument to trac-all. Sorry for the confusion.

On Fri, 30 Sep 2011, Ping-Hong Yeh wrote:


I edited the file under scripts/dmrirc.local

On Fri, Sep 30, 2011 at 12:00 PM, Anastasia Yendiki
 wrote:


Hi Ping - Thanks for trying that. When you say in the
dmrirc.local,
do
you
mean that you edit the file under scripts/dmrirc.

Re: [Freesurfer] problem with generating cesvar.nii

[SHAHIN NASR]

   Thanks Doug. Just one related question. Should I also generate a new
ffxdof.dat file for this map? I assumed that ffxdof depends on the number of
subjects (session) and since number of subjects (sessions) is the same
between the two groups then I can use those values, generated by
isxconcat-sess for either map1 or map2. Right?



On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve
wrote:

> Hi Shahin, it is not as simple as doing a subtraction of the cesvar files.
> What you are trying to get is the expected variance of your difference
> between the ces files (as a variance, it must be positive). To get this you
> need
>
> cesvardiff = (cesvar1+cesvar2)/(2^2)
>
> The 2^2 is the number of inputs (2) squared.
>
> doug
>
>
> SHAHIN NASR wrote:
>
>> Hi,
>>
>>  I have generated two different functional connectivity maps for two
>> different ROI-based seeds. These maps are based on group-average of the same
>> subjects (generated by using separate isxconcat-sess commands ), and now I
>> want to see the difference map. To do so, I used mris_calc as below.
>> > mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub
>> map2/rh.ces.nii
>>
>> Also, to generate the rh.cesvar.nii file I used this command:
>>  > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii   sub
>> map2/rh.cesvar.nii
>>
>> But then when I used the glmfit with WLS option as below:
>>
>> > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask
>> ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf
>> fsaverage rh --wls rh.cesvar.nii
>>
>>  I faced an error saying: "Error: MRInormWeights: values less than or eq
>> to 0" which I assumed is related to an error in rh.cesvar.nii file (am I
>> right?). Would you tell me how can I fix this problem?
>>
>> P.S.: please note that sequence of subjects and all MRI parameters are
>> exactly the same between the two maps.
>>
>> --
>> Shahin Nasr
>>
>> PhD in Cognitive Neuroscience
>> Martinos Imaging Center, MGH
>> Harvard Medical School
>>
>>
> --
> 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.
>
>


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
___
Freesurfer mailing list
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
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.

Re: [Freesurfer] problem with generating cesvar.nii

[Douglas N Greve]

It should be roughly the sum of the dofs of the individual subjects. Why 
are you using a fixed-effects model?
doug

SHAHIN NASR wrote:
>Thanks Doug. Just one related question. Should I also generate a 
> new ffxdof.dat file for this map? I assumed that ffxdof depends on the 
> number of subjects (session) and since number of subjects (sessions) 
> is the same between the two groups then I can use those values, 
> generated by isxconcat-sess for either map1 or map2. Right?
>
>
>
> On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Shahin, it is not as simple as doing a subtraction of the
> cesvar files. What you are trying to get is the expected variance
> of your difference between the ces files (as a variance, it must
> be positive). To get this you need
>
> cesvardiff = (cesvar1+cesvar2)/(2^2)
>
> The 2^2 is the number of inputs (2) squared.
>
> doug
>
>
> SHAHIN NASR wrote:
>
> Hi,
>
>  I have generated two different functional connectivity maps
> for two different ROI-based seeds. These maps are based on
> group-average of the same subjects (generated by using
> separate isxconcat-sess commands ), and now I want to see the
> difference map. To do so, I used mris_calc as below.
> > mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub  
> map2/rh.ces.nii
>
> Also, to generate the rh.cesvar.nii file I used this command:
>  > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii
>   sub   map2/rh.cesvar.nii
>
> But then when I used the glmfit with WLS option as below:
>
> > mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls
> --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii
> --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii
>
>  I faced an error saying: "Error: MRInormWeights: values less
> than or eq to 0" which I assumed is related to an error in
> rh.cesvar.nii file (am I right?). Would you tell me how can I
> fix this problem?
>
> P.S.: please note that sequence of subjects and all MRI
> parameters are exactly the same between the two maps.
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
> -- 
> 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.
>
>
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>

-- 
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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem with generating cesvar.nii

[SHAHIN NASR]

Do you suggest using random-effect model? Is there any problem with using a
fix-effect model (other than the fact that by using this model we can not
predict response of subjects outside our population)?

On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve
wrote:

>
> It should be roughly the sum of the dofs of the individual subjects. Why
> are you using a fixed-effects model?
> doug
>
> SHAHIN NASR wrote:
>
>>   Thanks Doug. Just one related question. Should I also generate a new
>> ffxdof.dat file for this map? I assumed that ffxdof depends on the number of
>> subjects (session) and since number of subjects (sessions) is the same
>> between the two groups then I can use those values, generated by
>> isxconcat-sess for either map1 or map2. Right?
>>
>>
>>
>> On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>>Hi Shahin, it is not as simple as doing a subtraction of the
>>cesvar files. What you are trying to get is the expected variance
>>of your difference between the ces files (as a variance, it must
>>be positive). To get this you need
>>
>>cesvardiff = (cesvar1+cesvar2)/(2^2)
>>
>>The 2^2 is the number of inputs (2) squared.
>>
>>doug
>>
>>
>>SHAHIN NASR wrote:
>>
>>Hi,
>>
>> I have generated two different functional connectivity maps
>>for two different ROI-based seeds. These maps are based on
>>group-average of the same subjects (generated by using
>>separate isxconcat-sess commands ), and now I want to see the
>>difference map. To do so, I used mris_calc as below.
>>> mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii   sub
>>  map2/rh.ces.nii
>>
>>Also, to generate the rh.cesvar.nii file I used this command:
>> > mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii
>>  sub   map2/rh.cesvar.nii
>>
>>But then when I used the glmfit with WLS option as below:
>>
>>> mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls
>>--nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii
>>--ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii
>>
>> I faced an error saying: "Error: MRInormWeights: values less
>>than or eq to 0" which I assumed is related to an error in
>>rh.cesvar.nii file (am I right?). Would you tell me how can I
>>fix this problem?
>>
>>P.S.: please note that sequence of subjects and all MRI
>>parameters are exactly the same between the two maps.
>>
>>-- Shahin Nasr
>>
>>PhD in Cognitive Neuroscience
>>Martinos Imaging Center, MGH
>>Harvard Medical School
>>
>>
>>-- 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.
>>
>>
>>
>>
>> --
>> Shahin Nasr
>>
>> PhD in Cognitive Neuroscience
>> Martinos Imaging Center, MGH
>> Harvard Medical School
>>
>>
> --
> 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
>
>


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
___
Freesurfer mailing list
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 Pa

Re: [Freesurfer] problem with generating cesvar.nii

[Douglas N Greve]

If you don't care about extending your results beyond your sample, then 
an FFx is fine.
doug

SHAHIN NASR wrote:
> Do you suggest using random-effect model? Is there any problem with 
> using a fix-effect model (other than the fact that by using this model 
> we can not predict response of subjects outside our population)? 
>
> On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> It should be roughly the sum of the dofs of the individual
> subjects. Why are you using a fixed-effects model?
> doug
>
> SHAHIN NASR wrote:
>
>   Thanks Doug. Just one related question. Should I also
> generate a new ffxdof.dat file for this map? I assumed that
> ffxdof depends on the number of subjects (session) and since
> number of subjects (sessions) is the same between the two
> groups then I can use those values, generated by
> isxconcat-sess for either map1 or map2. Right?
>
>
>
> On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>Hi Shahin, it is not as simple as doing a subtraction of the
>cesvar files. What you are trying to get is the expected
> variance
>of your difference between the ces files (as a variance, it
> must
>be positive). To get this you need
>
>cesvardiff = (cesvar1+cesvar2)/(2^2)
>
>The 2^2 is the number of inputs (2) squared.
>
>doug
>
>
>SHAHIN NASR wrote:
>
>Hi,
>
> I have generated two different functional connectivity
> maps
>for two different ROI-based seeds. These maps are based on
>group-average of the same subjects (generated by using
>separate isxconcat-sess commands ), and now I want to
> see the
>difference map. To do so, I used mris_calc as below.
>> mris_calc -o diff_map/rh.ces.nii   map1/rh.ces.nii  
> sub  map2/rh.ces.nii
>
>Also, to generate the rh.cesvar.nii file I used this
> command:
> > mris_calc -o diff_map1/rh.cesvar.nii  
>  map1/rh.cesvar.nii
>  sub   map2/rh.cesvar.nii
>
>But then when I used the glmfit with WLS option as below:
>
>> mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls
>--nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii
>--ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls
> rh.cesvar.nii
>
> I faced an error saying: "Error: MRInormWeights:
> values less
>than or eq to 0" which I assumed is related to an error in
>rh.cesvar.nii file (am I right?). Would you tell me how
> can I
>fix this problem?
>
>P.S.: please note that sequence of subjects and all MRI
>parameters are exactly the same between the two maps.
>
>-- Shahin Nasr
>
>PhD in Cognitive Neuroscience
>Martinos Imaging Center, MGH
>Harvard Medical School
>
>
>-- 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.
>
>
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 

Re: [Freesurfer] trac-all results

[Ping-Hong Yeh]

The mask sort of covers the whole brain (see attached). It may be due
to the display thresholding, when I viewed the path.pd.nii.gz using
fslview, the tract actually has been recovered as compared to the
previous one (old_path.png).

However, the path.pd still does seem normal, i.e. with quite a few
extraordinary high intensity (probability, yellow)?

Thanks.

ping

On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki
 wrote:
>
> Hi Ping - Do the corresponding brain masks in diffusion space
> (dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now
> cover the entire brain well, after the aparc+aseg fixes?
>
> a.y
>
> On Tue, 18 Oct 2011, Ping-Hong Yeh wrote:
>
>> Hi Anastasia,
>>
>> I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
>> problematic data and re-ran the trac-all following your suggestions.
>> However, the segmented forceps major using "FLIRT" still not getting
>> good result (see flt.png) though "BBR" one is OK (see bbr.png).
>> Similarly the segmented L CST using BBR looks weird, but the ones
>> using FLIRT seem OK.
>> It appear  the problems are not simply due to the poor segmentation
>> from the T1 recon-all.
>>
>> Any further suggestions?
>>
>> BR,
>> Ping
>>
>> On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki
>>  wrote:
>>>
>>> Hi Ping-Hong,
>>>
>>> Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
>>> will be extracted from the DWI data by the bet tool, instead of using the
>>> aparc+aseg.
>>>
>>> But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
>>> tractography solutions, i.e. the aparc+aseg is where the UnderLying
>>> Anatomy
>>> in TRACULA comes from. So the quality of the trac-all results depend on
>>> the
>>> quality of the aparc+aseg regardless of where your mask came from.
>>>
>>> a.y
>>>
>>> On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:
>>>
 Hi Anastasia,

 Can trac-all just use the mask in diffusion native space (by setting
 "usemaskanat = 0"?  ) so I get around the T1 segmentation problem from
 FS recon?

 It seems that there is no quick answer on fixing the aparc+aseg?

 Thank you,
 p




 On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki
  wrote:
>
> I'll have to refer you back to the freesurfer list for that one. There
> are
> people with much more expertise than me on troubleshooting the
> recon-all
> stream.
>
> Once you get your recons fixed, you'll have to rerun all trac-all steps
> except 1.1 (image corrections).
>
> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:
>
>> The original aparc+aseg are not good, at least for these two cases. So
>> which parameters in recon-all should be tweaked?
>>
>> On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
>>  wrote:
>>>
>>> Is the original aparc+aseg from the freesurfer recon not good either
>>> (from
>>> mri/aparc+aseg.mgz)? Or is it messed up only after registration into
>>> diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
>>> dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the
>>> freesurfer
>>> recon needs to be fixed or if the registration needs to fixed.
>>>
>>> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:
>>>
 yeap, the aparc+aseg_masks are not good.
 Any way to fix this? Thanks.

 On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
  wrote:
>
> I see, the mask may be the answer to the initialization failures!
> It
> seems
> like the fmajor you sent me also has its endings masked out? That'd
> cause
> it
> to fail. I wish I'd thought of this earlier!
>
> With usemaskanat = 1, the mask that's used is a slightly dilated
> version
> of
> the aparc+aseg from the FS recon, mapped to diffusion space. So if
> the
> aparc+aseg has those parts missing, or if the diffusion-anatomical
> registration is not good, parts will be masked out that shouldn't.
> The
> anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if
> you've
> run
> both flirt and bbregister registrations, there'll be 2 of them).
> Does
> this
> mask look like something went wrong?
>
> On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:
>
>> I used the default, i.e. set usemaskanat =1, but it looks that
>> tracts
>> were not reconstructed at the place where it was masked out (see
>> the
>> cross-bar at L_unc.png).
>>
>> I still have no luck in fixing the initialization issue (see
>> fmajor.png for example).
>>
>> Thanks.
>>
>>
>> On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
>>  wrote:
>>>
>>> Hi Ping - If you're using the anatomical b

[Freesurfer] FreeSurfer Questions

[Christopher McCarthy]

Dear FreeSurfer Gurus,

We are looking for a way to normalize the intensity histogram for our
subjects.  In the past we have used Brain Image Java, using FSL-Fast
inhomogeneity corrections.  Unfortunately we are unable to open the output
files (.img, .hdr) in FreeSurfer.  When trying to import the files (after
converting them to nii) we get a talaraich error:

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)

here is the mri_info for a subject we get this error with:

Volume information for S029_nii
  type: nii
dimensions: 256 x 256 x 100
   voxel sizes: 0.9375, 0.9375, 1.5000
  type: SHORT (4)
   fov: 240.000
   dof: 0
xstart: -120.0, xend: 120.0
ystart: -120.0, yend: 120.0
zstart: -75.0, zend: 75.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   1., z_a =   0., c_a =
0.
  : x_s =   0., y_s =   0., z_s =   1., c_s =
0.
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -0.9375   0.   0.   120.
0.   0.9375   0.  -120.
0.   0.   1.5000   -75.
0.   0.   0. 1.

voxel-to-ras determinant -1.31836

ras to voxel transform:
   -1.0667   0.   0.   128.
   -0.   1.0667  -0.   128.
   -0.  -0.   0.666750.
0.   0.   0. 1.

We are either looking to get the files we currently have to import correctly
in FreeSurfer, or import our DICOM files into a program and normalize the
intensity histogram and output a file freesurfer can read.  We are looking
to get rid of hyper intensities in the temporal and frontal lobes that cause
main and pial surface errors.

Thanks for whatever help you can give, now and in the future.

Chris McCarthy
___
Freesurfer mailing list
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
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.

Re: [Freesurfer] FreeSurfer Questions

[Bruce Fischl]

Hi Christopher

try outputing nifti from FSL instead of analyze and see if that helps. 
Don't go through analyze at all.


cheers,
Bruce


On Wed, 19 Oct 2011, 
Christopher McCarthy wrote:



Dear FreeSurfer Gurus,

We are looking for a way to normalize the intensity histogram for our
subjects.  In the past we have used Brain Image Java, using FSL-Fast
inhomogeneity corrections.  Unfortunately we are unable to open the output
files (.img, .hdr) in FreeSurfer.  When trying to import the files (after
converting them to nii) we get a talaraich error:

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. < threshold=0.0050)

here is the mri_info for a subject we get this error with:

Volume information for S029_nii
  type: nii
    dimensions: 256 x 256 x 100
   voxel sizes: 0.9375, 0.9375, 1.5000
  type: SHORT (4)
   fov: 240.000
   dof: 0
    xstart: -120.0, xend: 120.0
    ystart: -120.0, yend: 120.0
    zstart: -75.0, zend: 75.0
    TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.
  : x_a =   0., y_a =   1., z_a =   0., c_a =
0.
  : x_s =   0., y_s =   0., z_s =   1., c_s =
0.
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -0.9375   0.   0.   120.
    0.   0.9375   0.  -120.
    0.   0.   1.5000   -75.
    0.   0.   0. 1.

voxel-to-ras determinant -1.31836

ras to voxel transform:
   -1.0667   0.   0.   128.
   -0.   1.0667  -0.   128.
   -0.  -0.   0.6667    50.
    0.   0.   0. 1.

We are either looking to get the files we currently have to import correctly
in FreeSurfer, or import our DICOM files into a program and normalize the
intensity histogram and output a file freesurfer can read.  We are looking
to get rid of hyper intensities in the temporal and frontal lobes that cause
main and pial surface errors.

Thanks for whatever help you can give, now and in the future.

Chris McCarthy







___
Freesurfer mailing list
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
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.

Re: [Freesurfer] trac-all results

[Anastasia Yendiki]

Glad things are moving in the right direction. Now it looks like maybe one 
of the control points of the path is not moving around, which is why you 
get that very bright thin spot in the distribution. I can't tell by 
looking at that one slice of the mask only, but could it be that there 
voxels missing from the mask around there? If so you could fill them in 
and try again. You can also overlay the path.pd on the FA map and check if 
that part is off the white matter or on its edge.


On Wed, 19 Oct 2011, Ping-Hong Yeh wrote:


The mask sort of covers the whole brain (see attached). It may be due
to the display thresholding, when I viewed the path.pd.nii.gz using
fslview, the tract actually has been recovered as compared to the
previous one (old_path.png).

However, the path.pd still does seem normal, i.e. with quite a few
extraordinary high intensity (probability, yellow)?

Thanks.

ping

On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki
 wrote:


Hi Ping - Do the corresponding brain masks in diffusion space
(dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now
cover the entire brain well, after the aparc+aseg fixes?

a.y

On Tue, 18 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

I got fixed of the aparc+aseg (see aparc+aseg.png) in one of
problematic data and re-ran the trac-all following your suggestions.
However, the segmented forceps major using "FLIRT" still not getting
good result (see flt.png) though "BBR" one is OK (see bbr.png).
Similarly the segmented L CST using BBR looks weird, but the ones
using FLIRT seem OK.
It appear  the problems are not simply due to the poor segmentation
from the T1 recon-all.

Any further suggestions?

BR,
Ping

On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki
 wrote:


Hi Ping-Hong,

Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask
will be extracted from the DWI data by the bet tool, instead of using the
aparc+aseg.

But, and this is a big but, TRACULA uses the aparc+aseg to constrain the
tractography solutions, i.e. the aparc+aseg is where the UnderLying
Anatomy
in TRACULA comes from. So the quality of the trac-all results depend on
the
quality of the aparc+aseg regardless of where your mask came from.

a.y

On Fri, 14 Oct 2011, Ping-Hong Yeh wrote:


Hi Anastasia,

Can trac-all just use the mask in diffusion native space (by setting
"usemaskanat = 0"?  ) so I get around the T1 segmentation problem from
FS recon?

It seems that there is no quick answer on fixing the aparc+aseg?

Thank you,
p




On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki
 wrote:


I'll have to refer you back to the freesurfer list for that one. There
are
people with much more expertise than me on troubleshooting the
recon-all
stream.

Once you get your recons fixed, you'll have to rerun all trac-all steps
except 1.1 (image corrections).

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


The original aparc+aseg are not good, at least for these two cases. So
which parameters in recon-all should be tweaked?

On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki
 wrote:


Is the original aparc+aseg from the freesurfer recon not good either
(from
mri/aparc+aseg.mgz)? Or is it messed up only after registration into
diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz,
dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the
freesurfer
recon needs to be fixed or if the registration needs to fixed.

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


yeap, the aparc+aseg_masks are not good.
Any way to fix this? Thanks.

On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki
 wrote:


I see, the mask may be the answer to the initialization failures!
It
seems
like the fmajor you sent me also has its endings masked out? That'd
cause
it
to fail. I wish I'd thought of this earlier!

With usemaskanat = 1, the mask that's used is a slightly dilated
version
of
the aparc+aseg from the FS recon, mapped to diffusion space. So if
the
aparc+aseg has those parts missing, or if the diffusion-anatomical
registration is not good, parts will be masked out that shouldn't.
The
anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if
you've
run
both flirt and bbregister registrations, there'll be 2 of them).
Does
this
mask look like something went wrong?

On Tue, 11 Oct 2011, Ping-Hong Yeh wrote:


I used the default, i.e. set usemaskanat =1, but it looks that
tracts
were not reconstructed at the place where it was masked out (see
the
cross-bar at L_unc.png).

I still have no luck in fixing the initialization issue (see
fmajor.png for example).

Thanks.


On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki
 wrote:


Hi Ping - If you're using the anatomical brain as a mask (set
usemaskanat
=
1, which is the default), then the diffusion-based mask won't
have
an
effect
on your outputs.

BTW, have you had any luck with your initialization issues? Sorry
I
haven't
had another chance to look at your data since we last emailed, I
got
bogged
down with some other stuff.

a.y

On Tue, 1

Re: [Freesurfer] Group Average of Retinotopy Results

[Douglas N Greve]

Hi Michelle, try this:

isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup
cd retgroup/rtopy.fsaverage.lh

mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface 
fsaverage lh
mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface 
fsaverage lh
mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface 
fsaverage lh
mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface 
fsaverage lh

mri_fieldsign --fs lh.fieldsign.mgh \
  --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \
  --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \
  --s fsaverage --hemi lh --sphere --old

tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5



Michelle Umali wrote:
> Hi Doug and the Freesurfers,
> Thanks for your help.  I have 2 questions.:
>
> 1) I did the retinotopy analysis on the fsaverage surface as you 
> suggested below and then ran isxconcat-sess for my eccen and polar data:
>e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar 
> -sf sessid -o group_polar_lh
> but how do you do this for the fieldsign analysis, since the 
> cess.nii and other files don't exist?
>
> 2) So when trying to run a group mri_glmfit on the polar and eccen 
> maps with:
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface 
> fsaverage lh --glmdir group_eccen_lh.wls --nii.gz
>
> I got an error, because I have two ces.nii.gz and cesvar.nii.gz files 
> each.  I am not sure how this happened.  I only have one run each of 
> polar and wedge data.  What may have generated these two files and 
> which one do I use?
>
>
> Thanks.
> Michelle
>
>
> On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> When you run preproc-sess use -surface fsaverage lhrh instead of
> -surface self lhrh. Then create a new analysis with the same
> parameters, except use -surface fsaverage lh instead of -surface
> self lh.
> doug
>
> Michelle Umali wrote:
>
> Hi Doug,
> I'm a little confused as to how to assign functional data to
> the fsaverage space.
> 1) Do you mean just change each subject's subjectname file to
> fsaverage and then do the same thing as before for each person?
> 2) Also, when I specify the analysis do I change
> -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later
> be sensitive to analysis name?
>
> e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
> -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
> -force
>
> then the same for selxavg3-sess and fieldsign-sess
>
> and then isxconcat-sess would be:
> isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh
>
>
> Thanks.
> Michelle
>
> On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>If you want to combine across subjects, then you need to
> run the
>analysis on fsaverage (ie, rerun preproc-sess, create a new
>analysis, run selxavg3-sess, and then isxconcat-sess).
>doug
>
>Michelle Umali wrote:
>
>Dear Freesurfers,
>I've generated individual polar, eccentricity, and
> fieldsign
>maps for each of my subjects. I would like to generate
> group
>average maps of these that I can visualize on the
> fsaverage brain.
>
>When I ran:
>isxconcat-sess -sf sessid -analysis rtopy.self.lh -o
> group_lh
>
>I got:
>ERROR: analysis space is self surface, not supported
>
>How do I do a group average for the 3 different maps?
>
>Thanks.
>Michelle
>
>For each person I ran recon-all and flattened occipital
> patches.
>Then:
>mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
>-retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0
> -fsd bold
>-force
> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2
>-retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0
> -fsd bold
>-force
>
>preproc-sess -surface self lhrh -fwhm 5 -per-run -s
> sjXX -fsd
>bold -force
>
>selxavg3-sess -a rtopy.self.lh -s sjXX -force
>selxavg3-sess -a rtopy.self.rh -s sjXX -force
>
>fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX
>fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX
>
>  
>  
> --

Re: [Freesurfer] Group Average of Retinotopy Results

[Michelle Umali]

Hi Doug,
Thank you for your help with this.  So when I looked at the maps, two issues
arose.

1) The fieldsign map looks like it needs lots of smoothing.  When I ran the
individual subjects on the surface, I smoothed by 20 during fieldsign-sess.
Is it still appropriate/can one smooth at the mri_fieldsign step below?

2)Results ended up on the lateral side and way anterior from the occipital
lobe. Do I perform a separate registration between the individual subject
and fsaverage somewhere along the line?  Is this because I ran the
individual subject analyses on a flattened fsaverage occipital patch and not
on lh.sphere?

Thanks!
Michelle

On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali  wrote:

> Hi Doug,
> Two problems happened (I'm attaching a picture).
> 1) The fieldsign map looks like it needs lots of smoothing.  When I ran the
> individual subjects on the surface, I smoothed by 20 during fieldsign-sess.
> Is it still appropriate/can one smooth at the mri_fieldsign step below?
>
> 2)Results ended up on the lateral side and way anterior from the occipital
> lobe. Do I perform a separate registration between the individual subject
> and fsaverage somewhere along the line?  Is this because I ran the
> individual subject analyses on a flattened fsaverage occipital patch and not
> on lh.sphere?
>
> Thanks!
> Michelle
>
>
> On Wed, Oct 19, 2011 at 5:30 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Michelle, try this:
>>
>> isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup
>> cd retgroup/rtopy.fsaverage.lh
>>
>> mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface
>> fsaverage lh
>> mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface
>> fsaverage lh
>> mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface
>> fsaverage lh
>> mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface
>> fsaverage lh
>>
>> mri_fieldsign --fs lh.fieldsign.mgh \
>>  --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \
>>  --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \
>>  --s fsaverage --hemi lh --sphere --old
>>
>> tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5
>>
>>
>>
>> Michelle Umali wrote:
>>
>>> Hi Doug and the Freesurfers,
>>> Thanks for your help.  I have 2 questions.:
>>>
>>> 1) I did the retinotopy analysis on the fsaverage surface as you
>>> suggested below and then ran isxconcat-sess for my eccen and polar data:
>>>   e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf
>>> sessid -o group_polar_lh
>>>but how do you do this for the fieldsign analysis, since the cess.nii
>>> and other files don't exist?
>>>
>>> 2) So when trying to run a group mri_glmfit on the polar and eccen maps
>>> with:
>>> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage
>>> lh --glmdir group_eccen_lh.wls --nii.gz
>>>
>>> I got an error, because I have two ces.nii.gz and cesvar.nii.gz files
>>> each.  I am not sure how this happened.  I only have one run each of polar
>>> and wedge data.  What may have generated these two files and which one do I
>>> use?
>>>
>>>
>>> Thanks.
>>> Michelle
>>>
>>>
>>> On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu 
>>> >
>>> wrote:
>>>
>>>When you run preproc-sess use -surface fsaverage lhrh instead of
>>>-surface self lhrh. Then create a new analysis with the same
>>>parameters, except use -surface fsaverage lh instead of -surface
>>>self lh.
>>>doug
>>>
>>>Michelle Umali wrote:
>>>
>>>Hi Doug,
>>>I'm a little confused as to how to assign functional data to
>>>the fsaverage space.
>>>1) Do you mean just change each subject's subjectname file to
>>>fsaverage and then do the same thing as before for each person?
>>>2) Also, when I specify the analysis do I change
>>>-rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later
>>>be sensitive to analysis name?
>>>
>>>e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2
>>>-retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold
>>>-force
>>>
>>>then the same for selxavg3-sess and fieldsign-sess
>>>
>>>and then isxconcat-sess would be:
>>>isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh
>>>
>>>
>>>Thanks.
>>>Michelle
>>>
>>>On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve
>>>>> >> >
>>> >>
>>>>>
>>> wrote:
>>>
>>>   If you want to combine across subjects, then you need to
>>>run the
>>>   analysis on fsaverage (ie, rerun preproc-sess, create a new
>>>   analysis, run selxavg3-sess, and then isxconcat-sess).
>>>   doug
>>>
>>

[Freesurfer] Subcortical segmentation atlas

[cloud . ctrl]

Hello,

I am working on comparing hand-drawn subcortical volumes to those output 
automatically by FreeSurfer.  While reading about the segmentation process on 
the wiki, I came across this line: 

"The final segmentation is based on both a subject-independent probabilistic 
atlas and subject-specific measured values. The atlas is built from a training 
set, i.e., a set of subjects whose brains (surfaces or volumes) have been 
labeled by hand. These labels are then mapped into a common space (Talairach 
space for volumes..."   
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview)



Because of the way we decided to delineate our ROI, we need to compare the 
shapes we defined in AFNI to those defined by this training set and output by 
FreeSurfer.  I've been looking for more information about this probabilistic 
atlas, but I cannot find any more information about it.  The only thing I found 
was the last line of this thread from the mail archives:  



Am 23.08.2011 um 04:03 schrieb Anthony Dick:



> The subcortical segmentation identifies subcortical structures such as 

> thalamus, basal ganglia structures, hippocampus, amygdala, and 

> cerebellum. The cortical parcellation delineates different areas of the 

> cortex, such as the superior temporal sulcus, the central sulcus, the 

> pars triangularis, opercularis, and orbitalis of the inferior frontal 

> gyrus. A recommendation is to get a copy of the Duvernoy atlas, which 

> covers definitions of different parts of the cortex. The Mai atlas is 

> good for learning subcortical structures. 



Was the Mai atlas used to create the define the structures in the training set? 
 Could you provide me with any more information regarding the training set?
___
Freesurfer mailing list
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
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.

Re: [Freesurfer] Subcortical segmentation atlas

[Bruce Fischl]

no, we created our own atlas by manually labeling 39 subjects according 
to the CMA conventions, then iteratively going back over them to correct 
for consistent inaccuracies in the manual labelings. It's still an ongoing 
process as we are currently working on improving the manual putamen labels.


cheers
Bruce


On Wed, 19 Oct 2011, cloud.c...@me.com wrote:


Hello,

I am working on comparing hand-drawn subcortical volumes to those output
automatically by FreeSurfer.  While reading about the segmentation process
on the wiki, I came across this line: 

"The final segmentation is based on both a subject-independent probabilistic
atlas and subject-specific measured values. The atlas is built from a
training set, i.e., a set of subjects whose brains (surfaces or volumes)
have been labeled by hand. These labels are then mapped into a common space
(Talairach space for volumes..."  
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOvervie
w)


Because of the way we decided to delineate our ROI, we need to compare the
shapes we defined in AFNI to those defined by this training set and output
by FreeSurfer.  I've been looking for more information about this
probabilistic atlas, but I cannot find any more information about it.  The
only thing I found was the last line of this thread from the mail archives:
 


Am 23.08.2011 um 04:03 schrieb Anthony Dick:


> The subcortical segmentation identifies subcortical structures such as 

> thalamus, basal ganglia structures, hippocampus, amygdala, and 

> cerebellum. The cortical parcellation delineates different areas of the 

> cortex, such as the superior temporal sulcus, the central sulcus, the 

> pars triangularis, opercularis, and orbitalis of the inferior frontal 

> gyrus. A recommendation is to get a copy of the Duvernoy atlas, which 

> covers definitions of different parts of the cortex. The Mai atlas is 

> good for learning subcortical structures. 


Was the Mai atlas used to create the define the structures in the training
set?  Could you provide me with any more information regarding the training
set?


___
Freesurfer mailing list
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
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.