[Freesurfer] longitudinal study in counterbalance design

[lordowen]

Hi all:

We performed a thickness change study which related to the menstrual
cycle. We scanned subjects during different menstrual phases in a
counterbalance manner. Thus when we conduct a longitudinal analysis,
we need to set time point according to the actual scanning order
(i.e., 1st scan as Tp1 and so on) or according to the phase (i.e.,
menstruation phase as Tp1 and other phase as TpN)?

Thanks for your suggestion.

-- 
Best regards
--
杜政昊

Cheng-Hao Tu, PhD
Post Doctoral Research Fellow
Integrated Brain Research Unit
Department of Medical Research and Education
Taipei Veterans General Hospital
No.201, Sect.2, Shih-Pai Rd.
Taipei
Taiwan
Email: lordo...@ms10.hinet.net or lordowe...@gmail.com
Tel: +886-2-28712121 ext 3474
Fax: +886-2-28745182

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Re: [Freesurfer] problems with analysis after using fslmaths

[Caspar M. Schwiedrzik]

Hi,
is it possible that it is a data format problem? I tried forcing fslmaths
to give float output using -odt float. This changed mostly the
autocorrelations computed during selxavg, but not the pcc.
Caspar


2012/5/7 Caspar M. Schwiedrzik 

> the cutoff frequencies are 0.0025 Hz and 0.25 Hz.
> Caspar
>
> 2012/5/7 Douglas N Greve 
>
>> The mkanalysis command looks ok. I don't know how to interpret those
>> numbers for fslmaths. What are the cutoff frequencies?
>> doug
>>
>>
>> On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote:
>>
>>> Hi Doug,
>>> I use the following command for fslmaths
>>> fslmaths fmc.nii -bptf 200 2 fmcfilt.nii
>>>
>>> where 200*(TR+2) is 400s, and 2*(TR=2)=4s.
>>>
>>> and for mkanalysis-sess
>>> -force
>>> -fsd bold
>>> -funcstem fmcfilt
>>> -analysis name
>>> -notask
>>> -tr 2
>>> -runlistfile name
>>> -native
>>> -nskip 5
>>> -mask brain
>>> -tpef name
>>> -taskreg name
>>>
>>> for debugging, I did not include nuisance regressors.
>>> Caspar
>>>
>>>
>>> 2012/5/7 Douglas N Greve >> gr...@nmr.mgh.harvard.**edu >>
>>>
>>>
>>>What frequencies did you chose for the FSL bandpass filter? What
>>>is you mkanalysis-sess command?
>>>
>>>
>>>On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
>>>
>>>yes
>>>
>>>2012/5/7 Douglas N Greve >>
>>>>>>> >>>
>>>
>>>
>>>   Did you regenerate the seeds after filtering?
>>>
>>>
>>>   On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
>>>
>>>   I have tried analyses with only one seed time course
>>>(either 1
>>>   voxel, mean of a sphere of 1 voxel radius, or mean of a
>>>   functionally defined roi), as well as several seeds
>>>within the
>>>   same design matrix, with the same problem.
>>>   All of these analyses did yield higher pcc when done
>>>without
>>>   filtering.
>>>   Caspar
>>>
>>>   2012/5/7 Douglas N Greve >>
>>>>>>
>>>**.
>>> edu
>>>
>>>
>>>>>>> 
>>>
>>>
>>>  Is this doing all of those seeds simultaneously or
>>>one seed
>>>   at a time?
>>>
>>>  On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
>>>> Hi,
>>>> I am trying to use fslmaths to filter my data before I plug it
>>>  into a
>>>> resting state analysis. However, once I obtain a pcc map, all
>>>> correlation coefficients are <0.1, even the autocorrelation
>>>   with the
>>>> seed voxel.
>>>> The data look fine when I open them in Matlab using MRIread; the
>>>> correlations between individual voxel time courses obtained in
>>>  Matlab
>>>> is about 0.6.
>>>>
>>>> My analysis stream is as follows:
>>>> a) I filter the data using "fslmaths input -bptf highpass
>>>   lowpass
>>>> output"; from this I obtain a filtered nii.gz file
>>>> b) I extract a seed timecourse from the filtered data in Matlab
>>>> c) I run mkanalysis-sess with -notask
>>>> d) I run selxavg3-sess
>>>> e) I overlay the pcc.nii
>>>>
>>>> I have tried this with smoothed and unsmoothed data, with and
>>>  without
>>>> nuisance regressors, with different seeds, with mri_convert
>>>  after step
>>>> a. It is not a problem with the overlay since the max values
>>>   in pcc
>>>> are all <0.1.
>>>> I noticed that there are some differences in the nifti header
>>>  (as read
>>>> with MRIread) before and after filtering, but it seemed to
>>>   me that
>>>> they are gone after I used mri_convert.
>>>> I do find much higher correlations with unfiltered data.
>>>> Any advice what could be going wrong here? I am using
>>>   Freesurfer 5.1
>>>> and FSL 4.1.9 on Linux.
>>>> Thanks, Caspar
>>>>
>>>>
>>>>
>>>> __ _
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>
>>> >> >
>>>>>
>>> >> >>
>>>.
>>>harvard.edu 
>>>
>>>>>
>>> 

Re: [Freesurfer] problems with analysis after using fslmaths

[Caspar M. Schwiedrzik]

the cutoff frequencies are 0.0025 Hz and 0.25 Hz.
Caspar

2012/5/7 Douglas N Greve 

> The mkanalysis command looks ok. I don't know how to interpret those
> numbers for fslmaths. What are the cutoff frequencies?
> doug
>
>
> On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>> I use the following command for fslmaths
>> fslmaths fmc.nii -bptf 200 2 fmcfilt.nii
>>
>> where 200*(TR+2) is 400s, and 2*(TR=2)=4s.
>>
>> and for mkanalysis-sess
>> -force
>> -fsd bold
>> -funcstem fmcfilt
>> -analysis name
>> -notask
>> -tr 2
>> -runlistfile name
>> -native
>> -nskip 5
>> -mask brain
>> -tpef name
>> -taskreg name
>>
>> for debugging, I did not include nuisance regressors.
>> Caspar
>>
>>
>> 2012/5/7 Douglas N Greve > gr...@nmr.mgh.harvard.**edu >>
>>
>>
>>What frequencies did you chose for the FSL bandpass filter? What
>>is you mkanalysis-sess command?
>>
>>
>>On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
>>
>>yes
>>
>>2012/5/7 Douglas N Greve >
>>>>>
>>
>>
>>   Did you regenerate the seeds after filtering?
>>
>>
>>   On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
>>
>>   I have tried analyses with only one seed time course
>>(either 1
>>   voxel, mean of a sphere of 1 voxel radius, or mean of a
>>   functionally defined roi), as well as several seeds
>>within the
>>   same design matrix, with the same problem.
>>   All of these analyses did yield higher pcc when done
>>without
>>   filtering.
>>   Caspar
>>
>>   2012/5/7 Douglas N Greve >
>>>>
>>**.
>> edu
>>
>>
>>>> 
>>
>>
>>  Is this doing all of those seeds simultaneously or
>>one seed
>>   at a time?
>>
>>  On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
>>> Hi,
>>> I am trying to use fslmaths to filter my data before I plug it
>>  into a
>>> resting state analysis. However, once I obtain a pcc map, all
>>> correlation coefficients are <0.1, even the autocorrelation
>>   with the
>>> seed voxel.
>>> The data look fine when I open them in Matlab using MRIread; the
>>> correlations between individual voxel time courses obtained in
>>  Matlab
>>> is about 0.6.
>>>
>>> My analysis stream is as follows:
>>> a) I filter the data using "fslmaths input -bptf highpass
>>   lowpass
>>> output"; from this I obtain a filtered nii.gz file
>>> b) I extract a seed timecourse from the filtered data in Matlab
>>> c) I run mkanalysis-sess with -notask
>>> d) I run selxavg3-sess
>>> e) I overlay the pcc.nii
>>>
>>> I have tried this with smoothed and unsmoothed data, with and
>>  without
>>> nuisance regressors, with different seeds, with mri_convert
>>  after step
>>> a. It is not a problem with the overlay since the max values
>>   in pcc
>>> are all <0.1.
>>> I noticed that there are some differences in the nifti header
>>  (as read
>>> with MRIread) before and after filtering, but it seemed to
>>   me that
>>> they are gone after I used mri_convert.
>>> I do find much higher correlations with unfiltered data.
>>> Any advice what could be going wrong here? I am using
>>   Freesurfer 5.1
>>> and FSL 4.1.9 on Linux.
>>> Thanks, Caspar
>>>
>>>
>>>
>>> __ _
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>
>> > >
>>>
>> > >>
>>.
>>harvard.edu 
>>
>>>
>> > >>>
>>
>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/
>>   freesurfer
>>
>>>freesurfer
>>
>> 
>> >>
>>
>>  --
>>

Re: [Freesurfer] problems with analysis after using fslmaths

[Douglas N Greve]

The mkanalysis command looks ok. I don't know how to interpret those 
numbers for fslmaths. What are the cutoff frequencies?
doug

On 05/07/2012 03:25 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I use the following command for fslmaths
> fslmaths fmc.nii -bptf 200 2 fmcfilt.nii
>
> where 200*(TR+2) is 400s, and 2*(TR=2)=4s.
>
> and for mkanalysis-sess
> -force
> -fsd bold
> -funcstem fmcfilt
> -analysis name
> -notask
> -tr 2
> -runlistfile name
> -native
> -nskip 5
> -mask brain
> -tpef name
> -taskreg name
>
> for debugging, I did not include nuisance regressors.
> Caspar
>
>
> 2012/5/7 Douglas N Greve  >
>
> What frequencies did you chose for the FSL bandpass filter? What
> is you mkanalysis-sess command?
>
>
> On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
>
> yes
>
> 2012/5/7 Douglas N Greve  
>  >>
>
>
>Did you regenerate the seeds after filtering?
>
>
>On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
>
>I have tried analyses with only one seed time course
> (either 1
>voxel, mean of a sphere of 1 voxel radius, or mean of a
>functionally defined roi), as well as several seeds
> within the
>same design matrix, with the same problem.
>All of these analyses did yield higher pcc when done
> without
>filtering.
>Caspar
>
>2012/5/7 Douglas N Greve  
>  >
> . edu
>
>  
>
>   Is this doing all of those seeds simultaneously or
> one seed
>at a time?
>
>   On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
> > Hi,
> > I am trying to use fslmaths to filter my data before I plug it
>   into a
> > resting state analysis. However, once I obtain a pcc map, all
> > correlation coefficients are <0.1, even the autocorrelation
>with the
> > seed voxel.
> > The data look fine when I open them in Matlab using MRIread; the
> > correlations between individual voxel time courses obtained in
>   Matlab
> > is about 0.6.
> >
> > My analysis stream is as follows:
> > a) I filter the data using "fslmaths input -bptf highpass
>lowpass
> > output"; from this I obtain a filtered nii.gz file
> > b) I extract a seed timecourse from the filtered data in Matlab
> > c) I run mkanalysis-sess with -notask
> > d) I run selxavg3-sess
> > e) I overlay the pcc.nii
> >
> > I have tried this with smoothed and unsmoothed data, with and
>   without
> > nuisance regressors, with different seeds, with mri_convert
>   after step
> > a. It is not a problem with the overlay since the max values
>in pcc
> > are all <0.1.
> > I noticed that there are some differences in the nifti header
>   (as read
> > with MRIread) before and after filtering, but it seemed to
>me that
> > they are gone after I used mri_convert.
> > I do find much higher correlations with unfiltered data.
> > Any advice what could be going wrong here? I am using
>Freesurfer 5.1
> > and FSL 4.1.9 on Linux.
> > Thanks, Caspar
> >
> >
> >
> > __ _
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> .
> harvard.edu 
>  >>
>
> > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/
>freesurfer
>
>  freesurfer
> >
>
>   --
>   Douglas N. Greve, Ph.D.
>   MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
> 

Re: [Freesurfer] inability to pick points

[Bruce Fischl]

is it 1mm isotropic, 256^3? Run mri_info on it

On Mon, 7 May 2012, Borzello, Mia wrote:

> I'm not sure what you mean by "conformed"? My input volume is that one that I 
> coregistered if that's what you mean?
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:57 PM
> To: Borzello, Mia
> Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> is your input volume "conformed"? I think tkmedit disables some features
> if it is not
> On Mon, 7 May 2012, Borzello, Mia wrote:
>
>> "Select voxels" is actually highlighted already (and "Navigation" isn't), 
>> but it's still not working.
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 07, 2012 2:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] inability to pick points
>>
>> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
>> drop down tool menu). Sounds like you have the navigation button selected.
>> doug
>>
>> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>>> Hi,
>>>
>>> I'm just wondering if there is something that needs to be selected using 
>>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>>> right now i'm unable to move my cursor to a new location.
>>>
>>> Thanks so much,
>>> Mia
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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
>>
>>
>>
>
>
>
___
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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 you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] problems with analysis after using fslmaths

[Caspar M. Schwiedrzik]

Hi Doug,
I use the following command for fslmaths
fslmaths fmc.nii -bptf 200 2 fmcfilt.nii

where 200*(TR+2) is 400s, and 2*(TR=2)=4s.

and for mkanalysis-sess
-force
-fsd bold
-funcstem fmcfilt
-analysis name
-notask
-tr 2
-runlistfile name
-native
-nskip 5
-mask brain
-tpef name
-taskreg name

for debugging, I did not include nuisance regressors.
Caspar


2012/5/7 Douglas N Greve 

> What frequencies did you chose for the FSL bandpass filter? What is you
> mkanalysis-sess command?
>
>
> On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
>
>> yes
>>
>> 2012/5/7 Douglas N Greve > gr...@nmr.mgh.harvard.**edu >>
>>
>>
>>Did you regenerate the seeds after filtering?
>>
>>
>>On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
>>
>>I have tried analyses with only one seed time course (either 1
>>voxel, mean of a sphere of 1 voxel radius, or mean of a
>>functionally defined roi), as well as several seeds within the
>>same design matrix, with the same problem.
>>All of these analyses did yield higher pcc when done without
>>filtering.
>>Caspar
>>
>>2012/5/7 Douglas N Greve >
>>>
>>>>
>>
>>
>>   Is this doing all of those seeds simultaneously or one seed
>>at a time?
>>
>>   On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
>>> Hi,
>>> I am trying to use fslmaths to filter my data before I plug it
>>   into a
>>> resting state analysis. However, once I obtain a pcc map, all
>>> correlation coefficients are <0.1, even the autocorrelation
>>with the
>>> seed voxel.
>>> The data look fine when I open them in Matlab using MRIread; the
>>> correlations between individual voxel time courses obtained in
>>   Matlab
>>> is about 0.6.
>>>
>>> My analysis stream is as follows:
>>> a) I filter the data using "fslmaths input -bptf highpass
>>lowpass
>>> output"; from this I obtain a filtered nii.gz file
>>> b) I extract a seed timecourse from the filtered data in Matlab
>>> c) I run mkanalysis-sess with -notask
>>> d) I run selxavg3-sess
>>> e) I overlay the pcc.nii
>>>
>>> I have tried this with smoothed and unsmoothed data, with and
>>   without
>>> nuisance regressors, with different seeds, with mri_convert
>>   after step
>>> a. It is not a problem with the overlay since the max values
>>in pcc
>>> are all <0.1.
>>> I noticed that there are some differences in the nifti header
>>   (as read
>>> with MRIread) before and after filtering, but it seemed to
>>me that
>>> they are gone after I used mri_convert.
>>> I do find much higher correlations with unfiltered data.
>>> Any advice what could be going wrong here? I am using
>>Freesurfer 5.1
>>> and FSL 4.1.9 on Linux.
>>> Thanks, Caspar
>>>
>>>
>>>
>>> __ _
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>
>> > >
>>>
>> > >>
>>
>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/
>>freesurfer
>>
>>
>> 
>> >
>>
>>   --
>>   Douglas N. Greve, Ph.D.
>>   MGH-NMR Center
>>gr...@nmr.mgh.harvard.edu 
>> > >
>>>
>>>
>>   Phone Number: 617-724-2358 
>>>
>>   Fax: 617-726-7422  >>
>>
>>   Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting
>>
>> 
>> >
>>>
>> 
>> >>
>>   FileDrop: www.nmr.mgh.harvard.edu/
>>facility/filedrop/index.html
>>
>> 
>> >
>>>
>> 
>> >>
>>
>>   _

Re: [Freesurfer] matrix error

[Allie Rosen]

Hi,

I tested for a difference between the groups on age slope using DODS and
there was a difference. Does this mean I cannot re-run the model using
DOSS? Please let me know if there is a way I can still test for the
difference in thickness between groups.

Thanks again,
Allie



On Mon, May 7, 2012 at 3:01 PM, Douglas N Greve
wrote:

> The right way to do it is to remove the column entirely. You can't do this
> inside of the FSGD unless you use DOSS. You can use DOSS if there is no
> difference between the groups in the age slope. In fact, it is a good idea
> to run this test first. So, create an FSGD with just the age. Create a
> contrast to test for a difference between the groups on age slope (and use
> DODS). If there are no differences, then re-run your original model using
> DOSS (you will need to change the contrast vector).
>
> doug
>
>
> On 05/07/2012 02:50 PM, Allie Rosen wrote:
>
>> Hi Doug,
>>
>> Is there a different number I can substitute into the fifth column so the
>> numbers are not all zeroes?
>>
>> Thank you,
>> Allie
>>
>>
>>
>> On Mon, May 7, 2012 at 12:39 PM, Allie Rosen > rosen.al...@gmail.com>**> wrote:
>>
>>Hi Doug,
>>
>>Thanks for the help. The fifth column is all zeroes because the
>>covariate - length of disease - isn't applicable to control
>>subjects. In the end, I want to test the difference in thickness
>>between the two groups, regressing out the effect of both
>>covariates (age and length of disease). I think this means the
>>difference in intercepts between the two groups.
>>
>>Thanks again,
>>Allie
>>
>>
>>
>>On Mon, May 7, 2012 at 12:29 PM, Douglas N Greve
>>> >
>> wrote:
>>
>>Hi Allie, the 5th column of your design matrix is all 0s,
>>which causes
>>the ill conditioning. I don't think this design fits into our
>>standard
>>framework. You can still analyze and test, we'll just have to
>>figure out
>>exactly what needs to be done. In the end, what is it that you
>>want to
>>test? Just a difference in intercepts between the two groups?
>>doug
>>
>>On 05/07/2012 09:38 AM, Allie Rosen wrote:
>>> Hello,
>>>
>>> I am analyzing cortical thickness in a patient and control
>>group. I
>>> have two covariates: age and length of disease. I am using
>>the model from:
>>>
>>> 
>> http://surfer.nmr.mgh.harvard.**edu/fswiki/Fsgdf2G2V
>>>
>>> However, for the control group I put length of disease as 0
>>in my FSGD
>>> file. When I run the GLM, I get the following error message:
>>>
>>> matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>
>>> Can you please tell me what I am doing wrong? Below is the
>>required
>>> information.
>>>
>>> 1. Your command line:
>>>
>>> mri_glmfit --y lh.disease_length.thickness.**20.mgz --fsgd
>>> fsgd_disease_length.txt dods --glmdir
>>> lh.disease_length.thickness.**20.glmdir --surf fsaverage lh --C
>>> groupdiff_length_disease.mat
>>>
>>>   2. The FSGD file
>>>
>>> GroupDescriptorFile 1
>>> Title Anorexia vs Controls
>>> Class Control plus blue
>>> Class Patient circle green
>>> Variables Age Disease_Length
>>>
>>> Input C07 Control 37 0
>>> Input C28 Control 28 0
>>> Input C39 Control 37 0
>>> Input C54 Control 40 0
>>> Input C57 Control 32 0
>>> Input C10 Control 54 0
>>> Input C33 Control 31 0
>>> Input C29 Control 22 0
>>> Input A01 Patient 39 20
>>> Input A02 Patient 24 11
>>> Input A03 Patient 35 15
>>> Input A04 Patient 40 10
>>> Input A05 Patient 35 20
>>> Input A06 Patient 57 20
>>> Input A07 Patient 31 16
>>> Input A08 Patient 20 8
>>>
>>>   3. And the design matrix
>>>
>>> Design matrix --
>>>  1.000   0.000   37.000   0.000   0.000   0.000;
>>>  1.000   0.000   28.000   0.000   0.000   0.000;
>>>  1.000   0.000   37.000   0.000   0.000   0.000;
>>>  1.000   0.000   40.000   0.000   0.000   0.000;
>>>  1.000   0.000   32.000   0.000   0.000   0.000;
>>>  1.000   0.000   54.000   0.000   0.000   0.000;
>>>  1.000   0.000   31.000   0.000   0.000   0.000;
>>>  1.000   0.000   22.000   0.000   0.000   0.000;
>>>  0.000   1.000   0.000   39.000   0.000   20.000;
>>>  0.000   1.000   0.000   24.000   0.000   11.000;
>>>  0.000   1.000   0.000   35.000   0.000   15.000;
>>>  0.000   1.000   0.000   40.000   0.000   10.000;
>>>  0.000   1.000   0.000   35.000   0.000   20.000;
>> 

Re: [Freesurfer] trac-all -path error

[Priti Srinivasan]

So I'm assuming that you don't have any issues merged_ph* files anymore?

As far as the error below is concerned, this is typically the last step in
trac-paths, where it should merge all the 18 tracts to create a 4D tract
volume for visualization. The input for this should be all the 18
posterior distribution volumes. From what I see below, it does not look
like the tract reconstruction finished for any of the tracts (which is why
--in is empty). If you send us the trac-all.log, I can take a look. Also
do you see any tract volumes under dpath/ ?

Hope that helps,
Priti

> Yes, I figured out that I had previously run "trac-all -bedp" and it
> created "data_slice_0002". I deleted this directory, and bedpostx
> finished, but now I get this error from "trac-all-path":
> Segmentation fault (core dumped)
> /parietal/freesurfer/current/bin/dmri_mergepaths --indir
> /raid2/fmri8/control/H008B/dpath --in --out
> /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab
> /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15
> ERROR: must specify input volume(s)
>
> What should be specified here?
>
> Thanks,
> Chris
>
> PS When running bedpostx I was simply using the defaults, so "bedpostx
> H008B/dmri.bedpostX" was the command line.
>
> On 05/07/2012 02:28 PM, Priti Srinivasan wrote:
>> Hi Chris,
>>
>> The diff_slices folder is still there, which means that bedpostX
>> probably
>> did not finish processing. That folder usually gets deleted after
>> bedpostX
>> processing completes. It's strange that you have
>> merged_ph2samples.nii.gz
>> and not merged_ph1samples.nii.gz.
>>
>> Did you accidentally run bedpostX twice and exit out of it in the
>> middle?
>> It is quite possible that you'd already finished processing bedpostX(and
>> all files were properly created) and started running it again, which
>> would
>> explain the diff_slices and the absence of merged_ph1samples (but not
>> merged_ph2samples).
>>
>> You could potentially back up your current bedpostx folder and re-run
>> bedpostX to see if that solves your issue.
>>
>> Could you also send the commandline you're using for bedpostX?
>>
>> Thanks,
>> Priti
>>
>>> Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz"
>>> isn't getting created, I think. This is after I ran bedpostx on its
>>> own,
>>> per your instructions from this thread.
>>>
>>> Here are the last few lines of output from trac-all -path:
>>> Loading BEDPOST parameter samples from
>>> /raid2/fmri8/control/H008B/dmri.bedpostX
>>> niiRead(): error opening file
>>> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
>>> ERROR: Could not read
>>> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
>>> /parietal/freesurfer/current/bin/dmri_mergepaths --indir
>>> /raid2/fmri8/control/H008B/dpath --in --out
>>> /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab
>>> /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15
>>> ERROR: must specify input volume(s)
>>>
>>> This is what's in "dmri.bedpostX":
>>> bvals diff_slices   logs
>>> mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
>>> bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz
>>> mean_S0samples.nii.gz   merged_ph2samples.nii.gz
>>> nodif_brain_mask.nii.gz
>>> commands.txt  dyads2.nii.gz mean_f2samples.nii.gz
>>> mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms
>>>
>>> Thanks,
>>> Chris
>>>
>>> On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:
 Yes.

 On Fri, 23 Mar 2012, Chris Watson wrote:

> Ok. Do I run it with the defaults?
> # fibers per voxel = 2
> ARD weight = 1
> burn-in period = 1000
> # jumps = 1250
> sample every = 25
>
> On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:
>>Oh, ok. That's a known issue, it has to do with changes in the
>> command
>>line of the latest version of bedpostx. We've updated trac-all
>> and
>> it'll
>>be working in our next release but for now you'll have to run
>> bedpostx by
>>itself and not through trac-all. Sorry for the inconvenience!
>>
>>On Fri, 23 Mar 2012, Chris Watson wrote:
>>
>>>[freesurfer@occipital dmri.bedpostX]$ ls
>>> diff_slices/data_slice_0002/
>>>dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
>>>mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
>>>th1samples.nii.gz
>>>
>>>
>>>Come to think of it, when I ran bedpostx, it only output "1
>>> slice
>>>processed", but repeated 70 times, or however many slices there
>>> are. The
>>>data is from a Siemens 3T, by the way.
>>>
>>>On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:
 What's in the diff_slices directory? That's a temporary
 directory
 that
 bedpostx creates and that gets deleted after the results get

Re: [Freesurfer] inability to pick points

[Borzello, Mia]

tkmedit MGXX_SuferOutput_original norm.mgz lh.pial -aux ct.anat.mgz

I named the folder with the extra "_original" because this person already had a 
SurferOuput folder. Could that be the problem?

thanks.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 3:04 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

conformed means 1mm isotropic. What is your tkmedit cmd line?

On 05/07/2012 03:04 PM, Borzello, Mia wrote:
> I'm not sure what you mean by "conformed"? My input volume is that one that I 
> coregistered if that's what you mean?
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:57 PM
> To: Borzello, Mia
> Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> is your input volume "conformed"? I think tkmedit disables some features
> if it is not
> On Mon, 7 May 2012, Borzello, Mia wrote:
>
>> "Select voxels" is actually highlighted already (and "Navigation" isn't), 
>> but it's still not working.
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 07, 2012 2:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] inability to pick points
>>
>> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
>> drop down tool menu). Sounds like you have the navigation button selected.
>> doug
>>
>> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>>> Hi,
>>>
>>> I'm just wondering if there is something that needs to be selected using 
>>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>>> right now i'm unable to move my cursor to a new location.
>>>
>>> Thanks so much,
>>> Mia
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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
>>
>>
>>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] inability to pick points

[Douglas N Greve]

conformed means 1mm isotropic. What is your tkmedit cmd line?

On 05/07/2012 03:04 PM, Borzello, Mia wrote:
> I'm not sure what you mean by "conformed"? My input volume is that one that I 
> coregistered if that's what you mean?
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:57 PM
> To: Borzello, Mia
> Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> is your input volume "conformed"? I think tkmedit disables some features
> if it is not
> On Mon, 7 May 2012, Borzello, Mia wrote:
>
>> "Select voxels" is actually highlighted already (and "Navigation" isn't), 
>> but it's still not working.
>> Thanks,
>> m
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, May 07, 2012 2:43 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] inability to pick points
>>
>> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
>> drop down tool menu). Sounds like you have the navigation button selected.
>> doug
>>
>> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>>> Hi,
>>>
>>> I'm just wondering if there is something that needs to be selected using 
>>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>>> right now i'm unable to move my cursor to a new location.
>>>
>>> Thanks so much,
>>> Mia
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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
>>
>>
>>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] inability to pick points

[Borzello, Mia]

I'm not sure what you mean by "conformed"? My input volume is that one that I 
coregistered if that's what you mean?

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 2:57 PM
To: Borzello, Mia
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

is your input volume "conformed"? I think tkmedit disables some features
if it is not
On Mon, 7 May 2012, Borzello, Mia wrote:

> "Select voxels" is actually highlighted already (and "Navigation" isn't), but 
> it's still not working.
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
> drop down tool menu). Sounds like you have the navigation button selected.
> doug
>
> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>> Hi,
>>
>> I'm just wondering if there is something that needs to be selected using 
>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>> right now i'm unable to move my cursor to a new location.
>>
>> Thanks so much,
>> Mia
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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
>
>
>

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Re: [Freesurfer] problems with analysis after using fslmaths

[Douglas N Greve]

What frequencies did you chose for the FSL bandpass filter? What is you 
mkanalysis-sess command?

On 05/07/2012 02:58 PM, Caspar M. Schwiedrzik wrote:
> yes
>
> 2012/5/7 Douglas N Greve  >
>
> Did you regenerate the seeds after filtering?
>
>
> On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
>
> I have tried analyses with only one seed time course (either 1
> voxel, mean of a sphere of 1 voxel radius, or mean of a
> functionally defined roi), as well as several seeds within the
> same design matrix, with the same problem.
> All of these analyses did yield higher pcc when done without
> filtering.
> Caspar
>
> 2012/5/7 Douglas N Greve  
>  >>
>
>
>Is this doing all of those seeds simultaneously or one seed
> at a time?
>
>On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
> > Hi,
> > I am trying to use fslmaths to filter my data before I plug it
>into a
> > resting state analysis. However, once I obtain a pcc map, all
> > correlation coefficients are <0.1, even the autocorrelation
> with the
> > seed voxel.
> > The data look fine when I open them in Matlab using MRIread; the
> > correlations between individual voxel time courses obtained in
>Matlab
> > is about 0.6.
> >
> > My analysis stream is as follows:
> > a) I filter the data using "fslmaths input -bptf highpass
> lowpass
> > output"; from this I obtain a filtered nii.gz file
> > b) I extract a seed timecourse from the filtered data in Matlab
> > c) I run mkanalysis-sess with -notask
> > d) I run selxavg3-sess
> > e) I overlay the pcc.nii
> >
> > I have tried this with smoothed and unsmoothed data, with and
>without
> > nuisance regressors, with different seeds, with mri_convert
>after step
> > a. It is not a problem with the overlay since the max values
> in pcc
> > are all <0.1.
> > I noticed that there are some differences in the nifti header
>(as read
> > with MRIread) before and after filtering, but it seemed to
> me that
> > they are gone after I used mri_convert.
> > I do find much higher correlations with unfiltered data.
> > Any advice what could be going wrong here? I am using
> Freesurfer 5.1
> > and FSL 4.1.9 on Linux.
> > Thanks, Caspar
> >
> >
> >
> > __ _
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/
> freesurfer
> 
>
>--
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
>Phone Number: 617-724-2358 
> >
>Fax: 617-726-7422   >
>
>Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting
> 
>  >
>FileDrop: www.nmr.mgh.harvard.edu/
> facility/filedrop/index.html
> 
>  >
>
>__ _
>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
> 

Re: [Freesurfer] matrix error

[Douglas N Greve]

The right way to do it is to remove the column entirely. You can't do 
this inside of the FSGD unless you use DOSS. You can use DOSS if there 
is no difference between the groups in the age slope. In fact, it is a 
good idea to run this test first. So, create an FSGD with just the age. 
Create a contrast to test for a difference between the groups on age 
slope (and use DODS). If there are no differences, then re-run your 
original model using DOSS (you will need to change the contrast vector).

doug

On 05/07/2012 02:50 PM, Allie Rosen wrote:
> Hi Doug,
>
> Is there a different number I can substitute into the fifth column so 
> the numbers are not all zeroes?
>
> Thank you,
> Allie
>
>
>
> On Mon, May 7, 2012 at 12:39 PM, Allie Rosen  > wrote:
>
> Hi Doug,
>
> Thanks for the help. The fifth column is all zeroes because the
> covariate - length of disease - isn't applicable to control
> subjects. In the end, I want to test the difference in thickness
> between the two groups, regressing out the effect of both
> covariates (age and length of disease). I think this means the
> difference in intercepts between the two groups.
>
> Thanks again,
> Allie
>
>
>
> On Mon, May 7, 2012 at 12:29 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Allie, the 5th column of your design matrix is all 0s,
> which causes
> the ill conditioning. I don't think this design fits into our
> standard
> framework. You can still analyze and test, we'll just have to
> figure out
> exactly what needs to be done. In the end, what is it that you
> want to
> test? Just a difference in intercepts between the two groups?
> doug
>
> On 05/07/2012 09:38 AM, Allie Rosen wrote:
> > Hello,
> >
> > I am analyzing cortical thickness in a patient and control
> group. I
> > have two covariates: age and length of disease. I am using
> the model from:
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V
> >
> > However, for the control group I put length of disease as 0
> in my FSGD
> > file. When I run the GLM, I get the following error message:
> >
> > matrix is ill-conditioned or badly scaled, condno = 1e+08
> >
> > Can you please tell me what I am doing wrong? Below is the
> required
> > information.
> >
> > 1. Your command line:
> >
> > mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd
> > fsgd_disease_length.txt dods --glmdir
> > lh.disease_length.thickness.20.glmdir --surf fsaverage lh --C
> > groupdiff_length_disease.mat
> >
> >   2. The FSGD file
> >
> > GroupDescriptorFile 1
> > Title Anorexia vs Controls
> > Class Control plus blue
> > Class Patient circle green
> > Variables Age Disease_Length
> >
> > Input C07 Control 37 0
> > Input C28 Control 28 0
> > Input C39 Control 37 0
> > Input C54 Control 40 0
> > Input C57 Control 32 0
> > Input C10 Control 54 0
> > Input C33 Control 31 0
> > Input C29 Control 22 0
> > Input A01 Patient 39 20
> > Input A02 Patient 24 11
> > Input A03 Patient 35 15
> > Input A04 Patient 40 10
> > Input A05 Patient 35 20
> > Input A06 Patient 57 20
> > Input A07 Patient 31 16
> > Input A08 Patient 20 8
> >
> >   3. And the design matrix
> >
> > Design matrix --
> >  1.000   0.000   37.000   0.000   0.000   0.000;
> >  1.000   0.000   28.000   0.000   0.000   0.000;
> >  1.000   0.000   37.000   0.000   0.000   0.000;
> >  1.000   0.000   40.000   0.000   0.000   0.000;
> >  1.000   0.000   32.000   0.000   0.000   0.000;
> >  1.000   0.000   54.000   0.000   0.000   0.000;
> >  1.000   0.000   31.000   0.000   0.000   0.000;
> >  1.000   0.000   22.000   0.000   0.000   0.000;
> >  0.000   1.000   0.000   39.000   0.000   20.000;
> >  0.000   1.000   0.000   24.000   0.000   11.000;
> >  0.000   1.000   0.000   35.000   0.000   15.000;
> >  0.000   1.000   0.000   40.000   0.000   10.000;
> >  0.000   1.000   0.000   35.000   0.000   20.000;
> >  0.000   1.000   0.000   57.000   0.000   20.000;
> >  0.000   1.000   0.000   31.000   0.000   16.000;
> >  0.000   1.000   0.000   20.000   0.000   8.000;
> > 
> >
> > Thank you,
> > Allie
> >
> >
> >
> >
> > ___
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Re: [Freesurfer] problems with analysis after using fslmaths

[Douglas N Greve]

Did you regenerate the seeds after filtering?

On 05/07/2012 02:50 PM, Caspar M. Schwiedrzik wrote:
> I have tried analyses with only one seed time course (either 1 voxel, 
> mean of a sphere of 1 voxel radius, or mean of a functionally defined 
> roi), as well as several seeds within the same design matrix, with the 
> same problem.
> All of these analyses did yield higher pcc when done without filtering.
> Caspar
>
> 2012/5/7 Douglas N Greve  >
>
> Is this doing all of those seeds simultaneously or one seed at a time?
>
> On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
> > Hi,
> > I am trying to use fslmaths to filter my data before I plug it
> into a
> > resting state analysis. However, once I obtain a pcc map, all
> > correlation coefficients are <0.1, even the autocorrelation with the
> > seed voxel.
> > The data look fine when I open them in Matlab using MRIread; the
> > correlations between individual voxel time courses obtained in
> Matlab
> > is about 0.6.
> >
> > My analysis stream is as follows:
> > a) I filter the data using "fslmaths input -bptf highpass lowpass
> > output"; from this I obtain a filtered nii.gz file
> > b) I extract a seed timecourse from the filtered data in Matlab
> > c) I run mkanalysis-sess with -notask
> > d) I run selxavg3-sess
> > e) I overlay the pcc.nii
> >
> > I have tried this with smoothed and unsmoothed data, with and
> without
> > nuisance regressors, with different seeds, with mri_convert
> after step
> > a. It is not a problem with the overlay since the max values in pcc
> > are all <0.1.
> > I noticed that there are some differences in the nifti header
> (as read
> > with MRIread) before and after filtering, but it seemed to me that
> > they are gone after I used mri_convert.
> > I do find much higher correlations with unfiltered data.
> > Any advice what could be going wrong here? I am using Freesurfer 5.1
> > and FSL 4.1.9 on Linux.
> > Thanks, Caspar
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
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> 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
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> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
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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
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Re: [Freesurfer] inability to pick points

[Bruce Fischl]

is your input volume "conformed"? I think tkmedit disables some features 
if it is not
On Mon, 7 May 2012, Borzello, Mia wrote:

> "Select voxels" is actually highlighted already (and "Navigation" isn't), but 
> it's still not working.
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 07, 2012 2:43 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] inability to pick points
>
> Make sure that the "Select Voxel Tool" is activated in the tool bar (or
> drop down tool menu). Sounds like you have the navigation button selected.
> doug
>
> On 05/07/2012 02:05 PM, Borzello, Mia wrote:
>> Hi,
>>
>> I'm just wondering if there is something that needs to be selected using 
>> tkmedit to get electrode coordinates. I usually don't have this issue, but 
>> right now i'm unable to move my cursor to a new location.
>>
>> Thanks so much,
>> Mia
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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
>
>
>
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Re: [Freesurfer] inability to pick points

[Borzello, Mia]

"Select voxels" is actually highlighted already (and "Navigation" isn't), but 
it's still not working.
Thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 07, 2012 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inability to pick points

Make sure that the "Select Voxel Tool" is activated in the tool bar (or
drop down tool menu). Sounds like you have the navigation button selected.
doug

On 05/07/2012 02:05 PM, Borzello, Mia wrote:
> Hi,
>
> I'm just wondering if there is something that needs to be selected using 
> tkmedit to get electrode coordinates. I usually don't have this issue, but 
> right now i'm unable to move my cursor to a new location.
>
> Thanks so much,
> Mia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] matrix error

[Allie Rosen]

Hi Doug,

Is there a different number I can substitute into the fifth column so the
numbers are not all zeroes?

Thank you,
Allie



On Mon, May 7, 2012 at 12:39 PM, Allie Rosen  wrote:

> Hi Doug,
>
> Thanks for the help. The fifth column is all zeroes because the covariate
> - length of disease - isn't applicable to control subjects. In the end, I
> want to test the difference in thickness between the two groups, regressing
> out the effect of both covariates (age and length of disease). I think this
> means the difference in intercepts between the two groups.
>
> Thanks again,
> Allie
>
>
>
> On Mon, May 7, 2012 at 12:29 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Allie, the 5th column of your design matrix is all 0s, which causes
>> the ill conditioning. I don't think this design fits into our standard
>> framework. You can still analyze and test, we'll just have to figure out
>> exactly what needs to be done. In the end, what is it that you want to
>> test? Just a difference in intercepts between the two groups?
>> doug
>>
>> On 05/07/2012 09:38 AM, Allie Rosen wrote:
>> > Hello,
>> >
>> > I am analyzing cortical thickness in a patient and control group. I
>> > have two covariates: age and length of disease. I am using the model
>> from:
>> >
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V
>> >
>> > However, for the control group I put length of disease as 0 in my FSGD
>> > file. When I run the GLM, I get the following error message:
>> >
>> > matrix is ill-conditioned or badly scaled, condno = 1e+08
>> >
>> > Can you please tell me what I am doing wrong? Below is the required
>> > information.
>> >
>> > 1. Your command line:
>> >
>> > mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd
>> > fsgd_disease_length.txt dods --glmdir
>> > lh.disease_length.thickness.20.glmdir --surf fsaverage lh --C
>> > groupdiff_length_disease.mat
>> >
>> >   2. The FSGD file
>> >
>> > GroupDescriptorFile 1
>> > Title Anorexia vs Controls
>> > Class Control plus blue
>> > Class Patient circle green
>> > Variables Age Disease_Length
>> >
>> > Input C07 Control 37 0
>> > Input C28 Control 28 0
>> > Input C39 Control 37 0
>> > Input C54 Control 40 0
>> > Input C57 Control 32 0
>> > Input C10 Control 54 0
>> > Input C33 Control 31 0
>> > Input C29 Control 22 0
>> > Input A01 Patient 39 20
>> > Input A02 Patient 24 11
>> > Input A03 Patient 35 15
>> > Input A04 Patient 40 10
>> > Input A05 Patient 35 20
>> > Input A06 Patient 57 20
>> > Input A07 Patient 31 16
>> > Input A08 Patient 20 8
>> >
>> >   3. And the design matrix
>> >
>> > Design matrix --
>> >  1.000   0.000   37.000   0.000   0.000   0.000;
>> >  1.000   0.000   28.000   0.000   0.000   0.000;
>> >  1.000   0.000   37.000   0.000   0.000   0.000;
>> >  1.000   0.000   40.000   0.000   0.000   0.000;
>> >  1.000   0.000   32.000   0.000   0.000   0.000;
>> >  1.000   0.000   54.000   0.000   0.000   0.000;
>> >  1.000   0.000   31.000   0.000   0.000   0.000;
>> >  1.000   0.000   22.000   0.000   0.000   0.000;
>> >  0.000   1.000   0.000   39.000   0.000   20.000;
>> >  0.000   1.000   0.000   24.000   0.000   11.000;
>> >  0.000   1.000   0.000   35.000   0.000   15.000;
>> >  0.000   1.000   0.000   40.000   0.000   10.000;
>> >  0.000   1.000   0.000   35.000   0.000   20.000;
>> >  0.000   1.000   0.000   57.000   0.000   20.000;
>> >  0.000   1.000   0.000   31.000   0.000   16.000;
>> >  0.000   1.000   0.000   20.000   0.000   8.000;
>> > 
>> >
>> > Thank you,
>> > Allie
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> ___
>> 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.
>>
>>
>
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Re: [Freesurfer] inability to pick points

[Douglas N Greve]

Make sure that the "Select Voxel Tool" is activated in the tool bar (or 
drop down tool menu). Sounds like you have the navigation button selected.
doug

On 05/07/2012 02:05 PM, Borzello, Mia wrote:
> Hi,
>
> I'm just wondering if there is something that needs to be selected using 
> tkmedit to get electrode coordinates. I usually don't have this issue, but 
> right now i'm unable to move my cursor to a new location.
>
> Thanks so much,
> Mia
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] problems with analysis after using fslmaths

[Douglas N Greve]

Is this doing all of those seeds simultaneously or one seed at a time?

On 05/07/2012 02:25 PM, Caspar M. Schwiedrzik wrote:
> Hi,
> I am trying to use fslmaths to filter my data before I plug it into a 
> resting state analysis. However, once I obtain a pcc map, all 
> correlation coefficients are <0.1, even the autocorrelation with the 
> seed voxel.
> The data look fine when I open them in Matlab using MRIread; the 
> correlations between individual voxel time courses obtained in Matlab 
> is about 0.6.
>
> My analysis stream is as follows:
> a) I filter the data using "fslmaths input -bptf highpass lowpass 
> output"; from this I obtain a filtered nii.gz file
> b) I extract a seed timecourse from the filtered data in Matlab
> c) I run mkanalysis-sess with -notask
> d) I run selxavg3-sess
> e) I overlay the pcc.nii
>
> I have tried this with smoothed and unsmoothed data, with and without 
> nuisance regressors, with different seeds, with mri_convert after step 
> a. It is not a problem with the overlay since the max values in pcc 
> are all <0.1.
> I noticed that there are some differences in the nifti header (as read 
> with MRIread) before and after filtering, but it seemed to me that 
> they are gone after I used mri_convert.
> I do find much higher correlations with unfiltered data.
> Any advice what could be going wrong here? I am using Freesurfer 5.1 
> and FSL 4.1.9 on Linux.
> Thanks, Caspar
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] trac-all -path error

[Chris Watson]

Yes, I figured out that I had previously run "trac-all -bedp" and it 
created "data_slice_0002". I deleted this directory, and bedpostx 
finished, but now I get this error from "trac-all-path":

Segmentation fault (core dumped)
/parietal/freesurfer/current/bin/dmri_mergepaths --indir 
/raid2/fmri8/control/H008B/dpath --in --out 
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab 
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15

ERROR: must specify input volume(s)

What should be specified here?

Thanks,
Chris

PS When running bedpostx I was simply using the defaults, so "bedpostx 
H008B/dmri.bedpostX" was the command line.


On 05/07/2012 02:28 PM, Priti Srinivasan wrote:

Hi Chris,

The diff_slices folder is still there, which means that bedpostX probably
did not finish processing. That folder usually gets deleted after bedpostX
processing completes. It's strange that you have merged_ph2samples.nii.gz
and not merged_ph1samples.nii.gz.

Did you accidentally run bedpostX twice and exit out of it in the middle?
It is quite possible that you'd already finished processing bedpostX(and
all files were properly created) and started running it again, which would
explain the diff_slices and the absence of merged_ph1samples (but not
merged_ph2samples).

You could potentially back up your current bedpostx folder and re-run
bedpostX to see if that solves your issue.

Could you also send the commandline you're using for bedpostX?

Thanks,
Priti


Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz"
isn't getting created, I think. This is after I ran bedpostx on its own,
per your instructions from this thread.

Here are the last few lines of output from trac-all -path:
Loading BEDPOST parameter samples from
/raid2/fmri8/control/H008B/dmri.bedpostX
niiRead(): error opening file
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
/parietal/freesurfer/current/bin/dmri_mergepaths --indir
/raid2/fmri8/control/H008B/dpath --in --out
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15
ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX":
bvals diff_slices   logs
mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz
mean_S0samples.nii.gz   merged_ph2samples.nii.gz
nodif_brain_mask.nii.gz
commands.txt  dyads2.nii.gz mean_f2samples.nii.gz
mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms

Thanks,
Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:


Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

   Oh, ok. That's a known issue, it has to do with changes in the
command
   line of the latest version of bedpostx. We've updated trac-all and
it'll
   be working in our next release but for now you'll have to run
bedpostx by
   itself and not through trac-all. Sorry for the inconvenience!

   On Fri, 23 Mar 2012, Chris Watson wrote:


   [freesurfer@occipital dmri.bedpostX]$ ls
diff_slices/data_slice_0002/
   dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
   mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
   th1samples.nii.gz


   Come to think of it, when I ran bedpostx, it only output "1 slice
   processed", but repeated 70 times, or however many slices there
are. The
   data is from a Siemens 3T, by the way.

   On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

What's in the diff_slices directory? That's a temporary directory
that
bedpostx creates and that gets deleted after the results get
   "merged". So
my guess would be that bedpostx didn't finish processing.

On Fri, 23 Mar 2012, Chris Watson wrote:


Hello, I successfully ran trac-all -bedp, and when I run the
next

   step I

get the following error:

Loading BEDPOST parameter samples from

   /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX

niiRead(): error opening file


   
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

ERROR: Could not read

   
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed

   Mar 7

04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
Word too long.

   


Indeed, the "merged" file doesn't exist. I am running

   Freesurfer 5.1.0

and FSL 4.1.9.
Here's what's in the dmri.bedpostX directory:

[freesurf

Re: [Freesurfer] trac-all -path error

[Priti Srinivasan]

Hi Chris,

The diff_slices folder is still there, which means that bedpostX probably
did not finish processing. That folder usually gets deleted after bedpostX
processing completes. It's strange that you have merged_ph2samples.nii.gz
and not merged_ph1samples.nii.gz.

Did you accidentally run bedpostX twice and exit out of it in the middle?
It is quite possible that you'd already finished processing bedpostX(and
all files were properly created) and started running it again, which would
explain the diff_slices and the absence of merged_ph1samples (but not
merged_ph2samples).

You could potentially back up your current bedpostx folder and re-run
bedpostX to see if that solves your issue.

Could you also send the commandline you're using for bedpostX?

Thanks,
Priti

> Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz"
> isn't getting created, I think. This is after I ran bedpostx on its own,
> per your instructions from this thread.
>
> Here are the last few lines of output from trac-all -path:
> Loading BEDPOST parameter samples from
> /raid2/fmri8/control/H008B/dmri.bedpostX
> niiRead(): error opening file
> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
> ERROR: Could not read
> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
> /parietal/freesurfer/current/bin/dmri_mergepaths --indir
> /raid2/fmri8/control/H008B/dpath --in --out
> /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab
> /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15
> ERROR: must specify input volume(s)
>
> This is what's in "dmri.bedpostX":
> bvals diff_slices   logs
> mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
> bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz
> mean_S0samples.nii.gz   merged_ph2samples.nii.gz
> nodif_brain_mask.nii.gz
> commands.txt  dyads2.nii.gz mean_f2samples.nii.gz
> mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms
>
> Thanks,
> Chris
>
> On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:
>> Yes.
>>
>> On Fri, 23 Mar 2012, Chris Watson wrote:
>>
>>> Ok. Do I run it with the defaults?
>>> # fibers per voxel = 2
>>> ARD weight = 1
>>> burn-in period = 1000
>>> # jumps = 1250
>>> sample every = 25
>>>
>>> On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:
   Oh, ok. That's a known issue, it has to do with changes in the
 command
   line of the latest version of bedpostx. We've updated trac-all and
 it'll
   be working in our next release but for now you'll have to run
 bedpostx by
   itself and not through trac-all. Sorry for the inconvenience!

   On Fri, 23 Mar 2012, Chris Watson wrote:

>   [freesurfer@occipital dmri.bedpostX]$ ls
> diff_slices/data_slice_0002/
>   dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
>   mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
>   th1samples.nii.gz
>
>
>   Come to think of it, when I ran bedpostx, it only output "1 slice
>   processed", but repeated 70 times, or however many slices there
> are. The
>   data is from a Siemens 3T, by the way.
>
>   On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:
>>What's in the diff_slices directory? That's a temporary directory
>>that
>>bedpostx creates and that gets deleted after the results get
>>   "merged". So
>>my guess would be that bedpostx didn't finish processing.
>>
>>On Fri, 23 Mar 2012, Chris Watson wrote:
>>
>>>Hello, I successfully ran trac-all -bedp, and when I run the
>>> next
>>   step I
>>>get the following error:
Loading BEDPOST parameter samples from
>>   /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX
>>>niiRead(): error opening file
>>>
>>   
>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
>>   
>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz
Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed
>>   Mar 7
>>>04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
Word too long.
>>   
>> 
>>
Indeed, the "merged" file doesn't exist. I am running
>>   Freesurfer 5.1.0
>>>and FSL 4.1.9.
>>>Here's what's in the dmri.bedpostX directory:
[freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/
>>>bvals  bvecs  commands.txt  diff_slices  logs  monitor
>>>nodif_brain_mask.nii.gz  xfms
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>>>Freesurfer@nmr.mgh.harvard.edu
>

[Freesurfer] problems with analysis after using fslmaths

[Caspar M. Schwiedrzik]

Hi,
I am trying to use fslmaths to filter my data before I plug it into a
resting state analysis. However, once I obtain a pcc map, all correlation
coefficients are <0.1, even the autocorrelation with the seed voxel.
The data look fine when I open them in Matlab using MRIread; the
correlations between individual voxel time courses obtained in Matlab is
about 0.6.

My analysis stream is as follows:
a) I filter the data using "fslmaths input -bptf highpass lowpass output";
from this I obtain a filtered nii.gz file
b) I extract a seed timecourse from the filtered data in Matlab
c) I run mkanalysis-sess with -notask
d) I run selxavg3-sess
e) I overlay the pcc.nii

I have tried this with smoothed and unsmoothed data, with and without
nuisance regressors, with different seeds, with mri_convert after step a.
It is not a problem with the overlay since the max values in pcc are all
<0.1.
I noticed that there are some differences in the nifti header (as read with
MRIread) before and after filtering, but it seemed to me that they are gone
after I used mri_convert.
I do find much higher correlations with unfiltered data.
Any advice what could be going wrong here? I am using Freesurfer 5.1 and
FSL 4.1.9 on Linux.
Thanks, Caspar
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[Freesurfer] inability to pick points

[Borzello, Mia]

Hi,

I'm just wondering if there is something that needs to be selected using 
tkmedit to get electrode coordinates. I usually don't have this issue, but 
right now i'm unable to move my cursor to a new location.

Thanks so much,
Mia

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Re: [Freesurfer] trac-all -path error

[Chris Watson]

Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" 
isn't getting created, I think. This is after I ran bedpostx on its own, 
per your instructions from this thread.


Here are the last few lines of output from trac-all -path:
Loading BEDPOST parameter samples from 
/raid2/fmri8/control/H008B/dmri.bedpostX
niiRead(): error opening file 
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read 
/raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz
/parietal/freesurfer/current/bin/dmri_mergepaths --indir 
/raid2/fmri8/control/H008B/dpath --in --out 
/raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab 
/parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15

ERROR: must specify input volume(s)

This is what's in "dmri.bedpostX":
bvals diff_slices   logs   
mean_ph2samples.nii.gz  merged_f2samples.nii.gz   monitor
bvecs dyads2_dispersion.nii.gz  mean_dsamples.nii.gz   
mean_S0samples.nii.gz   merged_ph2samples.nii.gz  
nodif_brain_mask.nii.gz
commands.txt  dyads2.nii.gz mean_f2samples.nii.gz  
mean_th2samples.nii.gz  merged_th2samples.nii.gz  xfms


Thanks,
Chris

On 03/23/2012 01:25 PM, Anastasia Yendiki wrote:

Yes.

On Fri, 23 Mar 2012, Chris Watson wrote:


Ok. Do I run it with the defaults?
# fibers per voxel = 2
ARD weight = 1
burn-in period = 1000
# jumps = 1250
sample every = 25

On 03/23/2012 01:22 PM, Anastasia Yendiki wrote:

  Oh, ok. That's a known issue, it has to do with changes in the command
  line of the latest version of bedpostx. We've updated trac-all and it'll
  be working in our next release but for now you'll have to run bedpostx by
  itself and not through trac-all. Sorry for the inconvenience!

  On Fri, 23 Mar 2012, Chris Watson wrote:


  [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/
  dyads1.nii.gz  f1samples.nii.gz  logfile  mean_dsamples.nii.gz
  mean_f1samples.nii.gz  mean_S0samples.nii.gz  ph1samples.nii.gz
  th1samples.nii.gz


  Come to think of it, when I ran bedpostx, it only output "1 slice
  processed", but repeated 70 times, or however many slices there are. The
  data is from a Siemens 3T, by the way.

  On 03/23/2012 01:16 PM, Anastasia Yendiki wrote:

   What's in the diff_slices directory? That's a temporary directory
   that
   bedpostx creates and that gets deleted after the results get
  "merged". So
   my guess would be that bedpostx didn't finish processing.

   On Fri, 23 Mar 2012, Chris Watson wrote:


   Hello, I successfully ran trac-all -bedp, and when I run the next

  step I

   get the following error:

   Loading BEDPOST parameter samples from

  /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX

   niiRead(): error opening file


  
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

   ERROR: Could not read

  
/raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz

   Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed

  Mar 7

   04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

   trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012
   Word too long.

  


   Indeed, the "merged" file doesn't exist. I am running

  Freesurfer 5.1.0

   and FSL 4.1.9.
   Here's what's in the dmri.bedpostX directory:

   [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/

   bvals  bvecs  commands.txt  diff_slices  logs  monitor
   nodif_brain_mask.nii.gz  xfms

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  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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   properly
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Re: [Freesurfer] matrix error

[Douglas N Greve]

Hi Allie, the 5th column of your design matrix is all 0s, which causes 
the ill conditioning. I don't think this design fits into our standard 
framework. You can still analyze and test, we'll just have to figure out 
exactly what needs to be done. In the end, what is it that you want to 
test? Just a difference in intercepts between the two groups?
doug

On 05/07/2012 09:38 AM, Allie Rosen wrote:
> Hello,
>
> I am analyzing cortical thickness in a patient and control group. I 
> have two covariates: age and length of disease. I am using the model from:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V
>
> However, for the control group I put length of disease as 0 in my FSGD 
> file. When I run the GLM, I get the following error message:
>
> matrix is ill-conditioned or badly scaled, condno = 1e+08
>
> Can you please tell me what I am doing wrong? Below is the required 
> information.
>
> 1. Your command line:
>
> mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd 
> fsgd_disease_length.txt dods --glmdir 
> lh.disease_length.thickness.20.glmdir --surf fsaverage lh --C 
> groupdiff_length_disease.mat
>
>   2. The FSGD file
>
> GroupDescriptorFile 1
> Title Anorexia vs Controls
> Class Control plus blue
> Class Patient circle green
> Variables Age Disease_Length
>
> Input C07 Control 37 0
> Input C28 Control 28 0
> Input C39 Control 37 0
> Input C54 Control 40 0
> Input C57 Control 32 0
> Input C10 Control 54 0
> Input C33 Control 31 0
> Input C29 Control 22 0
> Input A01 Patient 39 20
> Input A02 Patient 24 11
> Input A03 Patient 35 15
> Input A04 Patient 40 10
> Input A05 Patient 35 20
> Input A06 Patient 57 20
> Input A07 Patient 31 16
> Input A08 Patient 20 8
>
>   3. And the design matrix
>
> Design matrix --
>  1.000   0.000   37.000   0.000   0.000   0.000;
>  1.000   0.000   28.000   0.000   0.000   0.000;
>  1.000   0.000   37.000   0.000   0.000   0.000;
>  1.000   0.000   40.000   0.000   0.000   0.000;
>  1.000   0.000   32.000   0.000   0.000   0.000;
>  1.000   0.000   54.000   0.000   0.000   0.000;
>  1.000   0.000   31.000   0.000   0.000   0.000;
>  1.000   0.000   22.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   39.000   0.000   20.000;
>  0.000   1.000   0.000   24.000   0.000   11.000;
>  0.000   1.000   0.000   35.000   0.000   15.000;
>  0.000   1.000   0.000   40.000   0.000   10.000;
>  0.000   1.000   0.000   35.000   0.000   20.000;
>  0.000   1.000   0.000   57.000   0.000   20.000;
>  0.000   1.000   0.000   31.000   0.000   16.000;
>  0.000   1.000   0.000   20.000   0.000   8.000;
> 
>
> Thank you,
> Allie
>
>
>
>
> ___
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Volume to surface

[Anderson Winkler]

Hi Gabriel,

Attached is a script that probably does what you need. Just make it 
executable and call it without arguments to get usage information. The 
label indices you can get from the aseg.stats file or from 
FreeSurferColorLUT.txt.


The surfaces will be saved in a subdirectory called "ascii" inside each 
subject's directory, and have extension .srf. They are internally the 
same as the .asc surfaces, just with a different extension.


Note that the idea of the script is to generate surfaces for 
visualization purposes only. If you'd like to do statistical analysis 
(e.g., compare shapes between patients and controls), these surfaces may 
not be appropriate.


Hope it helps!

All the best,

Anderson


On 07/05/12 12:15, Gabriel Gonzalez Escamilla wrote:

Hello all FS users and experts,

I'm wanting to get the sub cortical segmentation as ASCII files, so 
I'm trying convert the aseg.mgz into a surface file, to finally get an 
ASCII file,

For this I'm using the next commands:

First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii
To preserve  the aseg volume in native space

Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi 
lh --o ./lg.aseg2raw.mgh


And last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.asc

I'm Not sure if I should do this for the whole aseg or if should I try 
to separate the segmented structures first...


Many Thanks in advanced,
Gabriel


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#!/bin/bash

# Print usage if no argument is given
if [ -z "$1" ]; then
cat < [-l ] [-d]

Options:
-s  : Specify a list of subjects between quotes,
e.g. -s "john bill mary mark" or a text file
containing one subject per line.
-l  : Specify a list of labels between quotes,
e.g. "10 11 14 52 253", or a text file
containing one label per line, or ignore
this option to convert all labels.
-d  Debug mode. Leave all temporary files.

Requirements:
FreeSurfer must have been configured and the variables
FREESURFER_HOME and SUBJECTS_DIR must have been correctly set.

_
Anderson M. Winkler
Institute of Living / Yale University
Jul/2009
EOU
exit
fi

# List of labels to be converted  if no list is specified
LABLIST="4 5 7 8 10 11 12 13 14 15 16 17 18 26 28 43 44 46 47 49 50 51 52 53 54 
58 60 251 252 253 254 255"

# Check and accept arguments
SBJLIST=""
DEBUG=N
while getopts 's:l:d' OPTION
do
  case ${OPTION} in
s) SBJLIST=$( [[ -f ${OPTARG} ]] && cat ${OPTARG} || echo "${OPTARG}" ) ;;
l) LABLIST=$( [[ -f ${OPTARG} ]] && cat ${OPTARG} || echo "${OPTARG}" ) ;;
d) DEBUG=Y ;;
  esac
done

# Prepare a random string to save temporary files
RND0=$(head -n 1 /dev/random | md5sum)
RNDSTR=${RND0:0:12}

# Define a function for Ctrl+C as soon as the RNDSTR is defined
trap bashtrap INT
bashtrap()
{
  break ; break
  [[ "${s}" != "" ]] && rm -rf ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR} # try to 
delete temp files
  exit 1
}

# For each subject
for s in ${SBJLIST} ; do

  # Create directories for temp files and results
  mkdir -p ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}
  mkdir -p ${SUBJECTS_DIR}/${s}/ascii

  # For each label
  for lab in ${LABLIST} ; do

# Label string
lab0=$(printf %03d ${lab})

# Pre-tessellate
echo "==> Pre-tessellating: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mri_pretess \
   ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \
   ${SUBJECTS_DIR}/${s}/mri/norm.mgz \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz

# Tessellate
echo "==> Tessellating: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mri_tessellate \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \
   ${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth

# Smooth
echo "==> Smoothing: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mris_smooth -nw \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}

# Convert to ASCII
echo "==> Converting to ASCII: ${s}, ${lab0}"
${FREESURFER_HOME}/bin/mris_convert \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \
   ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc
mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \
   ${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf
  done

  # Get rid of temp files
  if [ "${DEBUG}" == "Y" ] ; 

[Freesurfer] matrix error

[Allie Rosen]

Hello,

I am analyzing cortical thickness in a patient and control group. I have
two covariates: age and length of disease. I am using the model from:

http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V

However, for the control group I put length of disease as 0 in my FSGD
file. When I run the GLM, I get the following error message:

matrix is ill-conditioned or badly scaled, condno = 1e+08

Can you please tell me what I am doing wrong? Below is the required
information.

1. Your command line:

mri_glmfit --y lh.disease_length.thickness.20.mgz --fsgd
fsgd_disease_length.txt dods --glmdir lh.disease_length.thickness.20.glmdir
--surf fsaverage lh --C groupdiff_length_disease.mat

  2. The FSGD file

GroupDescriptorFile 1
Title Anorexia vs Controls
Class Control plus blue
Class Patient circle green
Variables Age Disease_Length

Input C07 Control 37 0
Input C28 Control 28 0
Input C39 Control 37 0
Input C54 Control 40 0
Input C57 Control 32 0
Input C10 Control 54 0
Input C33 Control 31 0
Input C29 Control 22 0
Input A01 Patient 39 20
Input A02 Patient 24 11
Input A03 Patient 35 15
Input A04 Patient 40 10
Input A05 Patient 35 20
Input A06 Patient 57 20
Input A07 Patient 31 16
Input A08 Patient 20 8

  3. And the design matrix

Design matrix --
 1.000   0.000   37.000   0.000   0.000   0.000;
 1.000   0.000   28.000   0.000   0.000   0.000;
 1.000   0.000   37.000   0.000   0.000   0.000;
 1.000   0.000   40.000   0.000   0.000   0.000;
 1.000   0.000   32.000   0.000   0.000   0.000;
 1.000   0.000   54.000   0.000   0.000   0.000;
 1.000   0.000   31.000   0.000   0.000   0.000;
 1.000   0.000   22.000   0.000   0.000   0.000;
 0.000   1.000   0.000   39.000   0.000   20.000;
 0.000   1.000   0.000   24.000   0.000   11.000;
 0.000   1.000   0.000   35.000   0.000   15.000;
 0.000   1.000   0.000   40.000   0.000   10.000;
 0.000   1.000   0.000   35.000   0.000   20.000;
 0.000   1.000   0.000   57.000   0.000   20.000;
 0.000   1.000   0.000   31.000   0.000   16.000;
 0.000   1.000   0.000   20.000   0.000   8.000;


Thank you,
Allie
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[Freesurfer] Volume to surface 2

[Gabriel Gonzalez Escamilla]

I did forget to tell you that when I use the last command it always outputs the following error:ERROR: MRISread: cannot read surface data from file lh.aseg2raw.mgh! It gives me the same error when trying to load the surface into tksurfer, Is that I've made something wrong?Regards, Gabriel 
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[Freesurfer] Volume to surface

[Gabriel Gonzalez Escamilla]

Hello all FS users and experts,I'm wanting to get the sub cortical segmentation as ASCII files, so I'm trying convert the aseg.mgz into a surface file, to finally get an ASCII file,For this I'm using the next commands:First: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.niiTo preserve  the aseg volume in native space Second: mri_vol2surf --mov aseg2raw.nii --regheader mysubject --hemi lh --o ./lg.aseg2raw.mghAnd last: mris_convert lh.aseg2raw.mgh lh.aseg2raw.ascI'm Not sure if I should do this for the whole aseg or if should I try to separate the segmented structures first...Many Thanks in advanced,Gabriel
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