Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Douglas Greve

the dcmunpack command is right. You should make sure to analyze only the 
RMS in recon-all (ie , that is the only volume that goes into mri/orig
doug


On 5/9/13 6:48 PM, Bruce Fischl wrote:
> Hi Kayle
>
> you would run recon-all on the RMS, then run the dura stuff posthoc.
>
> cheers
> Bruce
> On Thu,
> 9 May 2013, Kayle Sawyer wrote:
>
>> Hi all,
>>
>> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been 
>> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we 
>> instead specify the multiecho scans for recon-all, do we need to give any 
>> additional parameters (e.g. the number of echoes) for it to utilize the 4 
>> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as 
>> described below? Or would we have to run recon-all with the RMS, then after 
>> it finishes re-run mris_make_surfaces manually with the -dura flag to refine 
>> the pial surface?
>>
>> Also, I'd like to make sure we are using dcmunpack properly. We take the
> scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run
> number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz
> file, and the RMS gets put into a separate mgz file.
>> Thanks,
>> -Kayle
>>
>> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>>> Message: 35
>>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
>>> From: Bruce Fischl 
>>> Subject: Re: [Freesurfer] Working with MEMPRAGE
>>> To: Jonathan Holt 
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Message-ID:
>>> 
>>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>>>
>>> it needs to be:
>>>
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
>>>
>>> note the "4" which tells it how many echoes to read
>>>
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>>
 I input:

 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh

 it returns:

 detecting dura using 0 echos from memprage_echo%d.mgz


 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.


 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:

> can you send me the full command line? It should say 4 echoes, not 0
> On Thu, 9 May 2013, Jonathan Holt wrote:
>
>> Thanks Bruce,
>>
>> should the hemisphere's be processed separately, or how do I signify lh 
>> and rh simultaneously?
>>
>> Also, should the fact that after running mris_make_surfaces, it says 
>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
>> I've got 4 different echos, all mgzs in the directory. I have a feeling 
>> I'm doing this incorrectly.
>>
>> jon
>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>>
>>> Hi Jon
>>>
>>> yes, the subject and hemi need to be defined (they are required 
>>> parameters)
>>> Bruce
>>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>>
 Hi all,
 combed through the mail archives to figure out how to work with multi 
 echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon

>>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
Hi Kayle

you would run recon-all on the RMS, then run the dura stuff posthoc.

cheers
Bruce
On Thu, 
9 May 2013, Kayle Sawyer wrote:

> Hi all,
>
> Can the MEMPRAGE be specified in recon-all with the -i flag? We have been 
> using the MEMPRAGE RMS scans and discarding the multiecho scans. If we 
> instead specify the multiecho scans for recon-all, do we need to give any 
> additional parameters (e.g. the number of echoes) for it to utilize the 4 
> echoes to detect dura and refine pial surfaces in mris_make_surfaces, as 
> described below? Or would we have to run recon-all with the RMS, then after 
> it finishes re-run mris_make_surfaces manually with the -dura flag to refine 
> the pial surface?
>
> Also, I'd like to make sure we are using dcmunpack properly. We take the 
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run 
number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz 
file, and the RMS gets put into a separate mgz file.
>
> Thanks,
> -Kayle
>
> On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>> Message: 35
>> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
>> From: Bruce Fischl 
>> Subject: Re: [Freesurfer] Working with MEMPRAGE
>> To: Jonathan Holt 
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>  
>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>>
>> it needs to be:
>>
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
>>
>> note the "4" which tells it how many echoes to read
>>
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>
>>> I input:
>>>
>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>>>
>>> it returns:
>>>
>>> detecting dura using 0 echos from memprage_echo%d.mgz
>>>
>>>
>>> Should I execute the command in the same directory as the mgz's? Should 
>>> they be set up or placed in a specific directory? I also, as with 
>>> recon-all, exported the proper subject directory beforehand.
>>>
>>>
>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>>>
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:

> Thanks Bruce,
>
> should the hemisphere's be processed separately, or how do I signify lh 
> and rh simultaneously?
>
> Also, should the fact that after running mris_make_surfaces, it says 
> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
> I've got 4 different echos, all mgzs in the directory. I have a feeling 
> I'm doing this incorrectly.
>
> jon
> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>
>> Hi Jon
>>
>> yes, the subject and hemi need to be defined (they are required 
>> parameters)
>> Bruce
>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>
>>> Hi all,
>>> combed through the mail archives to figure out how to work with multi 
>>> echo
>>> mprage, found what I need but I wanted to confirm which of these two
>>> commands is the appropriate
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>>> hemispheres need to be specified as per the 1st line?
>>> jon
>>>
>
>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Kayle Sawyer
Hi all,

Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using 
the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead 
specify the multiecho scans for recon-all, do we need to give any additional 
parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect 
dura and refine pial surfaces in mris_make_surfaces, as described below? Or 
would we have to run recon-all with the RMS, then after it finishes re-run 
mris_make_surfaces manually with the -dura flag to refine the pial surface?

Also, I'd like to make sure we are using dcmunpack properly. We take the 
scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run 
number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, 
and the RMS gets put into a separate mgz file.

Thanks,
-Kayle

On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 35
> Date: Thu, 9 May 2013 10:44:23 -0400 (EDT)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] Working with MEMPRAGE
> To: Jonathan Holt 
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>   
> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
> 
> it needs to be:
> 
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
> 
> note the "4" which tells it how many echoes to read
> 
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> I input:
>> 
>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>> 
>> it returns:
>> 
>> detecting dura using 0 echos from memprage_echo%d.mgz
>> 
>> 
>> Should I execute the command in the same directory as the mgz's? Should they 
>> be set up or placed in a specific directory? I also, as with recon-all, 
>> exported the proper subject directory beforehand.
>> 
>> 
>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>> 
>>> can you send me the full command line? It should say 4 echoes, not 0
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>> 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh 
 and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm 
 doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
> Hi Jon
> 
> yes, the subject and hemi need to be defined (they are required 
> parameters)
> Bruce
> On Wed, 8 May 2013, Jonathan Holt wrote:
> 
>> Hi all,
>> combed through the mail archives to figure out how to work with multi 
>> echo
>> mprage, found what I need but I wanted to confirm which of these two
>> commands is the appropriate
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>> hemispheres need to be specified as per the 1st line?
>> jon
>> 


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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Glen Lee
You are right, Doug.
The number of zero-value vertices got reduced more and more when I
increased the smoothing kernel size.

Thanks a lot for your help!
-Glen


On Thu, May 9, 2013 at 3:29 PM, Douglas N Greve
wrote:

>
> command looks ok. Just using a slab would create 0s in a lot of places,
> but those 0s should get smoothed with other non 0s
>
>
> On 05/09/2013 02:06 PM, Glen Lee wrote:
>
>
>>
>>
>> On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>>
>> Does the cortex label have any holes in it and do the holes in
>> your output correspond? Try it with out the --cortex flag.
>> doug
>> -> there was some improvement when I did smoothing after removed
>> '-- cortex flag', such that the number of vertex with '0' was
>> decreased from 35785 to 21898.
>>
>>   I piped in a slab EPI image (covering only temporal regions) to the
>> freesurfer using mri_vol2surf function (see below for more details).
>>   I'm guessing this has caused some holes (i.e., zero-value vertices) in
>> labels during 2D reconstruction?
>>   Or alternatively, do you see any problem in the command below?
>>
>>  mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold'
>> num2str(run) zero_digit num2str(TR) '.nii' ...
>> ' --srcreg ~/DMPC/3D/data/' Subj
>> '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o
>> ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR)
>> '_R.mgh'];
>>
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> https://gate.nmr.mgh.harvard.**edu/filedrop2
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
> greve/ 
>
>
>
> 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.
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> dispose of the e-mail.
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[Freesurfer] Postdoctoral Position at Boston/Children’s Hospital/Harvard Medical School

2013-05-09 Thread Gaab, Nadine
Postdoctoral Position at Boston/Children’s Hospital/Harvard Medical School

The Gaab Labhttp://childrenshospital.org/research/gaablab and 
(babymri.org)) at the Laboratories of Cognitive 
Neuroscience at Boston Children’s Hospital (Developmental Medicine Center) 
invites applications for a NIH funded post-doctoral associate in the area of 
developmental cognitive neuroscience/pediatric fMRI. Available resources 
include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis 
platforms based in MATLAB/UNIX. The candidate will be expected to oversee 
pediatric and infant (f)MRI experiments, analyze behavioral and fMRI data, 
prepare manuscripts for publication, and participate in conferences.

The NIH and foundation funded projects will focus on language processing in 
autism, neural and behavioral pre-markers of developmental dyslexia in infants 
and pre-reading children as well as typical reading and language development 
throughout childhood. The successful applicant should have a doctoral degree in 
a field related to developmental cognitive neuroscience (e.g., cognitive 
neuroscience, neuroscience, psychology, developmental psychology, medicine). 
Individuals with a background in electrical engineering, biomedical engineering 
or computer science will also be considered. The successful applicant must 
possess excellent English verbal and written communication skills. Applicants 
are expected to have a very strong research background in the design and 
statistical analysis of functional brain-imaging experiments. Experience with 
one of the fMRI analyses programs (SPM, FSL, Freesurfer) a must. Programming 
skills (MATLAB, C++; Python) are desirable and experience with MVPA or 
connectivity analyses a plus. Experience with pediatric functional neuroimaging 
and language and reading research are useful. Approximate start date is 
Summer/Early Fall 2013 (the earlier the better). Successful applicants will be 
appointed at Children’s Hospital Boston and Harvard Medical School. For 
consideration please send a statement of interest, a CV and a list of three 
potential referees via email to Nadine Gaab, PhD 
(nadine.g...@childrens.harvard.edu). 
The search will continue until the position is filled.


--
"If we knew what it was we were doing, it would not be called research, would 
it?" A. Einstein (1879-1955)

Nadine Gaab, PhD
Assistant Professor of Pediatrics
Harvard Medical School

Faculty Affiliate
Program in Neuroscience, Harvard Medical School

Member of the Faculty of Education
Harvard Graduate School of Education

Children's Hospital Boston
Department of Medicine/Division of Developmental Medicine
Laboratories of Cognitive Neuroscience
1 Autumn Street (Office 643)
Boston, MA 02115
nadine.g...@childrens.harvard.edu
phone: (857)-218-3021
Main Lab: 617-355-0400
fax: 617-730-0518
http://www.childrenshospital.org/research/gaablab
 www.babymri.org

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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Douglas N Greve

command looks ok. Just using a slab would create 0s in a lot of places, 
but those 0s should get smoothed with other non 0s


On 05/09/2013 02:06 PM, Glen Lee wrote:
>
>
>
> On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Does the cortex label have any holes in it and do the holes in
> your output correspond? Try it with out the --cortex flag.
> doug
> -> there was some improvement when I did smoothing after removed
> '-- cortex flag', such that the number of vertex with '0' was
> decreased from 35785 to 21898. 
>
>
>   I piped in a slab EPI image (covering only temporal regions) to the 
> freesurfer using mri_vol2surf function (see below for more details).
>   I'm guessing this has caused some holes (i.e., zero-value vertices) 
> in labels during 2D reconstruction?
>   Or alternatively, do you see any problem in the command below?
>
>  mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' 
> num2str(run) zero_digit num2str(TR) '.nii' ...
> ' --srcreg ~/DMPC/3D/data/' Subj 
> '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o 
> ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit 
> num2str(TR) '_R.mgh'];
>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Glen Lee
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
wrote:

>
> Does the cortex label have any holes in it and do the holes in your output
> correspond? Try it with out the --cortex flag.
> doug
> -> there was some improvement when I did smoothing after removed '--
> cortex flag', such that the number of vertex with '0' was decreased from
> 35785 to 21898.


  I piped in a slab EPI image (covering only temporal regions) to the
freesurfer using mri_vol2surf function (see below for more details).
  I'm guessing this has caused some holes (i.e., zero-value vertices) in
labels during 2D reconstruction?
  Or alternatively, do you see any problem in the command below?


 mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run)
zero_digit num2str(TR) '.nii' ...
' --srcreg ~/DMPC/3D/data/' Subj
'/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o
~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR)
'_R.mgh'];
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
Hi Jon

you need to run recon-all all the way through, then run the command I sent 
you with the echoes in the mri dir

cheers
Bruce
On Thu, 9 May 2013, Jonathan Holt wrote:

> No,
>
> I believe my PI simply ran mri_convert on the 4 nii's,
>
> Clearly there is a better approach?
>
> jon
> On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:
>
>> Did you run recon-all? It will create filled.mgz in the subject/mri dir
>>
>>
>>
>> On May 9, 2013, at 11:00 AM, Jonathan Holt  wrote:
>>
>>> That was my suspicion, I've got them in the wrong folder. None of them are 
>>> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
>>> nothing else.
>>>
>>> Also the exact error has it looking in 
>>> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz
>>>
>>> as opposed to /example/directory/subjects/subjid/mri/filled.mgz
>>>
>>> I can rename subject directory if need be.
>>>
>>>
>>> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
>>>
 is your SUBJECTS_DIR set properly? You need to put the memprage echoes in
 the subject's mri dir
 On Thu, 9 May 2013, Jonathan Holt wrote:

> Oh, simple mistake!
>
> However, now it spit's an error saying I need filled.mgz?
>
>
> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
>
>> it needs to be:
>>
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
>>
>> note the "4" which tells it how many echoes to read
>>
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>
>>> I input:
>>>
>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>>>
>>> it returns:
>>>
>>> detecting dura using 0 echos from memprage_echo%d.mgz
>>>
>>>
>>> Should I execute the command in the same directory as the mgz's? Should 
>>> they be set up or placed in a specific directory? I also, as with 
>>> recon-all, exported the proper subject directory beforehand.
>>>
>>>
>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>>>
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:

> Thanks Bruce,
>
> should the hemisphere's be processed separately, or how do I signify 
> lh and rh simultaneously?
>
> Also, should the fact that after running mris_make_surfaces, it says 
> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
> I've got 4 different echos, all mgzs in the directory. I have a 
> feeling I'm doing this incorrectly.
>
> jon
> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>
>> Hi Jon
>>
>> yes, the subject and hemi need to be defined (they are required 
>> parameters)
>> Bruce
>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>
>>> Hi all,
>>> combed through the mail archives to figure out how to work with 
>>> multi echo
>>> mprage, found what I need but I wanted to confirm which of these two
>>> commands is the appropriate
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>>> hemispheres need to be specified as per the 1st line?
>>> jon
>>>
>>
>>
>> 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] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Glen Lee
Thanks Doug.
I'll give it a try right away.

Glen


On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
wrote:

>
> Does the cortex label have any holes in it and do the holes in your output
> correspond? Try it with out the --cortex flag.
> doug
>
> ps. Please remember to send to the list and not to me directly. That way
> others can benefit from the exchange and the record goes into our mail
> archive.
>
>
>
>
> On 05/09/2013 11:07 AM, Glen Lee wrote:
>
>> Hi Doug
>>
>> See below for the command line that I used.
>>
>> smoothK=4;
>>
>> mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ...
>> num2str(smoothK) ' --cortex --sval ' Functional_dir
>> Subj '/GLM/all_base-sym_R.mgh '...
>>
>>
>>
>>
>> On Wed, May 8, 2013 at 11:31 PM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.**edu >> wrote:
>>
>> Hi Glen, can you give us more information about what you did? Eg,
>> command line?
>> doug
>>
>>
>>
>> On 5/8/13 8:53 PM, Glen Lee wrote:
>>
>>> Hello freesurfer experts,
>>>
>>> I'm a newbie for freesurfer and would like to ask a naive question.
>>>
>>> I've just applied smoothing onto a single surface mgh file using
>>> mri_surf2surf (with fwhm ==4) and examined the values in the
>>> output map.
>>>
>>> As it turns out, values become 0 in a number of vertices after
>>> smoothing while those in many other vertices look normal (i.e.,
>>> more or less similar to the values in the vertex of unsmoothed map).
>>> I'm not sure why this happened as smoothing average values
>>> locally within the kernel (4mm).
>>>
>>> Any helpful answers would be greatly appreciated.
>>>
>>> Glen
>>>
>>> p.s) fyi, the original EPI is a slap data covering only the
>>> temporal & occipital cortex.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> __**_
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu  >> harvard.edu >
>>> 
>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>>
>>
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu > 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.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> https://gate.nmr.mgh.harvard.**edu/filedrop2
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
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> greve/ 
>
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Re: [Freesurfer] recon-all completes without all the info..

2013-05-09 Thread Louis Nicholas Vinke
Hi Sudhin,
You will need to add -autorecon2 and -autorecon3 to the command you ran 
before, or just replace all -autorecon# flags with the -all flag.

for new subjects:

recon-all -s xyx -i xyz -autorecon1 -autorecon2 -autorecon3

for subjects who already have completed autorecon1:

recon-all -s xyx -autorecon2 -autorecon3

The T1 and brainmask volumes should already exist after completing 
autorecon1.  The rest of those files are creating during autorecon2 and 
autorecon3.
-Louis

On Thu, 9 May 2013, Sudhin A. Shah wrote:

> Hi! I am running this on ~26 datasets and some have exited with errors and 
> others have not completed (~ 2 days).
>
> Sorry, but what should I be running to get the following files?
>
> 1) T1.mgz
> 2) wm.mgz
> 3) aparc+aseg.mgz
> 4) brainmask.mgz
> 5) ribbon.mgz
> 6) And I need to run reg-feat2anat
>
> I am quite certain that what I ran (successfully) before
>
> was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the 
> files above did not populate.
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke 
> [vi...@nmr.mgh.harvard.edu]
> Sent: Tuesday, May 07, 2013 12:05 PM
> To: Sudhin A. Shah
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon-all completes without all the info..
>
> Yes, the -all flag will run autorecon1, autorecon2, and autorecon3.
>
> recon-all -all -i  -s 
>
> For that uncompleted subject you have though if sounds like you just need
> to run autorecon2 and 3
>
> recon-all -autorecon2 -autorecon3 -s 
>
> On Tue, 7 May 2013, Sudhin A. Shah wrote:
>
>> Is there 1 command line? I used to just run the 1 line.
>>
>>
>>
>> On May 7, 2013, at 10:19 AM, "Louis Nicholas Vinke" 
>>  wrote:
>>
>>> Hi Sudhin,
>>> You'll need to also run -autorecon2 and -autorecon3 in order to get 
>>> surfaces and all the cortical/sub-cortical measures.
>>> -Louis
>>>
>>> On Tue, 7 May 2013, Sudhin A. Shah wrote:
>>>
 On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:

  Hi, This is a new issue as it used to run well before.. I run
  recon-all ... ... -autorecon1 - force and it completes without
  error but I don't have all the files..

  Attached is a screenshot. On the right is the output from a file
  that worked before and on the left is a newer folder..
 ___
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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
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 properly
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>>
>>
>>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Jonathan Holt
No, 

I believe my PI simply ran mri_convert on the 4 nii's, 

Clearly there is a better approach?

jon
On May 9, 2013, at 11:04 AM, Bruce Fischl wrote:

> Did you run recon-all? It will create filled.mgz in the subject/mri dir
> 
> 
> 
> On May 9, 2013, at 11:00 AM, Jonathan Holt  wrote:
> 
>> That was my suspicion, I've got them in the wrong folder. None of them are 
>> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
>> nothing else.
>> 
>> Also the exact error has it looking in 
>> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 
>> 
>> as opposed to /example/directory/subjects/subjid/mri/filled.mgz
>> 
>> I can rename subject directory if need be.
>> 
>> 
>> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
>> 
>>> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
>>> the subject's mri dir
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>> 
 Oh, simple mistake!
 
 However, now it spit's an error saying I need filled.mgz?
 
 
 On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
 
> it needs to be:
> 
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
> 
> note the "4" which tells it how many echoes to read
> 
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> I input:
>> 
>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>> 
>> it returns:
>> 
>> detecting dura using 0 echos from memprage_echo%d.mgz
>> 
>> 
>> Should I execute the command in the same directory as the mgz's? Should 
>> they be set up or placed in a specific directory? I also, as with 
>> recon-all, exported the proper subject directory beforehand.
>> 
>> 
>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>> 
>>> can you send me the full command line? It should say 4 echoes, not 0
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>> 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify 
 lh and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
 I've got 4 different echos, all mgzs in the directory. I have a 
 feeling I'm doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
> Hi Jon
> 
> yes, the subject and hemi need to be defined (they are required 
> parameters)
> Bruce
> On Wed, 8 May 2013, Jonathan Holt wrote:
> 
>> Hi all,
>> combed through the mail archives to figure out how to work with 
>> multi echo
>> mprage, found what I need but I wanted to confirm which of these two
>> commands is the appropriate
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>> hemispheres need to be specified as per the 1st line?
>> jon
>> 
> 
> 
> 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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
>> 
>> 
>> 
>> 
 
 
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Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

2013-05-09 Thread Nicola Toschi
Thanks Nick,

well that did change something... here is what i get now with any fs 
command:

/bin/tcsh: /lib64/libfreebl3.so: version `NSSRAWHASH_3.12.3' not found 
(required by /work2/rootbackup/usr/local/freesurfer/lib/libcrypt.so.1)

Should I update/substitute /lib64/libfreebl3.so al well?

thanks a lot,

Nicola

PS when running ldd ./mri_convert inside the bin dir, I get

"not a dynamic executable"



On 05/09/2013 06:02 AM, Nick Schmansky wrote:
> Nicola and Nick,
>
> Hi, its Nick (the other Nick :)). This looks like a new issue we haven't
> seen before that is specific to opensuse.  Can you try downloading the
> file libcrypt.so.1 from this location:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>
> copy it to your freesurfer/lib dir, then set a lib path prior to
> setting-up (sourcing) freesurfer, like this:
>
> setenv FREESURFER_HOME 
> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> this libcrypt lib is from centos6, and i'm thinking that possibly opensuse
> implements crypt differently (working theory anyway).
>
> you can confirm that mri_convert is using this new lib by typing:
>
> cd $FREESURFER_HOME/bin
> ldd ./mri_convert
>
> and you should see libcrypt in the list with a path to the freesurfer/lib
> dir.
>
> Nick
>
>
>> Hi Nick (Schmansky),
>>
>> sorry to jump back in on this thread - I have exactly the same issue
>> (license file not valid) on the same OS (and not on others) with *all*
>> fs commands. I have tried multiple license files from other working
>> installations.
>>
>> Is there anything else i can try?
>>
>> Thanks a lot
>>
>> nicola
>>
>> On 5/8/2013 3:09 PM, Nick Schmansky wrote:
>>> Nick
>>>
>>> Can you email me the .license file that is being used?
>>>
>>> Thanks,
>>>
>>> N.
>>>
>>>
>>> On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote:
 Hi Nick,

 Truncated the email.  I'm getting a license error for both the
 mri_convert command and the tkmedit command that you provided.  The
 original also yields a license error (no segfault).  You are right, my
 earlier test called tkmedit.bin directly.

 Thanks

 Nick

 On 05/08/2013 12:07 PM, Nick Schmansky wrote:
> Nick,
>
> Hi, I found what might the source of the problem and posted new
> versions
> of mri_convert and tkmedit.bin to this directory:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>
> before trying the new mri_convert though, can you try the following?
>
> cd 
> mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz
>
> I'm guessing it will segfault or print the license problem.
>
> Now copy the new mri_convert (from the ftp link above) to the
> freesurfer/bin directory and try again.  It should work.  You can then
> also try the new tkmedit.bin.  Remember to copy the tkmedit.bin to the
> freesurfer/tktools directory and leave freesurfer/bin/tkmedit
> untouched
> (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs,
> so
> tkmedit.bin cannot be run directly)
>
> Thanks,
>
> Nick
>
>
>
>>>
>>>
>>> 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] Why does smoothing make non-zero intensity to zero in many vertices?

2013-05-09 Thread Douglas N Greve

Does the cortex label have any holes in it and do the holes in your 
output correspond? Try it with out the --cortex flag.
doug

ps. Please remember to send to the list and not to me directly. That way 
others can benefit from the exchange and the record goes into our mail 
archive.



On 05/09/2013 11:07 AM, Glen Lee wrote:
> Hi Doug
>
> See below for the command line that I used.
>
> smoothK=4;
>
> mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ...
> num2str(smoothK) ' --cortex --sval ' 
> Functional_dir Subj '/GLM/all_base-sym_R.mgh '...
>
>
>
>
> On Wed, May 8, 2013 at 11:31 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Glen, can you give us more information about what you did? Eg,
> command line?
> doug
>
>
>
> On 5/8/13 8:53 PM, Glen Lee wrote:
>> Hello freesurfer experts,
>>
>> I'm a newbie for freesurfer and would like to ask a naive question.
>>
>> I've just applied smoothing onto a single surface mgh file using
>> mri_surf2surf (with fwhm ==4) and examined the values in the
>> output map.
>>
>> As it turns out, values become 0 in a number of vertices after
>> smoothing while those in many other vertices look normal (i.e.,
>> more or less similar to the values in the vertex of unsmoothed map).
>> I'm not sure why this happened as smoothing average values
>> locally within the kernel (4mm).
>>
>> Any helpful answers would be greatly appreciated.
>>
>> Glen
>>
>> p.s) fyi, the original EPI is a slap data covering only the
>> temporal & occipital cortex.
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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-- 
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] recon-all completes without all the info..

2013-05-09 Thread Sudhin A. Shah
Hi! I am running this on ~26 datasets and some have exited with errors and 
others have not completed (~ 2 days).

Sorry, but what should I be running to get the following files?

1) T1.mgz
2) wm.mgz
3) aparc+aseg.mgz
4) brainmask.mgz
5) ribbon.mgz
6) And I need to run reg-feat2anat

I am quite certain that what I ran (successfully) before 

was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the 
files above did not populate.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke 
[vi...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 07, 2013 12:05 PM
To: Sudhin A. Shah
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all completes without all the info..

Yes, the -all flag will run autorecon1, autorecon2, and autorecon3.

recon-all -all -i  -s 

For that uncompleted subject you have though if sounds like you just need
to run autorecon2 and 3

recon-all -autorecon2 -autorecon3 -s 

On Tue, 7 May 2013, Sudhin A. Shah wrote:

> Is there 1 command line? I used to just run the 1 line.
>
>
>
> On May 7, 2013, at 10:19 AM, "Louis Nicholas Vinke" 
>  wrote:
>
>> Hi Sudhin,
>> You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces 
>> and all the cortical/sub-cortical measures.
>> -Louis
>>
>> On Tue, 7 May 2013, Sudhin A. Shah wrote:
>>
>>> On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote:
>>>
>>>  Hi, This is a new issue as it used to run well before.. I run
>>>  recon-all ... ... -autorecon1 - force and it completes without
>>>  error but I don't have all the files..
>>>
>>>  Attached is a screenshot. On the right is the output from a file
>>>  that worked before and on the left is a newer folder..
>>> ___
>>> Freesurfer mailing list
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> The information in this e-mail is intended only for the person to whom it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
Did you run recon-all? It will create filled.mgz in the subject/mri dir



On May 9, 2013, at 11:00 AM, Jonathan Holt  wrote:

> That was my suspicion, I've got them in the wrong folder. None of them are 
> 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
> nothing else.
> 
> Also the exact error has it looking in 
> /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 
> 
> as opposed to /example/directory/subjects/subjid/mri/filled.mgz
> 
> I can rename subject directory if need be.
> 
> 
> On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:
> 
>> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
>> the subject's mri dir
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>> 
>>> Oh, simple mistake!
>>> 
>>> However, now it spit's an error saying I need filled.mgz?
>>> 
>>> 
>>> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
>>> 
 it needs to be:
 
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
 
 note the "4" which tells it how many echoes to read
 
 On Thu, 9 May 2013, Jonathan Holt wrote:
 
> I input:
> 
> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
> 
> it returns:
> 
> detecting dura using 0 echos from memprage_echo%d.mgz
> 
> 
> Should I execute the command in the same directory as the mgz's? Should 
> they be set up or placed in a specific directory? I also, as with 
> recon-all, exported the proper subject directory beforehand.
> 
> 
> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
> 
>> can you send me the full command line? It should say 4 echoes, not 0
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>> 
>>> Thanks Bruce,
>>> 
>>> should the hemisphere's be processed separately, or how do I signify lh 
>>> and rh simultaneously?
>>> 
>>> Also, should the fact that after running mris_make_surfaces, it says 
>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
>>> I've got 4 different echos, all mgzs in the directory. I have a feeling 
>>> I'm doing this incorrectly.
>>> 
>>> jon
>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>>> 
 Hi Jon
 
 yes, the subject and hemi need to be defined (they are required 
 parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:
 
> Hi all,
> combed through the mail archives to figure out how to work with multi 
> echo
> mprage, found what I need but I wanted to confirm which of these two
> commands is the appropriate
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
> hemispheres need to be specified as per the 1st line?
> jon
> 
 
 
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 HelpLine at
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Jonathan Holt
That was my suspicion, I've got them in the wrong folder. None of them are 
'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and 
nothing else.

Also the exact error has it looking in 
/example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz 

as opposed to /example/directory/subjects/subjid/mri/filled.mgz

I can rename subject directory if need be.


On May 9, 2013, at 10:54 AM, Bruce Fischl wrote:

> is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
> the subject's mri dir
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> Oh, simple mistake!
>> 
>> However, now it spit's an error saying I need filled.mgz?
>> 
>> 
>> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
>> 
>>> it needs to be:
>>> 
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
>>> 
>>> note the "4" which tells it how many echoes to read
>>> 
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>> 
 I input:
 
 mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
 
 it returns:
 
 detecting dura using 0 echos from memprage_echo%d.mgz
 
 
 Should I execute the command in the same directory as the mgz's? Should 
 they be set up or placed in a specific directory? I also, as with 
 recon-all, exported the proper subject directory beforehand.
 
 
 On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
 
> can you send me the full command line? It should say 4 echoes, not 0
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> Thanks Bruce,
>> 
>> should the hemisphere's be processed separately, or how do I signify lh 
>> and rh simultaneously?
>> 
>> Also, should the fact that after running mris_make_surfaces, it says 
>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
>> I've got 4 different echos, all mgzs in the directory. I have a feeling 
>> I'm doing this incorrectly.
>> 
>> jon
>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>> 
>>> Hi Jon
>>> 
>>> yes, the subject and hemi need to be defined (they are required 
>>> parameters)
>>> Bruce
>>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>> 
 Hi all,
 combed through the mail archives to figure out how to work with multi 
 echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
 hemispheres need to be specified as per the 1st line?
 jon
 
>>> 
>>> 
>>> 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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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
 
 
 
 
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Re: [Freesurfer] Subcortical Choi 17 networks ROIs

2013-05-09 Thread Douglas N Greve
Hi Mario, you cannot use the m3z for this since the atlas is in mni152 
space. You can run mni152reg to register your subject to 152 space. Then 
use the resulting registration matrix and mri_label2vol to map the Choi 
atlas to the individual space. The registration will not be perfect 
since it is only 12dof. You could remove voxels that are not in the 
subject's striatum. You can then use fcseed-sess and specify this volume 
and an index in the volume.

doug




On 05/09/2013 10:42 AM, Mario Ortega wrote:
> HI Doug.
> So Im thinking of comparing the 7 striatal networks that are created 
> found here.
> http://ftp.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi2012
>  I want to transform the 7 netwrok striatal roi estimate to subject 
> space, then run fcseed-config and fcseed-sess. with an altered LUT and 
> segmentation.
> Im assuming the talairach.m3z can be used to transform the 7-networks 
> to subject space in each mri/transforms. to do this.
> Is this a feature that is coming into next version 5.3? Also, do I 
> have to go to subject space?
> Thank you for your response.
> -Mario

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
is your SUBJECTS_DIR set properly? You need to put the memprage echoes in 
the subject's mri dir
On Thu, 9 May 2013, Jonathan Holt wrote:

> Oh, simple mistake!
>
> However, now it spit's an error saying I need filled.mgz?
>
>
> On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:
>
>> it needs to be:
>>
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
>>
>> note the "4" which tells it how many echoes to read
>>
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>
>>> I input:
>>>
>>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>>>
>>> it returns:
>>>
>>> detecting dura using 0 echos from memprage_echo%d.mgz
>>>
>>>
>>> Should I execute the command in the same directory as the mgz's? Should 
>>> they be set up or placed in a specific directory? I also, as with 
>>> recon-all, exported the proper subject directory beforehand.
>>>
>>>
>>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>>>
 can you send me the full command line? It should say 4 echoes, not 0
 On Thu, 9 May 2013, Jonathan Holt wrote:

> Thanks Bruce,
>
> should the hemisphere's be processed separately, or how do I signify lh 
> and rh simultaneously?
>
> Also, should the fact that after running mris_make_surfaces, it says 
> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? 
> I've got 4 different echos, all mgzs in the directory. I have a feeling 
> I'm doing this incorrectly.
>
> jon
> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>
>> Hi Jon
>>
>> yes, the subject and hemi need to be defined (they are required 
>> parameters)
>> Bruce
>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>
>>> Hi all,
>>> combed through the mail archives to figure out how to work with multi 
>>> echo
>>> mprage, found what I need but I wanted to confirm which of these two
>>> commands is the appropriate
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>>> hemispheres need to be specified as per the 1st line?
>>> jon
>>>
>>
>>
>> The information in this e-mail is intended only for the person to whom 
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you 
>> in error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
>
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>>>
>>>
>>>
>>>
>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Jonathan Holt
Oh, simple mistake! 

However, now it spit's an error saying I need filled.mgz?


On May 9, 2013, at 10:44 AM, Bruce Fischl wrote:

> it needs to be:
> 
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh
> 
> note the "4" which tells it how many echoes to read
> 
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> I input:
>> 
>> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>> 
>> it returns:
>> 
>> detecting dura using 0 echos from memprage_echo%d.mgz
>> 
>> 
>> Should I execute the command in the same directory as the mgz's? Should they 
>> be set up or placed in a specific directory? I also, as with recon-all, 
>> exported the proper subject directory beforehand.
>> 
>> 
>> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>> 
>>> can you send me the full command line? It should say 4 echoes, not 0
>>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>> 
 Thanks Bruce,
 
 should the hemisphere's be processed separately, or how do I signify lh 
 and rh simultaneously?
 
 Also, should the fact that after running mris_make_surfaces, it says 
 "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've 
 got 4 different echos, all mgzs in the directory. I have a feeling I'm 
 doing this incorrectly.
 
 jon
 On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
 
> Hi Jon
> 
> yes, the subject and hemi need to be defined (they are required 
> parameters)
> Bruce
> On Wed, 8 May 2013, Jonathan Holt wrote:
> 
>> Hi all,
>> combed through the mail archives to figure out how to work with multi 
>> echo
>> mprage, found what I need but I wanted to confirm which of these two
>> commands is the appropriate
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
>> hemispheres need to be specified as per the 1st line?
>> jon
>> 
> 
> 
> 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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 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
>> 
>> 
>> 
>> 


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Re: [Freesurfer] Using FSL matrix for Talairach transform

2013-05-09 Thread Douglas N Greve
yep, can you upload the relevant datato our file drop?

On 05/09/2013 05:52 AM, Johannes Klein wrote:
> Hi Doug,
> Thanks! I've tried that now, but it didn't help. Looking at the output, I get 
> the impression that some of the axes might be swapped over. I've done a 
> manual registration now to process my subject.
> Maybe it's worth following this up for future use of FSL-supplied matrices - 
> however, the problem only applies to XFM-style output, and e.g. mri_vol2vol 
> works fine, so I guess there aren't many other users affected. If you like, I 
> can send you a few volumes and the associated registration matrix.
> Thanks for your help!
> Cheers,
> Johannes
>
> Douglas N Greve Wed, 08 May 2013 12:16:36 -0700
>
> Hi Johannes, as a quick fix can you try inverting the matrix?
> doug
>
> On 05/08/2013 01:31 PM, Johannes Klein wrote:
>> Hi Doug,
>> Thanks for your reply! I'm getting closer to a solution now, with
>> tkregister2's display showing a correctly transformed mni305 file,
>> but I still cannot get a valid talairach.xfm file out of this.
>>
>> Here's what I tried:
>> tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz
>>   --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg
>> works fine.
>>
>> Next, to obtain a suitable .xfm file, I ran
>> tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz
>>   --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg  --xfmout
>> testtal.xfm --noedit
>> and copied the output (testtal.xfm) into mri/transforms/talairach.xfm
>>
>> Now, when I view the result with
>> tkregister2 --s test --fstal --mgz
>> the transform is way off again. Apparently, tkregister2 reads and
>> interprets the FSL matrix correctly, but the output transform that I
>> get is not in the right format for transforms/talairach.xfm.
>> I wonder if I'm using the wrong output switch now - but looking at
>> tkregister2's documentation, it seems to be the one to use?
>> Thanks,
>> Johannes
>>
>>
>>
>> Date: Tue, 07 May 2013 14:11:27 -0400
>> From: Douglas N Greve > <
> mailto:gr...@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform
>> To: freesurfer@nmr.mgh.harvard.edu <
> mailto:freesurfer@nmr.mgh.harvard.edu
>> Message-ID: <518943cf.7050...@nmr.mgh.harvard.edu
>> <
> mailto:518943cf.7050...@nmr.mgh.harvard.edu
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure
>> what regdat2xfm is doing.
>> doug
>>
>> On 05/07/2013 12:42 PM, Johannes Klein wrote:
>>> Dear all,
>>> I have some tricky subjects that I cannot get to register properly
>>> with the standard Talairach process, or even the use-mritotal option.
>>> However, with some fiddling, I've produced a reasonable registration
>>> matrix with FSL's FLIRT.
>>>
>>> I'm now looking to convert my FSL registration matrix, and use it as
>>> Freesurfer's Talairach transform. From the documentation, I gathered
>>> that I need to get it into Freesurfer's xfm format, and I suppose
>>> this is a two step process.
>>>
>>> I converted the FLIRT-provided matrix cor2raw.xfm like so:
>>> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz
>>>   --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat
>>>
>>> I then converted register.dat to the xfm data format:
>>> regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz
>>> register.dat tal.xfm
>>>
>>> and finally replaced talairach.xfm in the transforms directory with
>>> the output of the last command. Unfortunately, this doesn't work, and
>>> the transform is very much off target when I view it in tkregister2.
>>> Obviously, I've made a mistake when converting between the different
>>> transforms - could anybody point me in the right direction?
>>> Thanks all,
>>> Johannes
>>>
>>>
>>>
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>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <
> mailto:gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop:
> https://gate.nmr.mgh.harvard.edu/filedrop2
>
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <
> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>>
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-- 
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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] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
it needs to be:

mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh

note the "4" which tells it how many echoes to read

On Thu, 9 May 2013, Jonathan Holt wrote:

> I input:
>
> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh
>
> it returns:
>
> detecting dura using 0 echos from memprage_echo%d.mgz
>
>
> Should I execute the command in the same directory as the mgz's? Should they 
> be set up or placed in a specific directory? I also, as with recon-all, 
> exported the proper subject directory beforehand.
>
>
> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:
>
>> can you send me the full command line? It should say 4 echoes, not 0
>> On Thu, 9 May 2013, Jonathan Holt wrote:
>>
>>> Thanks Bruce,
>>>
>>> should the hemisphere's be processed separately, or how do I signify lh and 
>>> rh simultaneously?
>>>
>>> Also, should the fact that after running mris_make_surfaces, it says 
>>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've 
>>> got 4 different echos, all mgzs in the directory. I have a feeling I'm 
>>> doing this incorrectly.
>>>
>>> jon
>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>>>
 Hi Jon

 yes, the subject and hemi need to be defined (they are required parameters)
 Bruce
 On Wed, 8 May 2013, Jonathan Holt wrote:

> Hi all,
> combed through the mail archives to figure out how to work with multi echo
> mprage, found what I need but I wanted to confirm which of these two
> commands is the appropriate
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and 
> hemispheres need to be specified as per the 1st line?
> jon
>


 The information in this e-mail is intended only for the person to whom it 
 is
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail
 contains patient information, please contact the Partners Compliance 
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.

>>>
>>>
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>>>
>>>
>>>
>
>
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Jonathan Holt
I input:

mris_make_surfaces -dura memprage_echo%d.mgz subjid lh

it returns:

detecting dura using 0 echos from memprage_echo%d.mgz


Should I execute the command in the same directory as the mgz's? Should they be 
set up or placed in a specific directory? I also, as with recon-all, exported 
the proper subject directory beforehand. 


On May 9, 2013, at 10:37 AM, Bruce Fischl wrote:

> can you send me the full command line? It should say 4 echoes, not 0
> On Thu, 9 May 2013, Jonathan Holt wrote:
> 
>> Thanks Bruce,
>> 
>> should the hemisphere's be processed separately, or how do I signify lh and 
>> rh simultaneously?
>> 
>> Also, should the fact that after running mris_make_surfaces, it says 
>> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've 
>> got 4 different echos, all mgzs in the directory. I have a feeling I'm doing 
>> this incorrectly.
>> 
>> jon
>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>> 
>>> Hi Jon
>>> 
>>> yes, the subject and hemi need to be defined (they are required parameters)
>>> Bruce
>>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>> 
 Hi all,
 combed through the mail archives to figure out how to work with multi echo
 mprage, found what I need but I wanted to confirm which of these two
 commands is the appropriate
 mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
 mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
 need to be specified as per the 1st line?
 jon
 
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>> 
>> 
>> 
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>> 
>> 


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Re: [Freesurfer] Labels and parcellations

2013-05-09 Thread Douglas N Greve

On 05/08/2013 05:24 PM, Tudor Popescu wrote:
> Sorry, one more iteration:
>
> 1) Command "mri_annotation2label --subject 01 --hemi lh --aparc.a2009s 
> --outdir $SUBJECTS_DIR/01/myLabelsDestrieux" doesn't recognise the 
> aparc.2009s flag (I tried a few other variations with no luck)!
The syntax is --annot aparc.2009s
If you run mri_annotation2label with --help it will tell you the syntax.
>
> 1') Assuming the above command works and I get .label files 
> corresponding to all Destrieux structures, what is the exact call to 
> mri_glmfit that will do the two contrasts I mentioned (group 
> comparison of CT, and comparison of CT-behaviour correlation)?
>
> 1'') How should the design matrix & contrast files (arguments for 
> calling mri_glmfit) be created, for these analyses?
Have you looked at our group analysis tutorials?
>
> 2) ..so when would I use a mask, in a ROI analysis, as opposed to a label?
Functionally, there is no difference. If you had a process that 
generated a mask, then you would just use that. You can convert any mask 
to a label with mri_cor2label. mri_glmfit will give you the same result.
>
> 3) I'm still not sure as to the answer to my question: regardless of 
> what space I do it in, does it pay off to create the label/mask that 
> I"ll use in the ROI analysis /manually /for each individual subject 
> (i.e. taking into account individual anatomy), as opposed to just 
> taking it from an atlas and using /the same /label/mask with /all 
> /subjects?
If you are using it as a mask for voxel-wise analysis, then you need a 
mask in the common space. You could get this mask by drawing the mask in 
the common space. Or you could draw the mask on each individual, then 
map the masks to the common space. But you would need to then merge all 
those masks together into a single binary mask. I don't know whether one 
would be better than the other, but the individual masks will surely be 
a lot more work.
>
> 4) Bingo - this creates an image as I wanted, but now the mouse cursor 
> no longer tells me the structure above which I hover the mouse (so a 
> legend to each color, much like in Fig 1 of the Desikan paper)
I don't understand what you mean here. The name of the structure should 
appear in the control window. It does not appear in the image window 
like in Fig 1.
doug
>
> I really appreciate your patience Doug, thanks :)
> Tudor
>
> On 8 May 2013 18:56, Douglas N Greve  > wrote:
>
>
> On 05/08/2013 01:28 PM, Tudor Popescu wrote:
>
>
> 2) ..and when would you use a surface mask versus a
> surface label?
>
> It is just a matter of convenience.
>
> Sorry, I meant I don't really understand what the difference
> is between a label and a mask, and in which circumstances each
> should be used. I tried finding an answer on the wiki but no
> luck..
>
> A label is a text file with a list of points in the label. A mask
> is binary file (eg, mgh or nii) with 1s where the mask is and 0s
> otherwise.
>
>
> 3) (it seems you skipped over this one:) )
>
> Sorry:) what are you going to do with the ROI?
>
> Use it mri_glmfit, in order to compare cortical thickness in
> that ROI between groups, and also (in a different design) to
> compare the correlations between thickness and a behavioural
> predictor
>
> If you're doing the final analysis in the group space, then just
> use the ROI in the group space.
>
>
> 4) This opens up a coronal slice rather than a 3D
> image as in
> the picture I linked to. Do I need to do anything else in
> tkmedit after it opens? (I tried pressing some
> buttons, and
> some menu options, with no luck)
>
> that was generated with tksurfer, something like tksurfer
> subject
> lh pial -aparc
>
> Using that command, I get a brain
>  that
> has only little of its surface coloured, unlike the image
> 
> 
> that I linked to, in which it seems each major structure is
> identified in its own colour, and these colours fill up the
> entire brain (there's no grey surface left)
>
> Change the annotation mode to be filled instead of outline mode.
> In the tksurfer control window, it is the 4th button from the
> right on the top row. It will say "Draw Filled Labels" when you
> put the mouse over it
>
>
>
>
> On 8 May 2013 16:54, Douglas N Greve
>  
>  >
>  

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
can you send me the full command line? It should say 4 echoes, not 0
On Thu, 
9 May 2013, Jonathan Holt wrote:

> Thanks Bruce,
>
> should the hemisphere's be processed separately, or how do I signify lh and 
> rh simultaneously?
>
> Also, should the fact that after running mris_make_surfaces, it says 
> "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've 
> got 4 different echos, all mgzs in the directory. I have a feeling I'm doing 
> this incorrectly.
>
> jon
> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:
>
>> Hi Jon
>>
>> yes, the subject and hemi need to be defined (they are required parameters)
>> Bruce
>> On Wed, 8 May 2013, Jonathan Holt wrote:
>>
>>> Hi all,
>>> combed through the mail archives to figure out how to work with multi echo
>>> mprage, found what I need but I wanted to confirm which of these two
>>> commands is the appropriate
>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
>>> need to be specified as per the 1st line?
>>> jon
>>>
>>
>>
>> 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] Qdec error and design problem

2013-05-09 Thread Douglas N Greve
Hi Sinead, you cannot use QDEC for this design since it has one factor 
with 3 levels (only 2 levels possible now). You can create an FSGD file, 
follow the example here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V

doug


On 05/09/2013 06:42 AM, Sinead Kelly wrote:
> Dear all,
>
> I am trying to run statistical analysis on cortical thickness data 
> using Qdec. I have one group of control subjects that are split into 
> three genotype groups. I want to investigate if cortical thickness 
> significantly between the three genotype groups. Is it possible to 
> look at differences between three groups using Qdec? I am getting the 
> following error when I try to analyse - ERROR: QdecGlmDesign::Create: 
> zero factors!
>
> I would really appreciate if anyone could shed some light on this for 
> me as this is the first time I have used Qdec and I don't know what is 
> causing this error.
>
> Thank you for your help.
>
> Sinead
>
> -- 
> Sinead Kelly
> Neuropsychiatric Genetics Group
> Trinity Centre
> St. James's Hospital
> Dublin 8
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Jonathan Holt
Thanks Bruce,

should the hemisphere's be processed separately, or how do I signify lh and rh 
simultaneously? 

Also, should the fact that after running mris_make_surfaces, it says "detecting 
dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different 
echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly.

jon
On May 9, 2013, at 8:50 AM, Bruce Fischl wrote:

> Hi Jon
> 
> yes, the subject and hemi need to be defined (they are required parameters)
> Bruce
> On Wed, 8 May 2013, Jonathan Holt wrote:
> 
>> Hi all,
>> combed through the mail archives to figure out how to work with multi echo
>> mprage, found what I need but I wanted to confirm which of these two
>> commands is the appropriate
>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres 
>> need to be specified as per the 1st line?
>> jon
>> 
> 
> 
> 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] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
Hi Jon

yes, the subject and hemi need to be defined (they are required 
parameters)
Bruce
On Wed, 8 May 2013, Jonathan Holt wrote:

> Hi all,
> combed through the mail archives to figure out how to work with multi echo
> mprage, found what I need but I wanted to confirm which of these two
> commands is the appropriate
> 
> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh
> 
> mris_make_surfaces -dura memprage_echo%d.mgz 
> 
> do the subjid and hemispheres need to be specified as per the 1st line?
> 
> jon
> 
> 
> 
> 
>
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[Freesurfer] Qdec error and design problem

2013-05-09 Thread Sinead Kelly
Dear all,

I am trying to run statistical analysis on cortical thickness data using
Qdec. I have one group of control subjects that are split into three
genotype groups. I want to investigate if cortical thickness significantly
between the three genotype groups. Is it possible to look at differences
between three groups using Qdec? I am getting the following error when I
try to analyse - ERROR: QdecGlmDesign::Create: zero factors!

I would really appreciate if anyone could shed some light on this for me as
this is the first time I have used Qdec and I don't know what is causing
this error.

Thank you for your help.

Sinead

-- 
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3

2013-05-09 Thread Nick Schmansky
Nicola and Nick,

Hi, its Nick (the other Nick :)). This looks like a new issue we haven't
seen before that is specific to opensuse.  Can you try downloading the
file libcrypt.so.1 from this location:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/

copy it to your freesurfer/lib dir, then set a lib path prior to
setting-up (sourcing) freesurfer, like this:

setenv FREESURFER_HOME 
setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib
source $FREESURFER_HOME/SetUpFreeSurfer.csh

this libcrypt lib is from centos6, and i'm thinking that possibly opensuse
implements crypt differently (working theory anyway).

you can confirm that mri_convert is using this new lib by typing:

cd $FREESURFER_HOME/bin
ldd ./mri_convert

and you should see libcrypt in the list with a path to the freesurfer/lib
dir.

Nick


> Hi Nick (Schmansky),
>
> sorry to jump back in on this thread - I have exactly the same issue
> (license file not valid) on the same OS (and not on others) with *all*
> fs commands. I have tried multiple license files from other working
> installations.
>
> Is there anything else i can try?
>
> Thanks a lot
>
> nicola
>
> On 5/8/2013 3:09 PM, Nick Schmansky wrote:
>> Nick
>>
>> Can you email me the .license file that is being used?
>>
>> Thanks,
>>
>> N.
>>
>>
>> On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote:
>>> Hi Nick,
>>>
>>> Truncated the email.  I'm getting a license error for both the
>>> mri_convert command and the tkmedit command that you provided.  The
>>> original also yields a license error (no segfault).  You are right, my
>>> earlier test called tkmedit.bin directly.
>>>
>>> Thanks
>>>
>>> Nick
>>>
>>> On 05/08/2013 12:07 PM, Nick Schmansky wrote:
 Nick,

 Hi, I found what might the source of the problem and posted new
 versions
 of mri_convert and tkmedit.bin to this directory:

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/

 before trying the new mri_convert though, can you try the following?

 cd 
 mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz

 I'm guessing it will segfault or print the license problem.

 Now copy the new mri_convert (from the ftp link above) to the
 freesurfer/bin directory and try again.  It should work.  You can then
 also try the new tkmedit.bin.  Remember to copy the tkmedit.bin to the
 freesurfer/tktools directory and leave freesurfer/bin/tkmedit
 untouched
 (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs,
 so
 tkmedit.bin cannot be run directly)

 Thanks,

 Nick



>>>
>>
>>
>>
>> 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] Using FSL matrix for Talairach transform

2013-05-09 Thread Johannes Klein
Hi Doug,
Thanks! I've tried that now, but it didn't help. Looking at the output, I get 
the impression that some of the axes might be swapped over. I've done a manual 
registration now to process my subject. 
Maybe it's worth following this up for future use of FSL-supplied matrices - 
however, the problem only applies to XFM-style output, and e.g. mri_vol2vol 
works fine, so I guess there aren't many other users affected. If you like, I 
can send you a few volumes and the associated registration matrix.
Thanks for your help!
Cheers,
Johannes

Douglas N Greve Wed, 08 May 2013 12:16:36 -0700

Hi Johannes, as a quick fix can you try inverting the matrix?
doug

On 05/08/2013 01:31 PM, Johannes Klein wrote:
> Hi Doug,
> Thanks for your reply! I'm getting closer to a solution now, with 
> tkregister2's display showing a correctly transformed mni305 file, 
> but I still cannot get a valid talairach.xfm file out of this.
>
> Here's what I tried:
> tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz 
>  --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg
> works fine.
>
> Next, to obtain a suitable .xfm file, I ran
> tkregister2 --mov  /usr/local/freesurfer/average/mni305.cor.mgz 
>  --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg  --xfmout 
> testtal.xfm --noedit
> and copied the output (testtal.xfm) into mri/transforms/talairach.xfm
>
> Now, when I view the result with
> tkregister2 --s test --fstal --mgz
> the transform is way off again. Apparently, tkregister2 reads and 
> interprets the FSL matrix correctly, but the output transform that I 
> get is not in the right format for transforms/talairach.xfm.
> I wonder if I'm using the wrong output switch now - but looking at 
> tkregister2's documentation, it seems to be the one to use?
> Thanks,
> Johannes
>
>
>
> Date: Tue, 07 May 2013 14:11:27 -0400
> From: Douglas N Greve  <
mailto:gr...@nmr.mgh.harvard.edu
>>
> Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform
> To: freesurfer@nmr.mgh.harvard.edu <
mailto:freesurfer@nmr.mgh.harvard.edu
>
> Message-ID: <518943cf.7050...@nmr.mgh.harvard.edu 
> <
mailto:518943cf.7050...@nmr.mgh.harvard.edu
>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure
> what regdat2xfm is doing.
> doug
>
> On 05/07/2013 12:42 PM, Johannes Klein wrote:
>> Dear all,
>> I have some tricky subjects that I cannot get to register properly 
>> with the standard Talairach process, or even the use-mritotal option. 
>> However, with some fiddling, I've produced a reasonable registration 
>> matrix with FSL's FLIRT.
>>
>> I'm now looking to convert my FSL registration matrix, and use it as 
>> Freesurfer's Talairach transform. From the documentation, I gathered 
>> that I need to get it into Freesurfer's xfm format, and I suppose 
>> this is a two step process.
>>
>> I converted the FLIRT-provided matrix cor2raw.xfm like so:
>> tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz 
>>  --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat
>>
>> I then converted register.dat to the xfm data format:
>> regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz 
>> register.dat tal.xfm
>>
>> and finally replaced talairach.xfm in the transforms directory with 
>> the output of the last command. Unfortunately, this doesn't work, and 
>> the transform is very much off target when I view it in tkregister2.
>> Obviously, I've made a mistake when converting between the different 
>> transforms - could anybody point me in the right direction?
>> Thanks all,
>> Johannes
>>
>>
>>
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>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <
mailto: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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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> <
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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