[Freesurfer] (no subject)

2017-09-11 Thread yl88 
Hi all,

I have finished the command “recon -all” without error. But I get an error that 
says:
“Received X error!
  Error code :158
  Request code : 148
  Minor code: 2
  Error text :’GLXBadLargeRequest’”

I am using the command “tksurfer sub lh inflated”.
Then clicking the File->Label->load label.->
and choosing document of “the lh.apare.a2009.annot”. 


I don’t know why I got this error so would you be able to explain why this is 
the case and how I can go about resolving this problem? 

Best,
Yvonne 
 
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Re: [Freesurfer] group analysis on thickness/mask

2017-09-11 Thread Xianwei Che 
Dear Doug,

After some trial and error I am still not able to run group analysis in ROI
manner.

Here is my understanding: I need to define a label (mri_binarize ?) in
which my ROIs should be labeled as 1 with other regions being 0. Then I can
take this label to glm with --lable and then run correction. If this is a
right way can you tell me a little bit more of how to do this. I am working
on cortical thickness data.

Thanks huge



*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia

On 12 September 2017 at 08:42, Xianwei Che  wrote:

> Dear Doug,
>
> Thank you for the answer. I will try it out.
>
> Regards
>
> *-*
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 01:44, Douglas N Greve 
> wrote:
>
>>
>>
>> On 09/10/2017 04:02 AM, Xianwei Che wrote:
>> > Dear experts,
>> >
>> > I am going to run a group analysis on thickness but limit the results
>> > to certain regions, say prefrontal  cortex. l did find this thread but
>> > failed to make it work on my data
>> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
>> /msg48693.html).
>> > I know I could extract the signal of the ROI but also interested in
>> > this way.
>> >
>> > Here are my questions:
>> > 1. mri_binarize should be working on the average data or the single
>> > data in each participant. If it should be on individual data, what the
>> > loop should be (if I have a text file SUBJECTS listing the
>> participants).
>> Actually, I don't know what [subjects] is supposed to mean. You should
>> include the index for the ROIs you want in the analysis
>> > 2. How the --match is used. I --helped the mri_binarize but did not
>> > get it. Is it for specifying the ROI by number, say the number of PFC?
>> There is no PFC ROI. You will have to piece it together from other ROIs.
>> You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt.
>> Look in the section for aparc+aseg.mgz
>> > 3. If I could finish the mask creation and merge to label; do I have
>> > to undergo the data concatenating stage (i.e. preproc, surf2surf) or
>> > directly move to glm. I saw another thread skipping these stages but
>> > it's on volume data
>> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
>> /msg32190.html).
>> Yu can move directly to the GLM
>> >
>> > Thank you so much!
>> >
>> >
>> > /-/
>> > Mr Xianwei Che
>> > PhD Candidate
>> > Monash Alfred Psychiatry Research Centre (MAPrc)
>> > Central Clinical School & the Alfred
>> > Monash University
>> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>>
>>
>> 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] group analysis on thickness/mask

2017-09-11 Thread Xianwei Che 
Dear Doug,

Thank you for the answer. I will try it out.

Regards

*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia

On 12 September 2017 at 01:44, Douglas N Greve 
wrote:

>
>
> On 09/10/2017 04:02 AM, Xianwei Che wrote:
> > Dear experts,
> >
> > I am going to run a group analysis on thickness but limit the results
> > to certain regions, say prefrontal  cortex. l did find this thread but
> > failed to make it work on my data
> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg48693.html).
> > I know I could extract the signal of the ROI but also interested in
> > this way.
> >
> > Here are my questions:
> > 1. mri_binarize should be working on the average data or the single
> > data in each participant. If it should be on individual data, what the
> > loop should be (if I have a text file SUBJECTS listing the participants).
> Actually, I don't know what [subjects] is supposed to mean. You should
> include the index for the ROIs you want in the analysis
> > 2. How the --match is used. I --helped the mri_binarize but did not
> > get it. Is it for specifying the ROI by number, say the number of PFC?
> There is no PFC ROI. You will have to piece it together from other ROIs.
> You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt.
> Look in the section for aparc+aseg.mgz
> > 3. If I could finish the mask creation and merge to label; do I have
> > to undergo the data concatenating stage (i.e. preproc, surf2surf) or
> > directly move to glm. I saw another thread skipping these stages but
> > it's on volume data
> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg32190.html).
> Yu can move directly to the GLM
> >
> > Thank you so much!
> >
> >
> > /-/
> > Mr Xianwei Che
> > PhD Candidate
> > Monash Alfred Psychiatry Research Centre (MAPrc)
> > Central Clinical School & the Alfred
> > Monash University
> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is 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] Talairach registration error

2017-09-11 Thread Ariana Vajdi 
Ok - thank you! I will speak to the person who generated the files then.

On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve 
wrote:

> I don't know how you (or someone else) generated the nifti files in the
> first place, so I can't help there. If you did not generate them, then
> talk to the person who did. I do not really recommend trying to do it by
> hand. You can get AP and SI correctly, but you'll never know whether
> they are LR reversed or not
>
>
> On 09/11/2017 04:12 PM, Ariana Vajdi wrote:
> > Ah, I see - how would I be able to do either of those? And would I
> > have to check the geometry of each scan individually? Not sure how
> > that works, but I have a substantially large dataset.
> >
> > Thank you for your response!
> >
> > On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve
> > > wrote:
> >
> > That means that geometry information (ie, what is left and right,
> > anterior or posterior) is not part of the nifti file. Without that
> > information, the anatomical analysis cannot be done. You will either
> > have to fix it yourself (ie, imbed that info into the file) or,
> > better,
> > recreate the file with the proper geometry info
> >
> >
> > On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
> > > Hello,
> > >
> > > Hope this message finds you well.
> > >
> > > I was beginning to run recon-all on a dataset and was encountering
> a
> > > problem with the talairach registration. I've encountered this
> error
> > > before here and there, but I've been receiving the same error for
> > > every scan that I've been trying to run, and I'm not sure why. It's
> > > also the first time I've used NIFTI files as the input - not sure
> if
> > > that's a contributing factor. I've also tried the -use-mritotal
> flag
> > > without any luck.
> > >
> > > These are the errors I receive:
> > >
> > > WARNING: neither NIfTI-1 qform or sform are valid
> > >
> > > WARNING: your volume will probably be incorrectly oriented
> > >
> > >
> > > ERROR: talairach_afd: Talairach Transform:
> > > transforms/talairach.xfm ***FAILED*** (p=0., pval=0. <
> > > threshold=0.0050)
> > >
> > > Manual Talairach alignment may be necessary, or
> > >
> > > include the -notal-check flag to skip this test,
> > >
> > > making sure the -notal-check flag follows -all
> > >
> > > or -autorecon1 in the command string.
> > >
> > >
> > > I would appreciate your help. Thank you!
> > >
> > > Warmly,
> > > Ariana
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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.
> >
> >
> >
> >
> > ___
> > 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
>
>

Re: [Freesurfer] Talairach registration error

2017-09-11 Thread Douglas N Greve 
I don't know how you (or someone else) generated the nifti files in the 
first place, so I can't help there. If you did not generate them, then 
talk to the person who did. I do not really recommend trying to do it by 
hand. You can get AP and SI correctly, but you'll never know whether 
they are LR reversed or not


On 09/11/2017 04:12 PM, Ariana Vajdi wrote:
> Ah, I see - how would I be able to do either of those? And would I 
> have to check the geometry of each scan individually? Not sure how 
> that works, but I have a substantially large dataset.
>
> Thank you for your response!
>
> On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve 
> > wrote:
>
> That means that geometry information (ie, what is left and right,
> anterior or posterior) is not part of the nifti file. Without that
> information, the anatomical analysis cannot be done. You will either
> have to fix it yourself (ie, imbed that info into the file) or,
> better,
> recreate the file with the proper geometry info
>
>
> On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
> > Hello,
> >
> > Hope this message finds you well.
> >
> > I was beginning to run recon-all on a dataset and was encountering a
> > problem with the talairach registration. I've encountered this error
> > before here and there, but I've been receiving the same error for
> > every scan that I've been trying to run, and I'm not sure why. It's
> > also the first time I've used NIFTI files as the input - not sure if
> > that's a contributing factor. I've also tried the -use-mritotal flag
> > without any luck.
> >
> > These are the errors I receive:
> >
> > WARNING: neither NIfTI-1 qform or sform are valid
> >
> > WARNING: your volume will probably be incorrectly oriented
> >
> >
> > ERROR: talairach_afd: Talairach Transform:
> > transforms/talairach.xfm ***FAILED*** (p=0., pval=0. <
> > threshold=0.0050)
> >
> > Manual Talairach alignment may be necessary, or
> >
> > include the -notal-check flag to skip this test,
> >
> > making sure the -notal-check flag follows -all
> >
> > or -autorecon1 in the command string.
> >
> >
> > I would appreciate your help. Thank you!
> >
> > Warmly,
> > Ariana
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve 
No, you at least have to run it through autorecon2


On 09/11/2017 04:06 PM, Sherrill, John T wrote:
> Sounds good. Unfortunately when I open many of my files that do not contain 
> an aseg file.  Many only have a scripts directory and nothing else. Is there 
> a way to process the files to just get the aseg data without doing a 
> recon-all?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, September 11, 2017 2:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> Yea, that's what I would do. You can run asegstats2table to get a list
> of the volume for all ROIs (so this gives you a matrix of 550 by about
> 50). For each row (subject),  compare the volumes to that of every other
> row. You'll need to come up with a comparison function; maybe mean
> percent difference (you might need to exclude very small structures like
> optic chiasm, vessels, etc -- or only include certain structures like
> hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects
> from lowest to highest difference and look at the ones with the lowest
> difference. You can probably think of other ways
>
>
> On 09/11/2017 03:17 PM, Sherrill, John T wrote:
>> I have run recon-all on all of the files. So I should start with 
>> asegstats2table ( 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_asegstats2table=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=MtJnnh5bFgsrOhtUjpvIR4hZ8YcefgfBG4f5F2sJI84=7l-5w5DwKzRbjsxDY-U40umkQFkb_J0u-1f06ML1V94=
>>   ) ?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Monday, September 11, 2017 2:07 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>>
>> One way is to perform a 6DOF registration between each pair. It is a lot
>> of pairs, but I don't think you can avoid it. Pairs that come from the
>> same subject will have an abnormally high (or low) objective function.
>> You could use mri_coreg (use --no-smooth) . If you've already run all
>> 550 through FS, then you might be able to look a the aseg.stats for
>> similar subjects.
>>
>>
>> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>>> I am trying to find the best way to identify likely duplicate subjects
>>> with in a database of about 550 subjects. Some subjects where
>>> duel-consented for studies and had multiple scans over a relatively
>>> short period of time. What is the best way to tease these out?
>>>
>>> John Sherrill
>>> jtsherr...@uams.edu
>>> john_sherr...@me.com
>>> (870) 761-0580
>>> 
>>> Confidentiality Notice: This e-mail message, including any
>>> attachments, is for the sole use of the intended recipient(s) and may
>>> contain confidential and privileged information. Any unauthorized
>>> review, use, disclosure or distribution is prohibited. If you are not
>>> the intended recipient, please contact the sender by reply e-mail and
>>> destroy all copies of the original message.
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
>> --
>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: 
>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=Mj9DAJaDWsk0JKAxs99YViYRgOnIG81THLDrpjx0zEM=
>>
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>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>

Re: [Freesurfer] Talairach registration error

2017-09-11 Thread Ariana Vajdi 
Ah, I see - how would I be able to do either of those? And would I have to
check the geometry of each scan individually? Not sure how that works, but
I have a substantially large dataset.

Thank you for your response!

On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve 
wrote:

> That means that geometry information (ie, what is left and right,
> anterior or posterior) is not part of the nifti file. Without that
> information, the anatomical analysis cannot be done. You will either
> have to fix it yourself (ie, imbed that info into the file) or, better,
> recreate the file with the proper geometry info
>
>
> On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
> > Hello,
> >
> > Hope this message finds you well.
> >
> > I was beginning to run recon-all on a dataset and was encountering a
> > problem with the talairach registration. I've encountered this error
> > before here and there, but I've been receiving the same error for
> > every scan that I've been trying to run, and I'm not sure why. It's
> > also the first time I've used NIFTI files as the input - not sure if
> > that's a contributing factor. I've also tried the -use-mritotal flag
> > without any luck.
> >
> > These are the errors I receive:
> >
> > WARNING: neither NIfTI-1 qform or sform are valid
> >
> > WARNING: your volume will probably be incorrectly oriented
> >
> >
> > ERROR: talairach_afd: Talairach Transform:
> > transforms/talairach.xfm ***FAILED*** (p=0., pval=0. <
> > threshold=0.0050)
> >
> > Manual Talairach alignment may be necessary, or
> >
> > include the -notal-check flag to skip this test,
> >
> > making sure the -notal-check flag follows -all
> >
> > or -autorecon1 in the command string.
> >
> >
> > I would appreciate your help. Thank you!
> >
> > Warmly,
> > Ariana
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T 
Sounds good. Unfortunately when I open many of my files that do not contain an 
aseg file.  Many only have a scripts directory and nothing else. Is there a way 
to process the files to just get the aseg data without doing a recon-all?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Monday, September 11, 2017 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database

Yea, that's what I would do. You can run asegstats2table to get a list
of the volume for all ROIs (so this gives you a matrix of 550 by about
50). For each row (subject),  compare the volumes to that of every other
row. You'll need to come up with a comparison function; maybe mean
percent difference (you might need to exclude very small structures like
optic chiasm, vessels, etc -- or only include certain structures like
hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects
from lowest to highest difference and look at the ones with the lowest
difference. You can probably think of other ways


On 09/11/2017 03:17 PM, Sherrill, John T wrote:
> I have run recon-all on all of the files. So I should start with 
> asegstats2table ( 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_asegstats2table=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=MtJnnh5bFgsrOhtUjpvIR4hZ8YcefgfBG4f5F2sJI84=7l-5w5DwKzRbjsxDY-U40umkQFkb_J0u-1f06ML1V94=
>   ) ?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, September 11, 2017 2:07 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> One way is to perform a 6DOF registration between each pair. It is a lot
> of pairs, but I don't think you can avoid it. Pairs that come from the
> same subject will have an abnormally high (or low) objective function.
> You could use mri_coreg (use --no-smooth) . If you've already run all
> 550 through FS, then you might be able to look a the aseg.stats for
> similar subjects.
>
>
> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>> I am trying to find the best way to identify likely duplicate subjects
>> with in a database of about 550 subjects. Some subjects where
>> duel-consented for studies and had multiple scans over a relatively
>> short period of time. What is the best way to tease these out?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>> 
>> Confidentiality Notice: This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential and privileged information. Any unauthorized
>> review, use, disclosure or distribution is prohibited. If you are not
>> the intended recipient, please contact the sender by reply e-mail and
>> destroy all copies of the original message.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=Mj9DAJaDWsk0JKAxs99YViYRgOnIG81THLDrpjx0zEM=
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>

Re: [Freesurfer] Talairach registration error

2017-09-11 Thread Douglas N Greve 
That means that geometry information (ie, what is left and right, 
anterior or posterior) is not part of the nifti file. Without that 
information, the anatomical analysis cannot be done. You will either 
have to fix it yourself (ie, imbed that info into the file) or, better, 
recreate the file with the proper geometry info


On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
> Hello,
>
> Hope this message finds you well.
>
> I was beginning to run recon-all on a dataset and was encountering a 
> problem with the talairach registration. I've encountered this error 
> before here and there, but I've been receiving the same error for 
> every scan that I've been trying to run, and I'm not sure why. It's 
> also the first time I've used NIFTI files as the input - not sure if 
> that's a contributing factor. I've also tried the -use-mritotal flag 
> without any luck.
>
> These are the errors I receive:
>
> WARNING: neither NIfTI-1 qform or sform are valid
>
> WARNING: your volume will probably be incorrectly oriented
>
>
> ERROR: talairach_afd: Talairach Transform:
> transforms/talairach.xfm ***FAILED*** (p=0., pval=0. <
> threshold=0.0050)
>
> Manual Talairach alignment may be necessary, or
>
> include the -notal-check flag to skip this test,
>
> making sure the -notal-check flag follows -all
>
> or -autorecon1 in the command string.
>
>
> I would appreciate your help. Thank you!
>
> Warmly,
> Ariana
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] labels used by freesurfer

2017-09-11 Thread Douglas N Greve 


On 09/11/2017 01:20 PM, Benjamin Luerweg wrote:
> dear fs community,
>
> as a kind of a freesurfer greenhorn i would kindly ask you to help me 
> out with identifying the different labels used by freesurfer.
> after using mri segstats most of the labels seem to be describing 
> thereselfs in proper way.
>
> what i don’t understand are for example the different volume values 
> showing up inside the console after entering the segstat command.
>
> VentChorVol what does this label explain?
Volume of all ventricles plus the volume of the chorioid plexus.
>
> CSFVolwhy is this volume differing to the one within the segstat file?
Volume of all ventricles (not well named because it does not include 
extra cerebral CSF)
>
> and finally i would really love to know how to calculate a correct 
> brain to liquor ratio?!
Do you mean brain volume to total CSF volume? See above
>
>
> kind regards,
> ben
>
>
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] mammillary bodies

2017-09-11 Thread Jacobs H (NP) 
Hello all!

I am looking for a automatic or semi-automatic segmentation tool for the 
mammillary bodies. Any suggestions?

Many thanks!
Heidi
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Re: [Freesurfer] Normalizing volumes

2017-09-11 Thread Douglas N Greve 
You can look here for what stats are available

https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

There is no one method that is considered the gold standard. Each will 
represent a different hypothesis to test. Eg, if you use whole brain 
volume, then you will be looking at changes with respect to whole brain 
atrophy. If you use eTIV, the whole brain atrophy will be included in 
your measure


On 09/11/2017 01:12 PM, Alexopoulos, Dimitrios wrote:
>
> Hi,
>
> We running FS 5.3 analyses on 2 cohorts (control vs. malnourished 
> adolescents) and I was wonderful what FS measure would be most 
> accurate for normalizing the volumes.
>
> (i.e total GM, total WM, suparatentorial, etc). The eTIV measures are 
> significantly different between the cohorts.
>
> Is eTIV the best way to normalize or perhaps BrainSegVol?
>
> What FS measure gives you total  brain volume?
>
> Jim
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
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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] mri_convert: line 3: 38445 Segmentation fault

2017-09-11 Thread Douglas N Greve 
Try running

unsetenv FS_LOAD_DWI


then re-running recon-all

On 09/11/2017 12:57 PM, M Janani wrote:
>
> Hi Team,
>
> Am getting segmentation error during the 
> reconstruction process.
>
> Please help in resolving the error.
>
> I have attached log for reference.
>
> Thanks,
>
> Janani
>
>
>
> ::DISCLAIMER::
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve 
Yea, that's what I would do. You can run asegstats2table to get a list 
of the volume for all ROIs (so this gives you a matrix of 550 by about 
50). For each row (subject),  compare the volumes to that of every other 
row. You'll need to come up with a comparison function; maybe mean 
percent difference (you might need to exclude very small structures like 
optic chiasm, vessels, etc -- or only include certain structures like 
hippo, put, pal, lat vent, cerebellum, etc). Then rank all the subjects 
from lowest to highest difference and look at the ones with the lowest 
difference. You can probably think of other ways


On 09/11/2017 03:17 PM, Sherrill, John T wrote:
> I have run recon-all on all of the files. So I should start with 
> asegstats2table ( https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table ) 
> ?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, September 11, 2017 2:07 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database
>
> One way is to perform a 6DOF registration between each pair. It is a lot
> of pairs, but I don't think you can avoid it. Pairs that come from the
> same subject will have an abnormally high (or low) objective function.
> You could use mri_coreg (use --no-smooth) . If you've already run all
> 550 through FS, then you might be able to look a the aseg.stats for
> similar subjects.
>
>
> On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>> I am trying to find the best way to identify likely duplicate subjects
>> with in a database of about 550 subjects. Some subjects where
>> duel-consented for studies and had multiple scans over a relatively
>> short period of time. What is the best way to tease these out?
>>
>> John Sherrill
>> jtsherr...@uams.edu
>> john_sherr...@me.com
>> (870) 761-0580
>> 
>> Confidentiality Notice: This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential and privileged information. Any unauthorized
>> review, use, disclosure or distribution is prohibited. If you are not
>> the intended recipient, please contact the sender by reply e-mail and
>> destroy all copies of the original message.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=3njeh9IV2-mOyQ5jJRFboeitp92qUpuOvYjURKAMuB8=
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=DwIBAg=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk=GlCsJ1nbrLG5ArDAnb2y529XqTlrni04Bu0-BvZuTm4=jGHTu2DMCG15a-BloX3mgf3XGM-EDWmdST6ob9hi1s4=ZP1E4cAyh8LcgkvzL-jfBxt2V8sZYJd9UcZdkViEAAk=
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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T 
I have run recon-all on all of the files. So I should start with 
asegstats2table ( https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table ) ?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Monday, September 11, 2017 2:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Finding Duplicate Subjects in a Database

One way is to perform a 6DOF registration between each pair. It is a lot
of pairs, but I don't think you can avoid it. Pairs that come from the
same subject will have an abnormally high (or low) objective function.
You could use mri_coreg (use --no-smooth) . If you've already run all
550 through FS, then you might be able to look a the aseg.stats for
similar subjects.


On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>
> I am trying to find the best way to identify likely duplicate subjects
> with in a database of about 550 subjects. Some subjects where
> duel-consented for studies and had multiple scans over a relatively
> short period of time. What is the best way to tease these out?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
> 
> Confidentiality Notice: This e-mail message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply e-mail and
> destroy all copies of the original message.
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>
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Re: [Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Douglas N Greve 
One way is to perform a 6DOF registration between each pair. It is a lot 
of pairs, but I don't think you can avoid it. Pairs that come from the 
same subject will have an abnormally high (or low) objective function. 
You could use mri_coreg (use --no-smooth) . If you've already run all 
550 through FS, then you might be able to look a the aseg.stats for 
similar subjects.


On 09/11/2017 02:50 PM, Sherrill, John T wrote:
>
> I am trying to find the best way to identify likely duplicate subjects 
> with in a database of about 550 subjects. Some subjects where 
> duel-consented for studies and had multiple scans over a relatively 
> short period of time. What is the best way to tease these out?
>
> John Sherrill
> jtsherr...@uams.edu
> john_sherr...@me.com
> (870) 761-0580
> 
> Confidentiality Notice: This e-mail message, including any 
> attachments, is for the sole use of the intended recipient(s) and may 
> contain confidential and privileged information. Any unauthorized 
> review, use, disclosure or distribution is prohibited. If you are not 
> the intended recipient, please contact the sender by reply e-mail and 
> destroy all copies of the original message.
>
>
> ___
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[Freesurfer] Finding Duplicate Subjects in a Database

2017-09-11 Thread Sherrill, John T 
I am trying to find the best way to identify likely duplicate subjects with in 
a database of about 550 subjects. Some subjects where duel-consented for 
studies and had multiple scans over a relatively short period of time. What is 
the best way to tease these out?

John Sherrill
jtsherr...@uams.edu
john_sherr...@me.com
(870) 761-0580

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[Freesurfer] Talairach registration error

2017-09-11 Thread Ariana Vajdi 
Hello,

Hope this message finds you well.

I was beginning to run recon-all on a dataset and was encountering a
problem with the talairach registration. I've encountered this error before
here and there, but I've been receiving the same error for every scan that
I've been trying to run, and I'm not sure why. It's also the first time
I've used NIFTI files as the input - not sure if that's a contributing
factor. I've also tried the -use-mritotal flag without any luck.

These are the errors I receive:

WARNING: neither NIfTI-1 qform or sform are valid

WARNING: your volume will probably be incorrectly oriented


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

Manual Talairach alignment may be necessary, or

include the -notal-check flag to skip this test,

making sure the -notal-check flag follows -all

or -autorecon1 in the command string.


I would appreciate your help. Thank you!

Warmly,
Ariana
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[Freesurfer] labels used by freesurfer

2017-09-11 Thread Benjamin Luerweg 
dear fs community,

as a kind of a freesurfer greenhorn i would kindly ask you to help me out with 
identifying the different labels used by freesurfer.
after using mri segstats most of the labels seem to be describing thereselfs in 
proper way.

what i don’t understand are for example the different volume values showing up 
inside the console after entering the segstat command.

VentChorVol what does this label explain?

CSFVol  why is this volume differing to the one within the segstat file?

and finally i would really love to know how to calculate a correct brain to 
liquor ratio?!


kind regards,
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[Freesurfer] Normalizing volumes

2017-09-11 Thread Alexopoulos, Dimitrios 
Hi,

We running FS 5.3 analyses on 2 cohorts (control vs. malnourished adolescents) 
and I was wonderful what FS measure would be most accurate for normalizing the 
volumes.
(i.e total GM, total WM, suparatentorial, etc). The eTIV measures are 
significantly different between the cohorts.

Is eTIV the best way to normalize or perhaps BrainSegVol?

What FS measure gives you total  brain volume?

Jim


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[Freesurfer] mri_convert: line 3: 38445 Segmentation fault

2017-09-11 Thread M Janani 
Hi Team,

Am getting segmentation error during the reconstruction process.

Please help in resolving the error.

I have attached log for reference.

Thanks,
Janani





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recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Longitunal analysis with FS-FAST

2017-09-11 Thread Douglas N Greve 
there is nothing special about doing long analysis in FSFAST. You just 
need to set up the group analysis appropriately.


On 09/11/2017 12:26 PM, std...@virgilio.it wrote:
> Hi list,
> I would like to perform longitudinal analysis with FS-FAST, fMRI data.
> Please could you list, in summary, the processes that I should done?
> Thanks
> Regards
> Stefano
>
>
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Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

2017-09-11 Thread Douglas N Greve 
ps, you can run it with -no-talairach to turn off checking (soit will 
run all the way through)


On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
> Dear freesurfer developers,
>
> I call recon-all -all from a matlab script using a system(cmd) which 
> is (apparently) correctly executed, as shown in the recon-all.log 
> (matlab_* attached), i.e.:
>
> /usr/local/freesurfer/bin/recon-all
> -all -cw256 -3T -multistrip -clean-bm -i 
> /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s 
> /home/gc/study/recon-all/400614dclass
>
> and apparently it run without errors as you can see in the 
> matlab_recon-all.log file, but I get (systematically) a wrong
>
> TalAviQA: 0.0
>
> while, if I run the above bash command directly I get a correct:
>
> TalAviQA: 0.97713
>
> as shown in the bash_recon-all.log (attached). I guessed that 
> something wrong happened  in
>
>  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
> --atlas 3T18yoSchwartzReactN32_as_orig
>
> and the error traced in talairach_avi.log (matlab_* and bash_* 
> attached). In fact matlab_talairach_avi.log is shorter and all 
> imgreg_4dfp end sections are missing which imply that TalAviQA can not 
> be extracted by awk and mritotal transform is performed instead. But 
> really I don't understand why this happens and whether similar issues 
> affects other recon-all subtask using matlab. I double checked this on 
> two linux sistems and with fs version 6.0 and 5.3 ... same results.
>
> Thanks in advance for any help,
>
> cheers,
>
>
>
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[Freesurfer] Longitunal analysis with FS-FAST

2017-09-11 Thread stdp82 
Hi list,I would like to perform longitudinal analysis with FS-FAST, fMRI 
data.Please could you list, in summary, the processes that I should 
done?ThanksRegardsStefano___
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Re: [Freesurfer] side effects launching recon-all from matlab system(cmd) call

2017-09-11 Thread Douglas N Greve 
  The tal_QC_AZS scripts expects the log file to have a specific format, 
and it looks like something changes when you run it inside matlab. 
sorry, the only idea I have is that the linux environments might be 
different in bash vs matlab.


On 09/11/2017 08:25 AM, Giuseppe Cabras wrote:
> Dear freesurfer developers,
>
> I call recon-all -all from a matlab script using a system(cmd) which 
> is (apparently) correctly executed, as shown in the recon-all.log 
> (matlab_* attached), i.e.:
>
> /usr/local/freesurfer/bin/recon-all
> -all -cw256 -3T -multistrip -clean-bm -i 
> /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s 
> /home/gc/study/recon-all/400614dclass
>
> and apparently it run without errors as you can see in the 
> matlab_recon-all.log file, but I get (systematically) a wrong
>
> TalAviQA: 0.0
>
> while, if I run the above bash command directly I get a correct:
>
> TalAviQA: 0.97713
>
> as shown in the bash_recon-all.log (attached). I guessed that 
> something wrong happened  in
>
>  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
> --atlas 3T18yoSchwartzReactN32_as_orig
>
> and the error traced in talairach_avi.log (matlab_* and bash_* 
> attached). In fact matlab_talairach_avi.log is shorter and all 
> imgreg_4dfp end sections are missing which imply that TalAviQA can not 
> be extracted by awk and mritotal transform is performed instead. But 
> really I don't understand why this happens and whether similar issues 
> affects other recon-all subtask using matlab. I double checked this on 
> two linux sistems and with fs version 6.0 and 5.3 ... same results.
>
> Thanks in advance for any help,
>
> cheers,
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] group analysis on thickness/mask

2017-09-11 Thread Douglas N Greve 


On 09/10/2017 04:02 AM, Xianwei Che wrote:
> Dear experts,
>
> I am going to run a group analysis on thickness but limit the results 
> to certain regions, say prefrontal  cortex. l did find this thread but 
> failed to make it work on my data 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). 
> I know I could extract the signal of the ROI but also interested in 
> this way.
>
> Here are my questions:
> 1. mri_binarize should be working on the average data or the single 
> data in each participant. If it should be on individual data, what the 
> loop should be (if I have a text file SUBJECTS listing the participants).
Actually, I don't know what [subjects] is supposed to mean. You should 
include the index for the ROIs you want in the analysis
> 2. How the --match is used. I --helped the mri_binarize but did not 
> get it. Is it for specifying the ROI by number, say the number of PFC?
There is no PFC ROI. You will have to piece it together from other ROIs. 
You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. 
Look in the section for aparc+aseg.mgz
> 3. If I could finish the mask creation and merge to label; do I have 
> to undergo the data concatenating stage (i.e. preproc, surf2surf) or 
> directly move to glm. I saw another thread skipping these stages but 
> it's on volume data 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).
Yu can move directly to the GLM
>
> Thank you so much!
>
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
>
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MGH-NMR Center
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[Freesurfer] Cortical thickness

2017-09-11 Thread Esteban, Eva(GE Healthcare) 
Hi Douglas,

Thank you very much for that, I will try it!

Eva

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 05 September 2017 22:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: EXT: Re: [Freesurfer] Cortical thickness

You need to map them into the same space. You can use mris_apply_reg to map one 
subject into the other or you can use mris_preproc to put them both into 
fsaverage space


On 09/01/2017 10:29 AM, Esteban, Eva(GE Healthcare) wrote:
>
> Hello everyone,
>
> I am trying to compare the difference in cortical thickness between 
> two subjects by overlaying the surfaces (lh.thickness and r
> rh.thickness) but -diff doesn't seem to be doing the work. Does anyone 
> know of any other commands which could be useful for this?
>
> Thank you!
>
> Eva
>
>
>
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Re: [Freesurfer] longitudinal freesurfer- different scanners

2017-09-11 Thread Martin Reuter 
below I meant you could run it only on the first two time points. Maybe 
there is already enough power to see effects.


Best, Martin


Am 08.09.2017 um 09:13 schrieb Martin Reuter:


Hi Michelle,

when scanners (or even scanner hardware, like head coil or software 
upgrades etc) change in a longitudinal study you will have 
difficulties finding out whether the changes you see are real 
anatomical changes or scanner effects. This is true for any software 
pipeline (longitudinal or not). Often these changes are regional, not 
linear and not just offsets. Often the seem to interact with disease, 
age etc (meaning they affect older or more diseased subjects 
differently from young or healthy subjects). Therefore even including 
a co-variate to correct for scanner upgrade in the statistics may not 
be sufficient.


In your case you can either run the analysis only with the first three 
time points. Or run it with all three and include a scanner covariate 
in the statistic with interaction terms. In both cases you would 
profit from using the longitudinal stream in Freesurfer.


Best, Martin




Am 05.09.2017 um 02:27 schrieb Michelle VanTieghem:

Hello,

Would it be ok to use the longitudinal pipeline for scans that were 
acquired on different scanners (e.g time 1 and time 2 on the same 
scanner, time 3 on different scanner)? Would the longitudinal 
pipeline help to account for different scanners, since it creates the 
average base image for all 3 time points? or is this not recommended?


Thank you,
Michelle

--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
mrv2...@columbia.edu 


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