Dear all,
I run a controls vs patients thickness analysis using qdec and got
several results. Now, it is not entirely clear to me how to refine my
surface-based analysis (still using qdec) into a ROI, the middle
orbitofrontal region.
Cheers,
Fabrizio
---------------------------
Fabrizio Piras Ph.D.
---------------------------
Fondazione I.R.C.C.S. Santa Lucia
Laboratorio di Neuropsichiatria
via Ardeatina 306
tel +390651501547
fax +390651501213
Il giorno 18/giu/11, alle ore 18:00, freesurfer-requ...@nmr.mgh.harvard.edu
ha scritto:
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> 1. Automated QC of Freesurfer Images (West, John D.)
> 2. [Fwd: Welcome to the "Freesurfer" mailing list (Digest mode)]
> (Antonella Kis)
> 3. Re: Automated QC of Freesurfer Images (Louis Nicholas Vinke)
> 4. Re: Automated QC of Freesurfer Images (Douglas N Greve)
> 5. Two timepoints - same subject, correlation matrix (Sudhin A.
> Shah)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 17 Jun 2011 20:11:55 +0000
> From: "West, John D." <jdw...@iupui.edu>
> Subject: [Freesurfer] Automated QC of Freesurfer Images
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <793d43fe7976404cb5e172709ab1f4080de8e...@iu-mssg-mbx102.ads.iu.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello.
>
> We are in the process of trying to develop a QC pipeline for our
> Freesurfer processed images. I was wondering if anyone has
> developed any type of automated QC they would be willing to share
> with us or have any suggestions on how to proceed.
>
> Any help would be most appreciated.
>
> Thanks.
> -John West
> Systems Admin/Imaging Analyst
> IU Center for Neuroimaging
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> ------------------------------
>
> Message: 2
> Date: Fri, 17 Jun 2011 16:38:44 -0400
> From: "Antonella Kis" <a...@utsc.utoronto.ca>
> Subject: [Freesurfer] [Fwd: Welcome to the "Freesurfer" mailing list
> (Digest mode)]
> To: freesurfer@nmr.mgh.harvard.edu
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> <41cee917c9e665cbdd5e5e848a036348.squir...@webmail.utsc.utoronto.ca>
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>
> Hello,
>
> I just received my confirmation for posting on the mailing list.
> ---------------------------- Original Message
> ----------------------------
> Subject: Welcome to the "Freesurfer" mailing list (Digest mode)
> From: freesurfer-requ...@nmr.mgh.harvard.edu
> Date: Fri, June 17, 2011 4:25 pm
> To: a...@utsc.utoronto.ca
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> --
> ------------------------------
> Dr.Antonella Kis, PhD
> Sessional Lecturer
> Life Sciences, Physics Department
> University of Toronto at Scarborough
>
> Clinical Research Project Coordinator
> The Hospital for Sick Children (SickKids)
> Diagnostic Imaging Department
> Neurosciences and Mental Health
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>
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 17 Jun 2011 16:41:59 -0400 (EDT)
> From: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Automated QC of Freesurfer Images
> To: "West, John D." <jdw...@iupui.edu>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <pine.lnx.4.64.1106171620380.11...@nyala.nmr.mgh.harvard.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Hi John,
> We do have a set of QA scripts which were created to check the
> version of
> FS used, the order of the output files, the order of all the steps
> in FS,
> take several snapshots, and then create a summary log file and an html
> file to view the snapshots. The scripts have been neglected for some
> time, but recently I've been updating them and weeding out a couple
> bugs
> left over.
>
> Here is the wiki page for the scripts:
> http://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>
> I'll send out an announcement when an updated and debugged version
> of the
> scripts has been posted. Should be relatively soon.
> -Louis
>
>
>
>
>
>
> On Fri, 17 Jun 2011, West, John D. wrote:
>
>> Hello.
>>
>> We are in the process of trying to develop a QC pipeline for our
>> Freesurfer processed images. I was wondering if anyone has
>> developed any type of automated QC they would be willing to share
>> with us or have any suggestions on how to proceed.
>>
>> Any help would be most appreciated.
>>
>> Thanks.
>> -John West
>> Systems Admin/Imaging Analyst
>> IU Center for Neuroimaging
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 17 Jun 2011 16:47:49 -0400
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Automated QC of Freesurfer Images
> To: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>,
> "West, John D." <jdw...@iupui.edu>
> Message-ID: <4dfbbd75.5000...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> you can also use wm-anat-snr. Run it with --help to get more info.
>
> Louis Nicholas Vinke wrote:
>> Hi John,
>> We do have a set of QA scripts which were created to check the
>> version of
>> FS used, the order of the output files, the order of all the steps
>> in FS,
>> take several snapshots, and then create a summary log file and an
>> html
>> file to view the snapshots. The scripts have been neglected for some
>> time, but recently I've been updating them and weeding out a couple
>> bugs
>> left over.
>>
>> Here is the wiki page for the scripts:
>> http://surfer.nmr.mgh.harvard.edu/fswiki/QATools
>>
>> I'll send out an announcement when an updated and debugged version
>> of the
>> scripts has been posted. Should be relatively soon.
>> -Louis
>>
>>
>>
>>
>>
>>
>> On Fri, 17 Jun 2011, West, John D. wrote:
>>
>>
>>> Hello.
>>>
>>> We are in the process of trying to develop a QC pipeline for our
>>> Freesurfer processed images. I was wondering if anyone has
>>> developed any type of automated QC they would be willing to share
>>> with us or have any suggestions on how to proceed.
>>>
>>> Any help would be most appreciated.
>>>
>>> Thanks.
>>> -John West
>>> Systems Admin/Imaging Analyst
>>> IU Center for Neuroimaging
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 17 Jun 2011 22:25:38 +0000 (GMT)
> From: "Sudhin A. Shah" <sut2...@med.cornell.edu>
> Subject: [Freesurfer] Two timepoints - same subject, correlation
> matrix
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <7420fc2c519fc.4dfbd...@med.cornell.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Can somebody please help me figure out how to correct this issue?
>
> 1 subject - 2 functional scans
>
> 1) run recon-all on subject anatomical.
>
> 2) process functional series (using AFNI/FSL) - each individually.
>
> 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html
> )
> @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each
> individually)
>
> This works (I don't know why since I am not doing anything to
> register them to a common space).
>
> 4) I get a square matrix of 109 (n x n correlation matrix) in 1
> timepoint and 112 in 2nd timepoint.
>
> I would like to get the exact same number so I can compare them! Of
> course I can manually adjust the rows/columns later, but I am not
> sure this is the smartest way to do this.
>
> Can I do all the steps in Freesurfer?
>
> Thank you,
> S
>
>
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