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Today's Topics:

  1. Re: Freesurfer Digest, Vol 89, Issue 52 (Jamaan Alghamdi)


----------------------------------------------------------------------

Message: 1
Date: Sat, 16 Jul 2011 19:38:40 +0100
From: Jamaan Alghamdi <jamaan.alghamdi@gmail.com>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 89, Issue 52
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAGLHyT7PGVWPqxNNXEwVAJnfiqV_H9LA13CYuMWa=PTCEBu3tA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi

Previous scripts are good but if you feel confused because you do not have
that experience with scripting you can try another way;

For creating directories;

for i in 01 02 03 04 05 .....; do mkdir -p C${i}/mri/orig ; done

replace dots (.....) with numbers as much as you want and replace C with
your subjects' ID


For runing mri_convert command;

for i in 01 02 03 04 05; do mri_convert C${i}.nii.gz  C${i}/mri/orig/001.mgz
 ; done

again replace dots (.....) with numbers as much as you want and replace C
with your subjects' ID

or even you can try the following applescript if you have mac system

*display dialog* "Choose your shell type" buttons {"bash", "csh or tcsh",
"Cancel"} ?

with title ""

*set* diag1button *to* button returned *of* result


*if* diag1button *is* "bash" *then*

*tell* *application* "Terminal"

*set* currentTab *to* *do script* "export
FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh"

*end* *tell*

 *else* *if* diag1button *is* "csh or tcsh" *then*

*tell* *application* "Terminal"

*set* currentTab *to* *do script* "setenv FREESURFER_HOME
/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh"

*end* *tell*

 *end* *if*


*set* destination *to* (*choose folder* with prompt "Choose the destination
folder")


*set* this_folder1 *to* *choose folder* with prompt "Data directory"

*set* dir *to* "mri/orig"

*tell* *application* "Finder"

*set* thePath1 *to* POSIX path *of* this_folder1

*set* mylist *to* *get* name *of* *folders* *of* this_folder1

*set* stringsList *to* mylist

 *set* theChoices *to* ?

*choose from list* stringsList with prompt "You can select more than one
subject's ID from the list below;

 Please use mous click and Command key to highlight your selection" with
title "" *with* multiple selections allowed

 *set* x *to* result *as* *string*

*repeat* *with* x *in* theChoices

*set* subjectid *to* x *as* *string*

*set* ThePath3 *to* POSIX path *of* this_folder1 & subjectid

*set* t *to* (*do shell script* "ls " & quoted form *of* ThePath3)

*set* beginningToEnd *to* *text* *of* *first* *paragraph* *of* t

*set* folderName *to* x *as* *string*

*tell* *application* "Finder"

*make* *folders* *in* destination with properties {name:folderName}

*set* this_folder *to* folderName

*set* ThePath *to* POSIX path *of* destination

*set* thePath2 *to* POSIX path *of* destination & this_folder

*tell* *application* "Terminal"

*set* currentTab *to* *do script* "cd" & space & quoted form *of* thePath2
in *window* 1

*set* currentTab *to* *do script* "mkdir -p" & space & quoted form *of* dir
in *window* 1

*set* currentTab *to* *do script* "mri_convert" & space & quoted form *of*
ThePath3 & "/" & quoted form *of* beginningToEnd & space & quoted form *of*
thePath2 & "/mri/orig/" & "001.mgz" in *window* 1

*end* *tell*

 *end* *tell*

 *end* *repeat*

 *end* *tell*




On 16 July 2011 18:28, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

> Send Freesurfer mailing list submissions to
>        freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>        freesurfer-request@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>        freesurfer-owner@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>   1. Re: how can do ''mri_convert''quickly when there are      too many
>      subjects (Peter J. Molfese)
>   2. Re :  Book with FreeSurfer chapter (Simmons, Andy)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 16 Jul 2011 12:40:27 -0400
> From: "Peter J. Molfese" <Peter.Molfese@yale.edu>
> Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there
>        are     too many subjects
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <703DA8F6-7DD5-41A2-BD5C-0180EA4802D6@yale.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> A script is definitely the easiest way to process quite a few subjects.
>  You can save some headache by using a recon-all command with an input for
> your image files.  For example: "recon-all -s sleep_001 -i sleep_001.nii
> -all" will create a subject folder in the correct location named sleep_001
> and begin the entire freesurfer pipeline taking the NIFTI image
> sleep_001.nii as the input.  You can modify it to just import the files by
> dropping the "-all".
>
> I've included a bash script below for simplifying this.  This script takes
> the NIFTI files you want to process as arguments and then automatically sets
> the Subject ID and begins processing.  Once it completes a single subject,
> it will start the next subject.  You can track the progress of subjects by
> seeing which folders have been created in the SUBJECTS_DIR.  If you have a
> multiprocessor system, you can run the script with different subjects in
> multiple terminal windows.
>
> To execute the script:
> 1. Save the script as fs_subject.sh
> 2. chmod +x fs_subject.sh
> 3. place the script in a folder with all of your NIFTI files (not required
> but may make your life easier)
> 4. execute the script with ./fs_subject.sh sleep_001.nii sleep_002.nii
> sleep_003.nii (don't forget to replace sleep_* with your NIFTI file names)
> 4a. If your subjects meet a standard naming convention you could do
> something like: ./fs_subject.sh sleep_*.nii (this would submit all subjects
> fitting the pattern of having "sleep_" at the beginning of the name.
>
>
> #!/bin/bash
> # ./fs_subject.sh
> # takes nifti files as arguments for submitting into freesurfer pipeline
>
> #setup Freesurfer if not currently loaded on path
> export FREESURFER_HOME=/usr/local/freesurfer
> #source $FREESURFER_HOME/SetUpFreeSurfer.sh
> . $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> for FS in $*
> do
>   subjectID=$(/bin/echo $FS | /usr/bin/sed 's/.nii//')
>   recon-all -s $subjectID -i $FS -all
> done
>
> Hope this helps!  Ultimately if you have a lot of computers and a lot of
> subjects, using Sun Grid Engine (SGE) or Apple's xgrid (if you have Macs)
> can really expedite the processing of subjects.
>
> Best,
> Peter
>
>
> > Date: Fri, 15 Jul 2011 12:22:38 -0500
> > From: Freesurfer Local Archive <freesurfer@jonca.org>
> > Subject: Re: [Freesurfer] how can do ''mri_convert''quickly when there
> >       are too many subjects
> > To: ??? <wgh0805@126.com>
> > Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>
> > Message-ID:
> >       <
> CABphhh-ZcMapCqq+0x66d0EXqQgdt-vPVojXt30O0P63kzoLAw@mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > I suspect that your subject directory/file names will match some
> > pattern. You can use combination of a loop and shell "ls" command to
> > cycle through all the subjects matching provided pattern. For example
> > if you have data in directories you would do something line this:
> >
> > #!/bin/tcsh
> >
> > cd /path/to/native/files
> >
> > for x in `ls -dA1 name_pattern_*`;
> > do
> > mkdir -p $SUBJECTS_DIR/${x}/mri/orig
> > $FREESURFER_HOME/bin/mri_convert ${x}.nii.gz
> $SUBJECTS_DIR/${x}/mri/orig/001.mgz
> > done
> >
> > If all files are in the same directory substitute '-dA1' for "-A1" and
> > it should work. Note this assumes that you have nifti files, for DICOM
> > you will need to modify it further.
> >
> > Cheers,
> >
> > Jacek
> >
> > 2011/7/15 ??? <wgh0805@126.com>:
> >> ??Hi Bruce,
> >>
> >> ?????In our research,if there are?100 subjects,how?can I ?process these
> data
> >> easily.For example?when I want to compare their thickness's
> difference?at
> >> first?I should do
> >> " mri_convert? bert.nii bert.nii.gz",but when there are too many
> subjects,is
> >> there a way to do all of these 100 subjects at the same time?
> >>
> >> ?Many thanks,
> >> ?Wang
> >>
> >>
> >>
> >> _______________________________________________
> >> 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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> >>
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> ------------------------------
>
> Message: 2
> Date: Sat, 16 Jul 2011 18:26:50 +0100
> From: "Simmons, Andy" <andy.simmons@kcl.ac.uk>
> Subject: [Freesurfer] Re :  Book with FreeSurfer chapter
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>        <
> EADA37A458FAEF4F8921F4A97317C8B19C2AFDB876@KCL-MAIL03.kclad.ds.kcl.ac.uk>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> There are also several other chapters of the same book using Freesurfer in
> AD, including
>
>
> Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy for
> Detection of Early Alzheimer's
> Disease / Eric Westman, Lars-Olof Wahlund, Catherine Foy, Michaela Poppe,
> Allison Cooper, Declan Murphy,
>
> Christian Spenger, Simon Lovestone and Andrew Simmons
>
>
> Combinatorial Markers of Mild Cognitive Impairment Conversion to
> Alzheimer's Disease - Cytokines and MRI
> Measures Together Predict Disease Progression / Simon J. Furney, Deborah
> Kronenberg, Andrew Simmons,
> Andreas G?ntert, Richard J. Dobson, Petroula Proitsi, Lars-Olof Wahlund,
> Iwona Kloszewska, Patrizia Mecocci,
>
> Hilkka Soininen, Magda Tsolaki, Bruno Vellas, Christian Spenger and Simon
> Lovestone
>
>
>
> Best wishes,
>
>
>
> Andy Simmons
>
>
>
> -----
>
>
>
> Date: Fri, 15 Jul 2011 20:36:01 -0300
>
> From: Pedro Paulo de Magalh?es Oliveira Junior <ppj@netfilter.com.br>
>
> Subject: [Freesurfer] Book with FreeSurfer chapter
>
> To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
>
> Message-ID:
>
>      <CAPSXCjqtiYDJMAFvxGWu=k9NuTE8zf1JdOAwMv3HSBiuAwQhSQ@mail.gmail.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Just for information:
>
>
>
> *Handbook of Imaging the Alzheimer Brain*
>
> *
>
> Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley,
>
> O. Sabri, A. Furst, S.E. Black and M. Weiner
>
> July 2011, 824 pp., hardcover
>
> ISBN 978-1-60750-792-5 (print)
>
> **
>
>
>
> The chapter that describes the usage of FreeSurfer in AD is "Automated
>
> Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de
> Magalh?es
>
> Oliveira Jr. et al.
>
> *
>
>
> ----
>
> Dr Andy Simmons
> Reader in Neuroimaging & Consultant Clinical Scientist
> Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre
> Institute of Psychiatry, Box P089
> Kings College London
> De Crespigny Park
> London, SE5 8AF, UK
>
> Email - andy.simmons@kcl.ac.uk
> Webpage  - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338
> Directions -
> http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-psychiatry/
> ResearcherID - http://www.researcherid.com/rid/B-8848-2008
> Fax +44 (0)203 228 2116
>
> [cid:image001.png@01CC43EE.317991F0]<http://msc-neuroimaging.com/>
>
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>
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>
> End of Freesurfer Digest, Vol 89, Issue 52
> ******************************************
>



--
Jamaan Alghamdi
07779801950
0151 795 4627
Magnetic Resonance & Image Analysis Research Centre (MARIARC)
University of Liverpool
Pembroke place
Liverpool
L69 3GE

http://web.mac.com/jamaan/Jamaan/Welcome.html
http://www.easyneuroimaging.com/
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