Hi Sampada
the recon-all script is designed to analyze T1-weighted structural data.
Once that has been done, it can be used to facilitate fMRI analysis. Is
that what you are trying to do? What are the 8 volumes?
cheers
Bruce
On Fri, 9 May 2014, Dr Sampada Sinha wrote:
Hello Freesurfer,
Thanks Shantanu I was able to convert the .nii to .mgz files . However, about
the recon-all
command do I run it separately for each .mgz file or run it one time for all
.mgz file(which
are eight in numbers)? And what command do I use for recon-all? I have tried
many but none
is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh <shant...@nmr.mgh.harvard.edu>
wrote:
sorry
try:
cd Users/sampada/Desktop/
mkdir test
cd test
mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii
sampada/Desktop/test/s400a1001.mgz
Hth,
shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
> You don't need the quotation marks in your path
> also, it seems you don't have a directory called
> /Users/sampada/Desktop/test/org
>
> try something like:
>
> cd Users/sampada/Desktop/
> mkdir test
> cd test
> mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii
> sampada/Desktop/test/s400a1001.nii
>
> Hth,
> shantanu
>
>
> On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
>> Hello Shantanu,
>>
>> Many thanks for your reply! This is my exact commandline which I give to
>> free surfer for the 1st of the eight nii files. When i am able to
>> convert
>> this nii to mgz then i will ask how to convert all the eight files at
>> one
>> go.
>>
>> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii'
>> '/Users/sampada/Desktop/test/mri/org/.mgz'
>>
>>
>> Regards,
>>
>> Sampada
>>
>>
>> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh
>> <shant...@nmr.mgh.harvard.edu
>>> wrote:
>>
>>> can you send your exact mri_convert commandline?
>>>
>>>
>>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
>>> > *Hello freesurfer*
>>> >
>>> > *Sorry for the personal message Shantanu. *
>>> >
>>> > *I managed to convert my dicom to nifti using mricron software,
>>> though
>>> had
>>> > to make some changes to the preferences. *
>>> >
>>> > *About the dcmunpack: The user manual on dcmunpack on fs site says
>>> that
>>> > the
>>> > unpackdcmdir is used only to unpack Siemens dicom files. We use
>>> Phillips
>>> > infinity for our PET scan.*
>>> >
>>> > *I am very new to Unix, free surfer and neuroimaging, so couldn't
>>> > understand what nipy would do...*
>>> >
>>> > *My FS is working fine as when I typed tkmedit bert orig.mngz for
>>> volume
>>> > view it was displaying image.*
>>> >
>>> > *But the when I tried to convert my .nii files to .mgz format , I get
>>> the
>>> > following error:*
>>> >
>>> >
>>> > Last login: Tue May 6 10:40:32 on ttys000
>>> > dhcp020-222-117:~ sampada$ export
>>> FREESURFER_HOME=/Applications/freesurfer
>>> > dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>> --------
>>> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> > FREESURFER_HOME /Applications/freesurfer
>>> > FSFAST_HOME /Applications/freesurfer/fsfast
>>> > FSF_OUTPUT_FORMAT nii.gz
>>> > SUBJECTS_DIR /Applications/freesurfer/subjects
>>> > MNI_DIR /Applications/freesurfer/mni
>>> > dhcp020-222-117:~ sampada$ mri_convert
>>> > '/Users/sampada/Desktop/d2n119495/s400a1001.nii'
>>> > '/Users/sampada/Desktop/test/mri/org/.mgz'
>>> > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii
>>> > /Users/sampada/Desktop/test/mri/org/.mgz
>>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii...
>>> > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00
>>> > i_ras = (0.0268034, -0.99958, 0.0110098)
>>> > j_ras = (0.0381548, 0.0120287, 0.999199)
>>> > k_ras = (0.998912, 0.0263618, -0.0384612)
>>> > writing to /Users/sampada/Desktop/test/mri/org/.mgz...
>>> > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
>>> open
>>> > file
>>> >
>>> > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
>>> >
>>> >
>>> > *Will you please let me know what command I need to use to mri
>>> convert
>>> and
>>> > recon all of my files? *
>>> > I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
>>> stage)>T2
>>> > (in the order of the acquisition acquired at the time of
>>> experiment).*
>>> >
>>> >
>>> > *Thanks and regards,*
>>> >
>>> > *Sampada*
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve
>>> > <gr...@nmr.mgh.harvard.edu
>>> >> wrote:
>>> >
>>> >>
>>> >> Have you tried using dcmunpack? You run it twice, once without any
>>> >> output to get a list of runs in the folder. The 2nd with how you
>>> want
>>> >> the data converted. Run it with --help to get more info
>>> >> doug
>>> >>
>>> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote:
>>> >> > Hello I have only recently started the fmri data analysis and I
>>> >> > downloaded freesurfer point by point from martinos site and
>>> >> > incorporated the license file as well into the
>>> Applications/freesurfer
>>> >> > directory. I have run into the first problem and that is of data
>>> >> > conversion. My file is in dcm format and I have 11,000 dcm files
>>> to
>>> >> > convert. However, before I was using Jamaan Alghamadi created gui
>>> and
>>> >> > it is not able to convert the mri dcm files. Then I shifted to
>>> UNIX
>>> >> > and again it is saying error.
>>> >> >
>>> >> > My file is on the desktop and I have given it subject id as Grace.
>>> My
>>> >> > directory to the dcm file is '/Users/sampada/desktop/Grace.
>>> >> >
>>> >> > My terminal look like this before I proceed with the file
>>> conversion
>>> >> >
>>> >> > Last login: Mon Apr 28 15:10:13 on ttys001
>>> >> >
>>> >> > dhcp020-223-179:~ sampada$ export
>>> >> FREESURFER_HOME=/Applications/freesurfer
>>> >> >
>>> >> > dhcp020-223-179:~ sampada$ source
>>> $FREESURFER_HOME/SetUpFreeSurfer.sh
>>> >> >
>>> >> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>> --------
>>> >> >
>>> >> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> >> >
>>> >> > FREESURFER_HOME /Applications/freesurfer
>>> >> >
>>> >> > FSFAST_HOME /Applications/freesurfer/fsfast
>>> >> >
>>> >> > FSF_OUTPUT_FORMAT nii.gz
>>> >> >
>>> >> > SUBJECTS_DIR /Applications/freesurfer/subjects
>>> >> >
>>> >> > MNI_DIR /Applications/freesurfer/mni
>>> >> >
>>> >> >
>>> >> >
>>> >> > Will anyone please let me know what I am doing wrong? I will be
>>> very
>>> >> > grateful for any input.
>>> >> >
>>> >> >
>>> >> > Thanks and regards,
>>> >> >
>>> >> >
>>> >> > Sampada
>>> >> > Senior research support specialist
>>> >> > Molecular and neuroimaging department
>>> >> > Department of Psychiatry
>>> >> > 451, biomedical research building
>>> >> > University at Buffalo (south campus)
>>> >> > Buffalo, NY-14216
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > _______________________________________________
>>> >> > 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
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>>>
>>> --
>>> Shantanu Ghosh, Ph.D.
>>> Harvard Medical School & Massachusetts General Hospital
>>> Martinos Center for Biomedical Imaging
>>> --
>>> Not only is the universe stranger than we think, it is stranger than we
>>> can think. -Werner Heisenberg
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Shantanu Ghosh, Ph.D.
> Harvard Medical School & Massachusetts General Hospital
> Martinos Center for Biomedical Imaging
> --
> Not only is the universe stranger than we think, it is stranger than we
> can think. -Werner Heisenberg
>
>
--
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is stranger than we
can think. -Werner Heisenberg
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