Re: [Freesurfer] convert FSFAST files to gifti format

[Douglas Greve]

not sure, maybe one of the HCP folks could weigh in. You might try 
converting the lh.nii.gz to mgh file first. Should not make a 
difference, but it might



On 9/14/16 10:24 AM, Sabin Khadka wrote:

Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white 
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz 
fmcpr.lh.gifit-file.gii


I still get freadFloat: frear failed error.

On separate note: Is is possible to convert these FSFAST generated 
files (fmcpr.odd.sm5.fsaverage.?h.nii.gz and 
 fmcpr.odd.sm5.mni305.2mm.nii.gz) into CIFTI format?


-Sabin

On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka > wrote:


Hi Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

Cheers,
Sabin Khadka

On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve
> wrote:

what is your mris_convert command line? You need to include vertex
position information (eg, -o lh.white)


On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> Hi all,
>
> Is there a way to convert FSFAST files
> (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
> format? I've tried mris_convert but it does not work.
>
> Thanks for help.
>
> Cheers,
> Sabin Khadka
>
>
> ___
> 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] convert FSFAST files to gifti format

[Sabin Khadka]

Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

On separate note: Is is possible to convert these FSFAST generated files
(fmcpr.odd.sm5.fsaverage.?h.nii.gz and  fmcpr.odd.sm5.mni305.2mm.nii.gz)
into CIFTI format?

-Sabin

On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka 
wrote:

> Hi Doug- I did try
> mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
> $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
> fmcpr.lh.gifit-file.gii
>
> I still get freadFloat: frear failed error.
>
> Cheers,
> Sabin Khadka
>
> On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> what is your mris_convert command line? You need to include vertex
>> position information (eg, -o lh.white)
>>
>>
>> On 09/12/2016 03:32 PM, Sabin Khadka wrote:
>> > Hi all,
>> >
>> > Is there a way to convert FSFAST files
>> > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
>> > format? I've tried mris_convert but it does not work.
>> >
>> > Thanks for help.
>> >
>> > Cheers,
>> > Sabin Khadka
>> >
>> >
>> > ___
>> > 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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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] convert FSFAST files to gifti format

[Sabin Khadka]

Hi Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

Cheers,
Sabin Khadka

On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve 
wrote:

> what is your mris_convert command line? You need to include vertex
> position information (eg, -o lh.white)
>
>
> On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> > Hi all,
> >
> > Is there a way to convert FSFAST files
> > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
> > format? I've tried mris_convert but it does not work.
> >
> > Thanks for help.
> >
> > Cheers,
> > Sabin Khadka
> >
> >
> > ___
> > 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] convert FSFAST files to gifti format

[Douglas N Greve]

what is your mris_convert command line? You need to include vertex 
position information (eg, -o lh.white)


On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> Hi all,
>
> Is there a way to convert FSFAST files 
> (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti 
> format? I've tried mris_convert but it does not work.
>
> Thanks for help.
>
> Cheers,
> Sabin Khadka
>
>
> ___
> 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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] convert FSFAST files to gifti format

[Sabin Khadka]

Hi all,

Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz)
files to convert into gifti format? I've tried mris_convert but it does not
work.

Thanks for help.

Cheers,
Sabin Khadka
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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.