?Hi All,
I am new to freeSurfer and need your guidance for some of the doubts I have.
I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file).
My questions are:
* ?Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? * ?Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there.
Thanks for your help,
Soumya.
Hi Soumya
Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce
On Jul 22, 2014, at 8:01 PM, "soumyabrata.dey" soumyabrata.dey@knights.ucf.edu wrote:
Hi All,
I am new to freeSurfer and need your guidance for some of the doubts I have.
I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file).
My questions are:
Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there. Thanks for your help, Soumya. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks a lot for replying.
The original data comes in .nii.gz format but when I unzipped it it become .hdr-.img (2 files). The freeSurfer is not understanding the .hdr-.img format but I am able to run it using .nii.gz format.
Thanks you again,
Soumya.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, July 23, 2014 2:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] Questions regarding recon-all command
Hi Soumya
Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce
On Jul 22, 2014, at 8:01 PM, "soumyabrata.dey" <soumyabrata.dey@knights.ucf.edumailto:soumyabrata.dey@knights.ucf.edu> wrote:
?Hi All,
I am new to freeSurfer and need your guidance for some of the doubts I have.
I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file).
My questions are:
* ?Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? * ?Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there.
Thanks for your help,
Soumya.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, there is no need to unzip it, we read gzipped nifti just fine Bruce On Wed, 23 Jul 2014, soumyabrata.dey wrote:
Hi Bruce,
Thanks a lot for replying.
The original data comes in .nii.gz format but when I unzipped it it become .hdr-.img (2 files). The freeSurfer is not understanding the .hdr-.img format but I am able to run it using .nii.gz format.
Thanks you again,
Soumya.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, July 23, 2014 2:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] Questions regarding recon-all command Hi Soumya
Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce
On Jul 22, 2014, at 8:01 PM, "soumyabrata.dey" soumyabrata.dey@knights.ucf.edu wrote:
Hi All, I am new to freeSurfer and need your guidance for some of the doubts I have. I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying <filename>.hdr is not found (I have also tried with inputting .img file). My questions are: o Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? o Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there. Thanks for your help, Soumya. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
soumyabrata.dey