Hello,
I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force
The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
I ran it several times but it never gave me that file. Also, it doesn't give me any errors.
I appreciate any help.
Ash
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz without performing any contrasts. I just need to look at the signal in some ROIs without performing any contrasts. I hope this makes sense.
Thanks, Ash
On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole coleashley00@gmail.com wrote:
Hello,
I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force
The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
I ran it several times but it never gave me that file. Also, it doesn't give me any errors.
I appreciate any help.
Ash
That file should be in the same dimensions, no?
On 1/30/18 12:19 AM, Ashley Cole wrote:
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz without performing any contrasts. I just need to look at the signal in some ROIs without performing any contrasts. I hope this makes sense.
Thanks, Ash
On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole <coleashley00@gmail.com mailto:coleashley00@gmail.com> wrote:
Hello, I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz. I ran it several times but it never gave me that file. Also, it doesn't give me any errors. I appreciate any help. Ash
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Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However, I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a contrast. If I am not mistaken, all is good now. Thank you for your response.
On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
That file should be in the same dimensions, no?
On 1/30/18 12:19 AM, Ashley Cole wrote:
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after selxavg3-sess. I was wondering how can I preprocess the functional image and have the output with the same dimension as the f.nii.gz without performing any contrasts. I just need to look at the signal in some ROIs without performing any contrasts. I hope this makes sense.
Thanks, Ash
On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole coleashley00@gmail.com wrote:
Hello,
I have several nifti files. I have preprocessed some of them before. I used this command: preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force
The output files contained fmc.odd.sm5.self.lh.nii.gz, fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file that I needed for my further analyses. However, when I run the same command on another nifti file which was obtained from the same scanner and the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
I ran it several times but it never gave me that file. Also, it doesn't give me any errors.
I appreciate any help.
Ash
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