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Hello to all, I am new to FreeSurfer. By executing recon-all I get the
permission error.
Is there a way to change the $SUBJECTS_DIR, such as /share/users/my
user/subject name ?
$ recon-all -subject 102109 -i T1w.nii.gz -all
mkdir: cannot create
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Hello to all of you
I ran recon-all:
$ recon-all -sd /share/users/mfakhri/FS/subjects -subject 102109 -i
T1w.nii.gz -all
Then I tried segmentation fornix and I used -f on the mri_cc command:
$ mri_cc -f -force -sdir /share/users/mfakhri/FS/subjects
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Hello to all,
I was wondering if I could create a binary mask of corpus callosum from T1w
images in subject space with FS.
Thanks for the help!
Mostafa
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Hi there,
I need just wm.seg.hgz image therefore I used autorecon2-cp:
recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject
102109_3T -i /share/users/mfakhri/freeSurfer-analys/102109_3T/T1w.nii.gz
-autorecon2-cp
but it doesn't work
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Hi Doug,
Thank You for your response
I have a new problem
I used -autorecon1 and autorecon2-cp:
recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject
fastWM -i /share/users/mfakhri/freeSurfer-analys/100610_7T/T1w.nii.gz
-autorecon1
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Hi Bruce,
It works.Thank you so much.
Actually I need just rawavrg.mgz and wm.seg.mgz, I think
using autorecon2 is quick way to to produce these images.
Is this correct?
Mostafa
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Thank you for sharing your expertise.
Mostafa
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