[Freesurfer] mri_glmfit & .nii files
Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks! ___ 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.
Re: [Freesurfer] mri_glmfit & .nii files
This is controlled by the $FSF_OUTPUT_FORMAT. By default this is compressed nifti (nii.gz). Both nii and nii.gz store the same information. The nii.gz is compressed, so you save some space. doug Chindhuri Selvadurai wrote: > Hi freesurfers, > > I am trying to run an analysis right now, however, after using isxconcat, > I am only finding ces.nii.gz files in the output directory and no .nii > files. > > output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 > subjects_dir: /cluster/manoach/milton/subjects > > command: mri_glmfit --y > /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir > group_analysis/volume/m1/ --osgm > > Not sure why this is the case.. any help would be appreciated! Thanks! > ___ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] mri_glmfit & .nii files
I am actually getting an error message when I type my mri_glmfit command: ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest ERROR: must specify input y file I did specify a y file and I do not know what fio_pushd is. > This is controlled by the $FSF_OUTPUT_FORMAT. By default this is > compressed nifti (nii.gz). Both nii and nii.gz store the same > information. The nii.gz is compressed, so you save some space. > > doug > > Chindhuri Selvadurai wrote: >> Hi freesurfers, >> >> I am trying to run an analysis right now, however, after using >> isxconcat, >> I am only finding ces.nii.gz files in the output directory and no .nii >> files. >> >> output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 >> subjects_dir: /cluster/manoach/milton/subjects >> >> command: mri_glmfit --y >> /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir >> group_analysis/volume/m1/ --osgm >> >> Not sure why this is the case.. any help would be appreciated! Thanks! >> ___ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ 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.
Re: [Freesurfer] mri_glmfit & .nii files
What's your command line? Looks like you might be putting a slash (/) as the first character to your glmdir. You will not have permissions to create this directory. doug Chindhuri Selvadurai wrote: > I am actually getting an error message when I type my mri_glmfit command: > > ERROR: fio_pushd: /group_analysis/volume/m1/mstmct_v_base/type_v_rest > ERROR: must specify input y file > > > I did specify a y file and I do not know what fio_pushd is. > > > >> This is controlled by the $FSF_OUTPUT_FORMAT. By default this is >> compressed nifti (nii.gz). Both nii and nii.gz store the same >> information. The nii.gz is compressed, so you save some space. >> >> doug >> >> Chindhuri Selvadurai wrote: >> >>> Hi freesurfers, >>> >>> I am trying to run an analysis right now, however, after using >>> isxconcat, >>> I am only finding ces.nii.gz files in the output directory and no .nii >>> files. >>> >>> output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 >>> subjects_dir: /cluster/manoach/milton/subjects >>> >>> command: mri_glmfit --y >>> /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir >>> group_analysis/volume/m1/ --osgm >>> >>> Not sure why this is the case.. any help would be appreciated! Thanks! >>> ___ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > > Best, > > Chindhuri Selvadurai > > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
