[Freesurfer] mri_mask output problem
Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ 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_mask output problem
what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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_mask output problem
Hi Doug, this is the command line input: mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii this is the terminal output: DoAbs = 0 Found 14652800 voxels in mask Writing masked volume to macaque_stripped_final2.nii...done. The same thing happens when I use nii.gz or mgz files. Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ 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_mask output problem
And macaque_25_model-MNI.nii is the non-binary image? And macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks right to me. doug On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote: Hi Doug, this is the command line input: mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii this is the terminal output: DoAbs = 0 Found 14652800 voxels in mask Writing masked volume to macaque_stripped_final2.nii...done. The same thing happens when I use nii.gz or mgz files. Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. ___ 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_mask output problem
Hi Doug, that's correct. I think the problem is perhaps that the original NIFTI file has a very narrow range of values, between 43.7308 and 43.8476, to cover the whole range of tissues in the image. It is an average over several subjects, and before skull stripping, there are hardly any zeros in the image. Is there a way to rescale the file? Thanks, Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu And macaque_25_model-MNI.nii is the non-binary image? And macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks right to me. doug On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote: Hi Doug, this is the command line input: mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii this is the terminal output: DoAbs = 0 Found 14652800 voxels in mask Writing masked volume to macaque_stripped_final2.nii...done. The same thing happens when I use nii.gz or mgz files. Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ 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_mask output problem
That should not be a problem. Certainly it should not cause everything to go to 1s and 0s. What version of FS are you using? And you say the same thing happens with FSL? Try using mri_convert to convert the nonbinary image to another nifti file and see if you get 1s and 0s. If not, then try that file as input. You can also try fscalc, something like fscalc input.nii mul mask.nii -o output.nii should accomplish the same thing doug On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's correct. I think the problem is perhaps that the original NIFTI file has a very narrow range of values, between 43.7308 and 43.8476, to cover the whole range of tissues in the image. It is an average over several subjects, and before skull stripping, there are hardly any zeros in the image. Is there a way to rescale the file? Thanks, Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu And macaque_25_model-MNI.nii is the non-binary image? And macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks right to me. doug On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote: Hi Doug, this is the command line input: mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii this is the terminal output: DoAbs = 0 Found 14652800 voxels in mask Writing masked volume to macaque_stripped_final2.nii...done. The same thing happens when I use nii.gz or mgz files. Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. ___ 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_mask output problem
Hi Doug, thanks for your input. I turns out that there is some problem when converting minc to NIFTI with float. I got a hold of the original minc file and converted it to NIFTI with minc2nii using integer, and now the values are in a reasonable range and the skull stripping works. Thanks! Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu That should not be a problem. Certainly it should not cause everything to go to 1s and 0s. What version of FS are you using? And you say the same thing happens with FSL? Try using mri_convert to convert the nonbinary image to another nifti file and see if you get 1s and 0s. If not, then try that file as input. You can also try fscalc, something like fscalc input.nii mul mask.nii -o output.nii should accomplish the same thing doug On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's correct. I think the problem is perhaps that the original NIFTI file has a very narrow range of values, between 43.7308 and 43.8476, to cover the whole range of tissues in the image. It is an average over several subjects, and before skull stripping, there are hardly any zeros in the image. Is there a way to rescale the file? Thanks, Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu And macaque_25_model-MNI.nii is the non-binary image? And macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks right to me. doug On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote: Hi Doug, this is the command line input: mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii this is the terminal output: DoAbs = 0 Found 14652800 voxels in mask Writing masked volume to macaque_stripped_final2.nii...done. The same thing happens when I use nii.gz or mgz files. Caspar 2013/12/30 Douglas Greve gr...@nmr.mgh.harvard.edu what is your command line and terminal output? On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ 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] citation for smoothing method
Hi Yumi, you can site Hagler, 2006, NI, Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data doug On 12/26/2013 08:01 PM, YUMI MAEDA wrote: Hi, I have a question about citation for smoothing methods. In the following link, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer there are statement This data was smoothed in the volume at 5mm, but when preparing for a group surface-based analysis, we recommend that you smooth on the surface prior to group analysis and not smooth in the volume at all (or less than the voxel size) Is there any reference paper that I can cite when I write a manuscript? thank you very much. YUMI ___ 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.
[Freesurfer] freeview error
Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha___ 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.
[Freesurfer] freeview error
Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha ___ 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.
[Freesurfer] Fwd: freeview error
Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button configure overlay. Then freeview were suspended. The CPU ran 100%,and memory ran 23%. There was nothing to do but terminated it manually in the command console by ctrl + c. I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is NVIDIA GeForce 8600 GT, and CPU is Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz, and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha ___ 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.
