Re: [Freesurfer] Voxel to Surface Coordinates
External Email - Use Caution I apologize for the confusion. We are doing a ROI based analysis with our EEG data that have been transformed onto a ICBM152 surface map. Using an atlas that we have incorporated into our FreeSurfer pipeline, we are trying to convert our ROIs from the atlas onto the same surface map space. What would be the best way to perform this? Thank you so much in advance. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, May 14, 2019 5:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel to Surface Coordinates KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. -- what are MNI surface coords? On 5/14/19 5:30 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > We have an anatomical atlas that we have incorporated in the > FreeSurfer pipeline. Is it possible to convert this voxel based atlas > into MNI152 surface coordinates? Any suggestions or comments would be > greatly appreciated. > > Thank you, > > Da-Yea > > -- > -- > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=l > JrVZti-TOeTf7hUk6B3NYU0YzhxYYCHFA5TncjzvtQ=O35TQxOdkCe3vr_5GyB4U0YN9 > ObdUpciGlk2QDX_r3o= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=lJrVZti-TOeTf7hUk6B3NYU0YzhxYYCHFA5TncjzvtQ=O35TQxOdkCe3vr_5GyB4U0YN9ObdUpciGlk2QDX_r3o= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Voxel to Surface Coordinates
External Email - Use Caution Hello, We have an anatomical atlas that we have incorporated in the FreeSurfer pipeline. Is it possible to convert this voxel based atlas into MNI152 surface coordinates? Any suggestions or comments would be greatly appreciated. Thank you, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Partial volume correction for aseg.mgz files
External Email - Use Caution Hello, I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz files and compare them to our manual segmentations. I've warped these ROI masks onto our native space. I've noticed on the forum that there were mentions of discrepancies in the volumes from aseg.mgz and aseg.stats due to partial volume correction. If I were to calculate the volume using the ROI extracted masks (that have been warped on to the native space), how can I calculate for partial volume correction? Any suggestions would be greatly appreciated! Thank you, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_binarize --replace
External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace -128 2 The problem I'm having is that the values (V1) for each binary mask is not constant. For example, for one participant the values may be -117 whereas the values are -128 for another participant. Is there a way to set a range for the --replace option so that I can loop it through the subjects rather than having to do this command for each one separately? Any suggestions would be greatly appreciated! Thank you, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert --in_center
External Email - Use Caution Hello, Is it possible to change the origin of the aseg.mgz file? I tried mri_convert --in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img file the origin seems to be at 0 -127 0. Any suggestions would be greatly appreciated! Thank you, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Calculating volume using pial files
External Email - Use Caution Hello, I'm trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii formats? Or is there a command to calculate the volume? Thank you so much in advance for your help. Best regards, Da-Yea Song -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extracting both the GM and WM ROIs
External Email - Use Caution Hello, Does the fsaverage subject have a wmparc.mgz file? Thank you, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 5:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting both the GM and WM ROIs what do you mean by the white matter region? The aparc only labels cortex, which is, of course, GM. If you mean the WM adjacent to the aparc, have you looked at the wmparc.mgz file? On 12/11/2018 05:16 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > I've been trying to extract ROIs directly from the Desikan atlas by > using the mri_annotation2label and the aparc.annot files from the > fsaverage folder. > > I noticed that this pulls out the grey matter portion for these > regions but was wondering if there was a command or file that I could > use to do the same for both the grey and white matter. For example, is > it possible to extract the grey and white matter region of the > posteriorcingulate (in one file)? > > Thank you so much in advance for your help! > > Best regards, > > Da-yea > > -- > -- > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=W > G_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb > 1WjybRLvFdC-zozuSs= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=WG_88ScamnRxidGvqosdhzeRZCdZQnuX2xLbYo_XwPY=k9Hs5g6IDuazjyIsUC1lbrxPb1WjybRLvFdC-zozuSs= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting both the GM and WM ROIs
External Email - Use Caution Hello, I've been trying to extract ROIs directly from the Desikan atlas by using the mri_annotation2label and the aparc.annot files from the fsaverage folder. I noticed that this pulls out the grey matter portion for these regions but was wondering if there was a command or file that I could use to do the same for both the grey and white matter. For example, is it possible to extract the grey and white matter region of the posteriorcingulate (in one file)? Thank you so much in advance for your help! Best regards, Da-yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution Hi Bruce, Will the mri_annotation2label work on /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot? Thanks, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > I really appreciate the quick reply back Bruce! > > I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 > --o ctx-lh-posteriorcingulate and got the error message saying > mri_read(): couldn't determine type of file > /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot > > Any suggestions? > > Thank you, > Da-yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Friday, December 07, 2018 3:39 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Extracting ROI from atlases > > $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot > > > On Fri, 7 Dec 2018, > Song, Da-Yea wrote: > >>External Email - Use Caution >> >> Could you please direct me on where I could find the fsaverage annot file >> for the Desikan atlas? >> >> Thank you, >> Da-Yea >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Friday, December 07, 2018 3:36 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Extracting ROI from atlases >> >> yes, use the fsaverage annot file. That is essentially what you want >> >> cheers >> Bruce >> >> >> On Fri, 7 Dec 2018, Song, Da-Yea wrote: >> >>>External Email - Use Caution >>> >>> Hi Bruce, >>> >>> We are hoping to pull out ROIs (the left and right PCC in particular) from >>> the Desikan atlas (rather than from a particular subject). Do you have any >>> suggestions on what file I could use? >>> >>> Thank you, >>> Da-Yea >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >>> Fischl >>> Sent: Friday, December 07, 2018 3:33 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Extracting ROI from atlases >>> >>> Hi Da-yea >>> >>> what are you trying to achieve? We provide annotations of the >>> fsaverage subject you can use, and of course we automatically >>> parcellate each subject that is run through recon-all. The gcs is >>> contains a lot of information that isn't easily displayed as an ROI, >>> so you can't really just extract one from it >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 7 Dec 2018, Song, Da-Yea wrote: >>> >>>>External Email - Use Caution >>>> >>>> I tried this on the >>>> ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an >>>> error message that mri_read could not determine the type of file. Do I >>>> need to convert the gcs file into another format to use? >>>> >>>> Thank you so much in advance for your help! >>>> >>>> Best, >>>> Da-yea >>>> >>>> -Original Message- >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, >>>> Douglas N.,Ph.D. >>>> Sent: Thursday, December 06, 2018 11:50 AM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Extracting ROI from atlases >>>> >>>> You can use >>>> mri_binarize --i aparc+aseg.mgz --match 1028 --o >>>> ctx-lh-superiorfrontal.nii.gz See >>>> $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to >>>> use >>>> >>>> >>>> On 12/04/2018 12:51 PM, Song, Da-Yea wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hello, >>>>> >>>>> Is there a command to extr
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution Hi Bruce, I've taken a look at the mri_annotation2label command and it seems like it requires a specific subject to run this command. We were looking to pull out the ROI from the Desikan atlas (rather than from a particular participant). Is there a way to do that? Thank you so much in advance, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases the annot is not a volume. Try mri_annotation2label cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > I really appreciate the quick reply back Bruce! > > I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 > --o ctx-lh-posteriorcingulate and got the error message saying > mri_read(): couldn't determine type of file > /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot > > Any suggestions? > > Thank you, > Da-yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Friday, December 07, 2018 3:39 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Extracting ROI from atlases > > $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot > > > On Fri, 7 Dec 2018, > Song, Da-Yea wrote: > >>External Email - Use Caution >> >> Could you please direct me on where I could find the fsaverage annot file >> for the Desikan atlas? >> >> Thank you, >> Da-Yea >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Friday, December 07, 2018 3:36 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Extracting ROI from atlases >> >> yes, use the fsaverage annot file. That is essentially what you want >> >> cheers >> Bruce >> >> >> On Fri, 7 Dec 2018, Song, Da-Yea wrote: >> >>>External Email - Use Caution >>> >>> Hi Bruce, >>> >>> We are hoping to pull out ROIs (the left and right PCC in particular) from >>> the Desikan atlas (rather than from a particular subject). Do you have any >>> suggestions on what file I could use? >>> >>> Thank you, >>> Da-Yea >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >>> Fischl >>> Sent: Friday, December 07, 2018 3:33 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Extracting ROI from atlases >>> >>> Hi Da-yea >>> >>> what are you trying to achieve? We provide annotations of the >>> fsaverage subject you can use, and of course we automatically >>> parcellate each subject that is run through recon-all. The gcs is >>> contains a lot of information that isn't easily displayed as an ROI, >>> so you can't really just extract one from it >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 7 Dec 2018, Song, Da-Yea wrote: >>> >>>>External Email - Use Caution >>>> >>>> I tried this on the >>>> ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an >>>> error message that mri_read could not determine the type of file. Do I >>>> need to convert the gcs file into another format to use? >>>> >>>> Thank you so much in advance for your help! >>>> >>>> Best, >>>> Da-yea >>>> >>>> -Original Message- >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, >>>> Douglas N.,Ph.D. >>>> Sent: Thursday, December 06, 2018 11:50 AM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Extracting ROI from atlases >>>> >>>> You can use >>>> mri_binarize --i aparc+aseg.mgz --match 1028 --o >>>> ctx-lh-superiorfrontal.nii.gz See >>>> $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to >>>> use >>>> >>>> >>>> On 12/04/2018 12:51 PM, Song, Da-Yea wrote: >>>
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution I really appreciate the quick reply back Bruce! I tried the following: mri_binaraize --i lh.aparc.annot --match 1023 --o ctx-lh-posteriorcingulate and got the error message saying mri_read(): couldn't determine type of file /usr/local/Freesurfer/subjects/fsaverage/label/lh.aparc.annot Any suggestions? Thank you, Da-yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases $FREESURFER_HOME/subjects/fsaverage/label/?h.aparc.annot On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > Could you please direct me on where I could find the fsaverage annot file > for the Desikan atlas? > > Thank you, > Da-Yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Friday, December 07, 2018 3:36 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Extracting ROI from atlases > > yes, use the fsaverage annot file. That is essentially what you want > > cheers > Bruce > > > On Fri, 7 Dec 2018, Song, Da-Yea wrote: > >>External Email - Use Caution >> >> Hi Bruce, >> >> We are hoping to pull out ROIs (the left and right PCC in particular) from >> the Desikan atlas (rather than from a particular subject). Do you have any >> suggestions on what file I could use? >> >> Thank you, >> Da-Yea >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Friday, December 07, 2018 3:33 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Extracting ROI from atlases >> >> Hi Da-yea >> >> what are you trying to achieve? We provide annotations of the >> fsaverage subject you can use, and of course we automatically >> parcellate each subject that is run through recon-all. The gcs is >> contains a lot of information that isn't easily displayed as an ROI, >> so you can't really just extract one from it >> >> cheers >> Bruce >> >> >> On Fri, 7 Dec 2018, Song, Da-Yea wrote: >> >>>External Email - Use Caution >>> >>> I tried this on the >>> ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an >>> error message that mri_read could not determine the type of file. Do I need >>> to convert the gcs file into another format to use? >>> >>> Thank you so much in advance for your help! >>> >>> Best, >>> Da-yea >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas >>> N.,Ph.D. >>> Sent: Thursday, December 06, 2018 11:50 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Extracting ROI from atlases >>> >>> You can use >>> mri_binarize --i aparc+aseg.mgz --match 1028 --o >>> ctx-lh-superiorfrontal.nii.gz See >>> $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use >>> >>> >>> On 12/04/2018 12:51 PM, Song, Da-Yea wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hello, >>>> >>>> Is there a command to extract ROIs from atlases (ex. desikan) in >>>> nifti file formats? >>>> >>>> Thank you so much in advance for your time. >>>> >>>> Best, >>>> >>>> Da-Yea >>>> >>>> --- >>>> - >>>> - >>>> --- >>>> Disclaimer: >>>> >>>> >>>> The materials in this e-mail are private and may contain Protected >>>> Information. Please note that e-mail communication is not encrypted >>>> by default. You have the right to request further emails be >>>> encrypted by notifying the sender. Your continued use of e-mail >>>> constitutes your acknowledgment of these confidentiality and >>>> security limitations. If you are not the intended recipient, be >>>> advised that any unauthorized use, disclosure, copying, >>>> distributio
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution Could you please direct me on where I could find the fsaverage annot file for the Desikan atlas? Thank you, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases yes, use the fsaverage annot file. That is essentially what you want cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > Hi Bruce, > > We are hoping to pull out ROIs (the left and right PCC in particular) from > the Desikan atlas (rather than from a particular subject). Do you have any > suggestions on what file I could use? > > Thank you, > Da-Yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Friday, December 07, 2018 3:33 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Extracting ROI from atlases > > Hi Da-yea > > what are you trying to achieve? We provide annotations of the > fsaverage subject you can use, and of course we automatically > parcellate each subject that is run through recon-all. The gcs is > contains a lot of information that isn't easily displayed as an ROI, > so you can't really just extract one from it > > cheers > Bruce > > > On Fri, 7 Dec 2018, Song, Da-Yea wrote: > >>External Email - Use Caution >> >> I tried this on the >> ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an >> error message that mri_read could not determine the type of file. Do I need >> to convert the gcs file into another format to use? >> >> Thank you so much in advance for your help! >> >> Best, >> Da-yea >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas >> N.,Ph.D. >> Sent: Thursday, December 06, 2018 11:50 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Extracting ROI from atlases >> >> You can use >> mri_binarize --i aparc+aseg.mgz --match 1028 --o >> ctx-lh-superiorfrontal.nii.gz See >> $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use >> >> >> On 12/04/2018 12:51 PM, Song, Da-Yea wrote: >>> >>> External Email - Use Caution >>> >>> Hello, >>> >>> Is there a command to extract ROIs from atlases (ex. desikan) in >>> nifti file formats? >>> >>> Thank you so much in advance for your time. >>> >>> Best, >>> >>> Da-Yea >>> >>> >>> - >>> --- >>> Disclaimer: >>> >>> >>> The materials in this e-mail are private and may contain Protected >>> Information. Please note that e-mail communication is not encrypted >>> by default. You have the right to request further emails be >>> encrypted by notifying the sender. Your continued use of e-mail >>> constitutes your acknowledgment of these confidentiality and >>> security limitations. If you are not the intended recipient, be >>> advised that any unauthorized use, disclosure, copying, >>> distribution, or the taking of any action in reliance on the contents of >>> this information is strictly prohibited. >>> If you have received this e-mail in error, please immediately notify >>> the sender via telephone or return e-mail. >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.ha >>> r >>> vard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPG >>> l >>> LDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8 >>> & >>> m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw=7LTBome-I69Xsk1RhHcX >>> 5 >>> eTUXnQrBP5am9WANIUlhe4= >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har >> v >> ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlL >> D >> GrbTByhvtrs9nrrENlxA=Ej6I9f50S
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution Hi Bruce, We are hoping to pull out ROIs (the left and right PCC in particular) from the Desikan atlas (rather than from a particular subject). Do you have any suggestions on what file I could use? Thank you, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, December 07, 2018 3:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] Extracting ROI from atlases Hi Da-yea what are you trying to achieve? We provide annotations of the fsaverage subject you can use, and of course we automatically parcellate each subject that is run through recon-all. The gcs is contains a lot of information that isn't easily displayed as an ROI, so you can't really just extract one from it cheers Bruce On Fri, 7 Dec 2018, Song, Da-Yea wrote: >External Email - Use Caution > > I tried this on the > ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an > error message that mri_read could not determine the type of file. Do I need > to convert the gcs file into another format to use? > > Thank you so much in advance for your help! > > Best, > Da-yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas > N.,Ph.D. > Sent: Thursday, December 06, 2018 11:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Extracting ROI from atlases > > You can use > mri_binarize --i aparc+aseg.mgz --match 1028 --o > ctx-lh-superiorfrontal.nii.gz See > $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use > > > On 12/04/2018 12:51 PM, Song, Da-Yea wrote: >> >> External Email - Use Caution >> >> Hello, >> >> Is there a command to extract ROIs from atlases (ex. desikan) in >> nifti file formats? >> >> Thank you so much in advance for your time. >> >> Best, >> >> Da-Yea >> >> - >> --- >> Disclaimer: >> >> >> The materials in this e-mail are private and may contain Protected >> Information. Please note that e-mail communication is not encrypted >> by default. You have the right to request further emails be encrypted >> by notifying the sender. Your continued use of e-mail constitutes >> your acknowledgment of these confidentiality and security >> limitations. If you are not the intended recipient, be advised that >> any unauthorized use, disclosure, copying, distribution, or the >> taking of any action in reliance on the contents of this information is >> strictly prohibited. >> If you have received this e-mail in error, please immediately notify >> the sender via telephone or return e-mail. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har >> vard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGl >> LDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8& >> m=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw=7LTBome-I69Xsk1RhHcX5 >> eTUXnQrBP5am9WANIUlhe4= > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=j > jRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw=7LTBome-I69Xsk1RhHcX5eTUX > nQrBP5am9WANIUlhe4= > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer=DwIDAw=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=tL1NYVnvNpTUbtMM7_ogOOHsPQV2dLc6POouLtuKLSs=umuIN7eRbxiiTsuM6-vQ7BDZ5Vmt5nwPIL5NPyilKyo= > > > -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclos
Re: [Freesurfer] Extracting ROI from atlases
External Email - Use Caution I tried this on the ?h.curvature.buckner40.filled.desikan_killinary.2010_03-25.gcs but got an error message that mri_read could not determine the type of file. Do I need to convert the gcs file into another format to use? Thank you so much in advance for your help! Best, Da-yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, December 06, 2018 11:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting ROI from atlases You can use mri_binarize --i aparc+aseg.mgz --match 1028 --o ctx-lh-superiorfrontal.nii.gz See $FREESURFER_HOME/FreeSurferColorLUT.txt for the list of codes to use On 12/04/2018 12:51 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > Is there a command to extract ROIs from atlases (ex. desikan) in nifti > file formats? > > Thank you so much in advance for your time. > > Best, > > Da-Yea > > > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw=7LTBome-I69Xsk1RhHcX5eTUXnQrBP5am9WANIUlhe4= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=jjRZ8y9irhkswoHg_a5_5xXIjS27bQ3ZLTeP0rUPqfw=7LTBome-I69Xsk1RhHcX5eTUXnQrBP5am9WANIUlhe4= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extracting ROI from atlases
External Email - Use Caution Hello, Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats? Thank you so much in advance for your time. Best, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CerebralWhiteMatterVol {Disarmed}
External Email - Use Caution Hello, I had a follow up question regarding the CerebralWhiteMatter variable from aseg.stats. 1. Does this include the white matter underlying the cortex? 2. How about the subcortical white matter? (For example, I noticed that there was a separate value for gray matter -SubCortGray- but not for white matter. Is it because this is already included in the CerebralWhiteMatter?) Thank you so much in advance for your help! Best regards, Da-Yea From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, November 20, 2018 6:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] CerebralWhiteMatterVol No, it does not. On 11/20/18 3:54 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=XgbRUsEg8ebS5CgX7P0Jwzin6EJw6rXbty3aL1AxeDo=zle6gZjcU92U8NgxtJd3MnN9x6Ni33_K-OpY42yTvOg=> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] CerebralWhiteMatterVol
External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aseg.stats calculations {Disarmed}
External Email - Use Caution Thank you for pointing that out! I took another look and was able to get the following; TotalGray (from the aseg.stats) = 751765.612392 298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.00 (SubCortGray) + 52358.1 (L_cerebellum-cortex) + 52661.8 (R_cerebellum-cortex) = 750096.512392 There is still a difference of 1669.1. What could account for the difference? Best, Da-Yea From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, November 20, 2018 1:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aseg.stats calculations On 11/20/18 1:37 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried calculating this based on the formula but got different results. a. TotalGray (from the aseg.stats) = 751765.612392 b. 298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.00 (SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 645176.103792 Check your value for cerebellum cortex. It should be more like 60,000 mm3. You probably are looking at the mean intensity. 2. We have subjects that were processed in v4.0.4 and v6.0.0. Since the TotalGray measure did not exist in the v.4.0.4, what could we use to calculate the volume? How about the above formula? Thank you so much in advance for your help! Best, Da-Yea Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwMF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=4p_j1sHU-AtqQ0C_3_02b2SagUxdq2XXikaBKycMOxc=4yXPGritPZx9nr6CriB8e4Tu8QeBL3Hkvnv7gEbtBtM=> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aseg.stats calculations
External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried calculating this based on the formula but got different results. a. TotalGray (from the aseg.stats) = 751765.612392 b. 298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.00 (SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 645176.103792 2. We have subjects that were processed in v4.0.4 and v6.0.0. Since the TotalGray measure did not exist in the v.4.0.4, what could we use to calculate the volume? Thank you so much in advance for your help! Best, Da-Yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all error
External Email - Use Caution Hello, I'm running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions would be really appreciated. Here is the recon-all.cmd error message: #- # New invocation of recon-all Fri Sep 7 09:34:58 EDT 2018 mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz # #@# MotionCor Fri Sep 7 09:35:30 EDT 2018 cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz /g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform mri_add_xform_to_header -c /g5/dcn/freesurfer /subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz # #@# Talairach Fri Sep 7 09:35:44 EDT 2018 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 #- # New invocation of recon-all Fri Sep 7 09:36:58 EDT 2018 #- # New invocation of recon-all Fri Sep 7 09:37:03 EDT 2018 #- # New invocation of recon-all Fri Sep 7 09:39:43 EDT 2018 #- # New invocation of recon-all Fri Sep 7 09:39:47 EDT 2018 #- # New invocation of recon-all Fri Sep 7 09:42:58 EDT 2018 #- # New invocation of recon-all Fri Sep 7 09:43:02 EDT 2018 Best, Da-yea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return 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.
[Freesurfer] Unknown Region_Stats
External Email - Use Caution Hello, I read on the website FAQ that "if you use the values in the ?h.aparac.stats, it already factors out the 'unknown' region, so you don't have to do it yourself". Is there a way to view stats (ex. thickness, area, volume) for these unknown regions? Thank you, Dayea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return 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.
[Freesurfer] Stats Error
External Email - Use Caution Hello, I'm extracting some stats from recon-all but noticed that it would stop running in the middle (error message: end: Not in while/foreach) . Any suggestions on how I could solve this problem would be greatly appreciated! Thank you so much in advance. Best regards, Da-Yea computing statistics for each annotation in rantaFL.annot. reading volume /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/mri/wm.mgz... reading input surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... Using TH3 vertex volume calc Total face volume 249500 Total vertex volume 245871 (mask=0) reading input pial surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.pial... reading input white surface /g5/dcn/freesurfer_testing/subjects//3095_3T_011216_0/surf/lh.white... reading colortable from annotation file... colortable with 11 entries read (originally /freesurfer/FrontalLobeColorLUT.txt) atlas_icv (eTIV) = 1377325 mm^3(det: 1.414413 ) lhCtxGM: 245607.578 244866.000 diff= 741.6 pctdiff= 0.302 rhCtxGM: 253269.330 252721.000 diff= 548.3 pctdiff= 0.217 lhCtxWM: 199421.968 199714.500 diff= -292.5 pctdiff=-0.147 rhCtxWM: 198426.788 199552.500 diff=-1125.7 pctdiff=-0.567 SubCortGMVol 53103.000 SupraTentVol 962619.664 (961451.000) diff=1168.664 pctdiff=0.121 SupraTentVolNotVent 951172.664 (950004.000) diff=1168.664 pctdiff=0.123 BrainSegVol 1091475.000 (1088903.000) diff=2572.000 pctdiff=0.236 BrainSegVolNotVent 1076628.000 (1076311.664) diff=316.336 pctdiff=0.029 BrainSegVolNotVent 1076628.000 CerebellumVol 126436.000 VentChorVol 11447.000 3rd4th5thCSF 3400.000 CSFVol 828.000, OptChiasmVol 188.000 MaskVol 1502516.000 structure is "anterior_cingulate" number of vertices = 3531 total surface area = 2414 mm^2 total gray matter volume= 6657 mm^3 average cortical thickness = 2.742 mm +- 0.824 mm average integrated rectified mean curvature = 0.116 average integrated rectified Gaussian curvature = 0.017 folding index = 37 intrinsic curvature index = 2.5 structure is "dlpfc" number of vertices = 10762 total surface area = 7059 mm^2 total gray matter volume= 20651 mm^3 average cortical thickness = 2.426 mm +- 0.665 mm average integrated rectified mean curvature = 0.125 average integrated rectified Gaussian curvature = 0.025 folding index = 150 intrinsic curvature index = 10.8 structure is "frontal_eye_field" number of vertices = 1371 total surface area = 927 mm^2 total gray matter volume= 2587 mm^3 average cortical thickness = 2.654 mm +- 0.526 mm average integrated rectified mean curvature = 0.111 average integrated rectified Gaussian curvature = 0.020 folding index = 12 intrinsic curvature index = 1.0 structure is "inferolateral_pfc" number of vertices = 4430 total surface area = 2928 mm^2 total gray matter volume= 9914 mm^3 average cortical thickness = 2.662 mm +- 0.654 mm average integrated rectified mean curvature = 0.124 average integrated rectified Gaussian curvature = 0.022 folding index = 64 intrinsic curvature index = 4.1 structure is "lateral_OFC" number of vertices = 5859 total surface area = 3926 mm^2 total gray matter volume= 11128 mm^3 average cortical thickness = 2.493 mm +- 0.732 mm average integrated rectified mean curvature = 0.128 average integrated rectified Gaussian curvature = 0.029 folding index = 74 intrinsic curvature index = 6.6 structure is "medial_OFC" number of vertices = 1871 total surface area = 1217 mm^2 total gray matter volume= 3722 mm^3 average cortical thickness = 2.641 mm +- 0.791 mm average integrated rectified mean curvature = 0.121 average integrated rectified Gaussian curvature = 0.036 folding index = 27 intrinsic curvature index = 2.9 structure is "mpfc" number of vertices = 6801 total surface area = 4531 mm^2 total gray matter volume= 15597 mm^3 average cortical thickness = 2.761 mm +- 0.652 mm average integrated rectified mean curvature = 0.127 average integrated rectified Gaussian curvature = 0.027 folding index = 86 intrinsic curvature index = 7.4 structure is "primary_motor" number of vertices = 6578 total surface area = 3910 mm^2 total
Re: [Freesurfer] MRIread error
External Email - Use Caution There is enough disk space and it works fine with the other subjects. But for a few subjects in particular I seem to get the same error message. I checked once more and it seems that the rh.white files are being saved in the stats folder (rather than being in the "surf" folder) . The size of the files are 0KB. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Wednesday, August 29, 2018 4:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MRIread error Check permissions first. Look at the size of the file. Is it much smaller than other rh.white files in other subjects? Have you run out of disk space? On 08/29/2018 04:37 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hi everyone, > > I'm trying to pre-process subjects through the pipeline but keep > getting a handful of subjects that error out within seconds of running > them. The error message I get is: > > MRISread(/subjects/002_1006/surf/rh.white):could not open file > > When I go into the subject's folder, I find the rh.white file in the > stats folder. I've run about 100 subjects without an issue but for > some reason there are a few subjects that will stop processing with > the same error message. Any suggestions or comments would be greatly > appreciated. > > Thanks! > > Dayea > > -- > -- > Disclaimer: > > > The materials in this e-mail are private and may contain Protected > Information. Please note that e-mail communication is not encrypted by > default. You have the right to request further emails be encrypted by > notifying the sender. Your continued use of e-mail constitutes your > acknowledgment of these confidentiality and security limitations. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying, distribution, or the taking of any action in > reliance on the contents of this information is strictly prohibited. > If you have received this e-mail in error, please immediately notify > the sender via telephone or return e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLD > GrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=e > 98J_H-7BF0EKDAVuJ-2kvx3azQNKX1ulVz4U_li3Gk=LpELKCdVe1n-qbC8ZUaMHYMLZ > N3Fra2zLobAGw6K3tI= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=e98J_H-7BF0EKDAVuJ-2kvx3azQNKX1ulVz4U_li3Gk=LpELKCdVe1n-qbC8ZUaMHYMLZN3Fra2zLobAGw6K3tI= 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=DwIF-g=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8=e98J_H-7BF0EKDAVuJ-2kvx3azQNKX1ulVz4U_li3Gk=OWWchzmA_noIdnscfxQPEUfHeGAEL_D8RplFnwNr7j0= . 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.
[Freesurfer] MRIread error
External Email - Use Caution Hi everyone, I'm trying to pre-process subjects through the pipeline but keep getting a handful of subjects that error out within seconds of running them. The error message I get is: MRISread(/subjects/002_1006/surf/rh.white):could not open file When I go into the subject's folder, I find the rh.white file in the stats folder. I've run about 100 subjects without an issue but for some reason there are a few subjects that will stop processing with the same error message. Any suggestions or comments would be greatly appreciated. Thanks! Dayea -- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return 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.
