Re: [Freesurfer] mapping ROI to surface space
Apologies I meant from a label to a .mgh Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 08/11/2016 17:35, "Andrews, Derek" <derek.andr...@kcl.ac.uk> wrote: >This sender failed our fraud detection checks and may not be who they >appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing > >Thank you Doug that worked perfectly. > >Is it possible then to go back to a .w from a label? > > > >Derek Sayre Andrews, MSc >PhD Candidate > >The Sackler Institute for Translational Neurodevelopment >Department of Forensic and Neurodevelopmental Sciences >Institute of Psychiatry, Psychology & Neuroscience, King's College London > >Telephone: +44 (0)20 7848 5701 >Email: derek.andr...@kcl.ac.uk > > > > > >On 08/11/2016 16:10, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >>Use mri_surf2surf to convert it to an mgh or mgz file, then use >>mri_cor2label with the --surf option to convert it to a label >> >> >>On 11/8/16 9:41 AM, Andrews, Derek wrote: >>> Hi Bruce and Freesurfer developers, >>> >>> Thank you. Any suggestions on converting a binary .w file to a label >>>would >>> be very helpful. >>> >>> Best, Derek >>> >>> >>> >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> Department of Forensic and Neurodevelopmental Sciences >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: derek.andr...@kcl.ac.uk >>> >>> >>> >>> >>> >>> On 08/11/2016 14:04, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Derek >>>> >>>> I'll cc the FS list so others can answer. It depends on the reason the >>>> holes exist. It also depends on the size of the holes. The dev >>>>version >>>> of >>>> mri_label2labels supports morphological close operations. It takes an >>>> integer parameter which should be about the radius of the holes you >>>>would >>>> like to fill in. Note that this will also fill in some concavities in >>>>the >>>> boundary of the label. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 8 Nov 2016, Andrews, Derek wrote: >>>> >>>>> Hi Bruce, >>>>> >>>>> Apologies for contacting you directly but I’m not sure if my message >>>>>is >>>>> getting through to the list. >>>>> >>>>> I have gotten ahold of the dev version of mri_label2label. >>>>> >>>>> Currently I have a .w file that I need to “fill in the holes” on. >>>>>Could >>>>> you please specify the steps I will need to take to make my .w file >>>>>an >>>>> acceptable input for mri_label2label, and any recommendations you may >>>>> have >>>>> for the value of N for the —close flag. >>>>> >>>>> Any help you could provide would be appreciated. >>>>> >>>>> Best, Derek >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Derek Sayre Andrews, MSc >>>>> PhD Candidate >>>>> >>>>> The Sackler Institute for Translational Neurodevelopment >>>>> Department of Forensic and Neurodevelopmental Sciences >>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>>> London >>>>> >>>>> Telephone: +44 (0)20 7848 5701 >>>>> Email: derek.andr...@kcl.ac.uk >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>>>>wrote: >>>>> >>>>>> Hi Derek >>>>&
Re: [Freesurfer] mapping ROI to surface space
Thank you Doug that worked perfectly. Is it possible then to go back to a .w from a label? Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 08/11/2016 16:10, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote: >Use mri_surf2surf to convert it to an mgh or mgz file, then use >mri_cor2label with the --surf option to convert it to a label > > >On 11/8/16 9:41 AM, Andrews, Derek wrote: >> Hi Bruce and Freesurfer developers, >> >> Thank you. Any suggestions on converting a binary .w file to a label >>would >> be very helpful. >> >> Best, Derek >> >> >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >> On 08/11/2016 14:04, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Derek >>> >>> I'll cc the FS list so others can answer. It depends on the reason the >>> holes exist. It also depends on the size of the holes. The dev version >>> of >>> mri_label2labels supports morphological close operations. It takes an >>> integer parameter which should be about the radius of the holes you >>>would >>> like to fill in. Note that this will also fill in some concavities in >>>the >>> boundary of the label. >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 8 Nov 2016, Andrews, Derek wrote: >>> >>>> Hi Bruce, >>>> >>>> Apologies for contacting you directly but I’m not sure if my message >>>>is >>>> getting through to the list. >>>> >>>> I have gotten ahold of the dev version of mri_label2label. >>>> >>>> Currently I have a .w file that I need to “fill in the holes” on. >>>>Could >>>> you please specify the steps I will need to take to make my .w file an >>>> acceptable input for mri_label2label, and any recommendations you may >>>> have >>>> for the value of N for the —close flag. >>>> >>>> Any help you could provide would be appreciated. >>>> >>>> Best, Derek >>>> >>>> >>>> >>>> >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> Department of Forensic and Neurodevelopmental Sciences >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: derek.andr...@kcl.ac.uk >>>> >>>> >>>> >>>> >>>> >>>> On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>>>wrote: >>>> >>>>> Hi Derek >>>>> >>>>> I think the dev version of mri_label2label supports >>>>> open/close/dilate/erode >>>>> operations: >>>>> >>>>> mri_label2label --help >>>>> USAGE: mri_label2label.bin >>>>> >>>>> --srclabel input label file >>>>> >>>>> --erode N erode the label N times before writing >>>>> --open N open the label N times before writing >>>>> --close N close the label N times before writing >>>>> --dilate Ndilate the label N times before writing >>>>> . >>>>> . >>>>> . >>>>> >>>>> if your version doesn't have these operations let us know and we can >>>>> get >>>>> you an updated one >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> >>>>> On Fri, 28 Oct 2016, >>>>> Andrews,
Re: [Freesurfer] mapping ROI to surface space
Hi Bruce and Freesurfer developers, Thank you. Any suggestions on converting a binary .w file to a label would be very helpful. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 08/11/2016 14:04, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Derek > >I'll cc the FS list so others can answer. It depends on the reason the >holes exist. It also depends on the size of the holes. The dev version >of >mri_label2labels supports morphological close operations. It takes an >integer parameter which should be about the radius of the holes you would >like to fill in. Note that this will also fill in some concavities in the >boundary of the label. > >cheers >Bruce > > >On Tue, 8 Nov 2016, Andrews, Derek wrote: > >> Hi Bruce, >> >> Apologies for contacting you directly but I’m not sure if my message is >> getting through to the list. >> >> I have gotten ahold of the dev version of mri_label2label. >> >> Currently I have a .w file that I need to “fill in the holes” on. Could >> you please specify the steps I will need to take to make my .w file an >> acceptable input for mri_label2label, and any recommendations you may >>have >> for the value of N for the —close flag. >> >> Any help you could provide would be appreciated. >> >> Best, Derek >> >> >> >> >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >> On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Derek >>> >>> I think the dev version of mri_label2label supports >>> open/close/dilate/erode >>> operations: >>> >>> mri_label2label --help >>> USAGE: mri_label2label.bin >>> >>>--srclabel input label file >>> >>>--erode N erode the label N times before writing >>>--open N open the label N times before writing >>>--close N close the label N times before writing >>>--dilate Ndilate the label N times before writing >>> . >>> . >>> . >>> >>> if your version doesn't have these operations let us know and we can >>>get >>> you an updated one >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Fri, 28 Oct 2016, >>> Andrews, Derek wrote: >>> >>>> Hi Bruce, >>>> >>>> As always thank you for your prompt reply. >>>> >>>> For the morphological close operation, would you suggest using >>>>mris_fill >>>> on the surface ROI I created and then running mri_vol2surf again on >>>>the >>>> volume output by mris_fill? >>>> >>>> Best, Derek >>>> >>>> >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> Department of Forensic and Neurodevelopmental Sciences >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: derek.andr...@kcl.ac.uk >>>> >>>> >>>> >>>> >>>> >>>> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>>>wrote: >>>> >>>>> p.s. you could remove many/most of these holes using a morphological >>>>> close operation >>>>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>>>> >>>>>> Hello Freesurfer Developers and Community, >>>>>> >>>>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>>>> fsaverage >>>>>&g
Re: [Freesurfer] mapping ROI to surface space
Hello Freesurfer Developers, I have gotten ahold of the dev version of mri_label2label. Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag. Thank you. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk > On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Derek > > I think the dev version of mri_label2label supports > open/close/dilate/erode > operations: > > mri_label2label --help > USAGE: mri_label2label.bin > > --srclabel input label file > > --erode N erode the label N times before writing > --open N open the label N times before writing > --close N close the label N times before writing > --dilate Ndilate the label N times before writing > . > . > . > > if your version doesn't have these operations let us know and we can get > you an updated one > > cheers > Bruce > > > > On Fri, 28 Oct 2016, > Andrews, Derek wrote: > >> Hi Bruce, >> >> As always thank you for your prompt reply. >> >> For the morphological close operation, would you suggest using mris_fill >> on the surface ROI I created and then running mri_vol2surf again on the >> volume output by mris_fill? >> >> Best, Derek >> >> >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >> London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >>> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >>> >>> p.s. you could remove many/most of these holes using a morphological >>> close operation >>>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>>> >>>> Hello Freesurfer Developers and Community, >>>> >>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>> fsaverage >>>> pial surface. >>>> >>>> I have used the following commands >>>> >>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>> ‹12 >>>> ‹t1 >>>> >>>> Then >>>> >>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>> >>>> The ROI appears to be in the right place however is very blotchy. >>>> Have I >>>> missed a step? Or is this correct? >>>> >>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>> after >>>> mapped using the above. >>>> >>>> Thank you for your support, >>>> >>>> Best, Derek >>>> >>>> [IMAGE] >>>> >>>> >>>> >>>> >>>> >>>> ___ >>>> __ >>>> ___ >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> >>>> Department of Forensic and Neurodevelopmental Sciences >>>> >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: derek.andr...@kcl.ac.uk >>>> >>>> >>>> >>>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>> nm >>> >>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek >>> .a >>> >>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f3
Re: [Freesurfer] mapping ROI to surface space
Hello Freesurfer Developers, I have gotten ahold of the dev version of mri_label2label. Currently I have a .w file that I need to “fill in the holes” on. Could you please specify the steps I will need to take to make my .w file an acceptable input for mri_label2label, and any recommendations you may have for the value of N for the —close flag. Thank you. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Derek > >I think the dev version of mri_label2label supports >open/close/dilate/erode >operations: > >mri_label2label --help >USAGE: mri_label2label.bin > >--srclabel input label file > >--erode N erode the label N times before writing >--open N open the label N times before writing >--close N close the label N times before writing >--dilate Ndilate the label N times before writing > . >. >. > >if your version doesn't have these operations let us know and we can get >you an updated one > >cheers >Bruce > > > >On Fri, 28 Oct 2016, >Andrews, Derek wrote: > >> Hi Bruce, >> >> As always thank you for your prompt reply. >> >> For the morphological close operation, would you suggest using mris_fill >> on the surface ROI I created and then running mri_vol2surf again on the >> volume output by mris_fill? >> >> Best, Derek >> >> >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> p.s. you could remove many/most of these holes using a morphological >>> close operation >>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>> >>>> Hello Freesurfer Developers and Community, >>>> >>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>> fsaverage >>>> pial surface. >>>> >>>> I have used the following commands >>>> >>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>>‹12 >>>> ‹t1 >>>> >>>> Then >>>> >>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>> >>>> The ROI appears to be in the right place however is very blotchy. >>>>Have I >>>> missed a step? Or is this correct? >>>> >>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>>after >>>> mapped using the above. >>>> >>>> Thank you for your support, >>>> >>>> Best, Derek >>>> >>>> [IMAGE] >>>> >>>> >>>> >>>> >>>> >>>>___ >>>>__ >>>> ___ >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> >>>> Department of Forensic and Neurodevelopmental Sciences >>>> >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: derek.andr...@kcl.ac.uk >>>> >>>> >>>> >>>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>>nm >>> >>>r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek >>>.a >>> >>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 >>>b8 >>> >>>3c724071654356%7C0=liaieNpnjB7M4w9favIeZ9B0
Re: [Freesurfer] mapping ROI to surface space
Hi Bruce, It doesn’t look like I have those operations. If you could provide me with a copy of the dev version of the function I would very much appreciate it. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 28/10/2016 15:53, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Derek > >I think the dev version of mri_label2label supports >open/close/dilate/erode >operations: > >mri_label2label --help >USAGE: mri_label2label.bin > >--srclabel input label file > >--erode N erode the label N times before writing >--open N open the label N times before writing >--close N close the label N times before writing >--dilate Ndilate the label N times before writing > . >. >. > >if your version doesn't have these operations let us know and we can get >you an updated one > >cheers >Bruce > > > >On Fri, 28 Oct 2016, >Andrews, Derek wrote: > >> Hi Bruce, >> >> As always thank you for your prompt reply. >> >> For the morphological close operation, would you suggest using mris_fill >> on the surface ROI I created and then running mri_vol2surf again on the >> volume output by mris_fill? >> >> Best, Derek >> >> >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> Department of Forensic and Neurodevelopmental Sciences >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> p.s. you could remove many/most of these holes using a morphological >>> close operation >>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>> >>>> Hello Freesurfer Developers and Community, >>>> >>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>> fsaverage >>>> pial surface. >>>> >>>> I have used the following commands >>>> >>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>>‹12 >>>> ‹t1 >>>> >>>> Then >>>> >>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>> >>>> The ROI appears to be in the right place however is very blotchy. >>>>Have I >>>> missed a step? Or is this correct? >>>> >>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>>after >>>> mapped using the above. >>>> >>>> Thank you for your support, >>>> >>>> Best, Derek >>>> >>>> [IMAGE] >>>> >>>> >>>> >>>> >>>> >>>>___ >>>>__ >>>> ___ >>>> >>>> Derek Sayre Andrews, MSc >>>> PhD Candidate >>>> >>>> The Sackler Institute for Translational Neurodevelopment >>>> >>>> Department of Forensic and Neurodevelopmental Sciences >>>> >>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>> London >>>> >>>> Telephone: +44 (0)20 7848 5701 >>>> Email: derek.andr...@kcl.ac.uk >>>> >>>> >>>> >>>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>>nm >>> >>>r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek >>>.a >>> >>>ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 >>>b8 >>> >>>3c724071654356%7C0=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D& >>>re >>> served=0 >>> >>> >>> The information in this e-mail is intended only for the person to whom >>>
Re: [Freesurfer] mapping ROI to surface space
The ROI volume is not binary however I binarized it after mapping to the surface space. Should I have binarized the ROI prior to running mri_vol2surf? Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 28/10/2016 15:59, "dgw" <dgwake...@gmail.com> wrote: >another thing to check is that you are using a binary ROI file. The >Volume based image looked like it had a range of values. > >hth >d > >On Fri, Oct 28, 2016 at 10:53 AM, Bruce Fischl ><fis...@nmr.mgh.harvard.edu> wrote: >> Hi Derek >> >> I think the dev version of mri_label2label supports >>open/close/dilate/erode >> operations: >> >> mri_label2label --help >> USAGE: mri_label2label.bin >> >>--srclabel input label file >> >>--erode N erode the label N times before writing >>--open N open the label N times before writing >>--close N close the label N times before writing >>--dilate Ndilate the label N times before writing >> . >> . >> . >> >> if your version doesn't have these operations let us know and we can >>get you >> an updated one >> >> cheers >> Bruce >> >> >> >> >> On Fri, 28 Oct 2016, Andrews, Derek wrote: >> >>> Hi Bruce, >>> >>> As always thank you for your prompt reply. >>> >>> For the morphological close operation, would you suggest using >>>mris_fill >>> on the surface ROI I created and then running mri_vol2surf again on the >>> volume output by mris_fill? >>> >>> Best, Derek >>> >>> >>> >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> Department of Forensic and Neurodevelopmental Sciences >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: derek.andr...@kcl.ac.uk >>> >>> >>> >>> >>> >>> On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >>> >>>> p.s. you could remove many/most of these holes using a morphological >>>> close operation >>>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>>> >>>>> Hello Freesurfer Developers and Community, >>>>> >>>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>>> fsaverage >>>>> pial surface. >>>>> >>>>> I have used the following commands >>>>> >>>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>>>‹12 >>>>> ‹t1 >>>>> >>>>> Then >>>>> >>>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>>> >>>>> The ROI appears to be in the right place however is very blotchy. >>>>>Have I >>>>> missed a step? Or is this correct? >>>>> >>>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>>>after >>>>> mapped using the above. >>>>> >>>>> Thank you for your support, >>>>> >>>>> Best, Derek >>>>> >>>>> [IMAGE] >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>__ >>>>>___ >>>>> ___ >>>>> >>>>> Derek Sayre Andrews, MSc >>>>> PhD Candidate >>>>> >>>>> The Sackler Institute for Translational Neurodevelopment >>>>> >>>>> Department of Forensic and Neurodevelopmental Sciences >>>>> >>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>>> London >>>>> >>>>> Telephone: +44 (0)20 7848 5701 >>>>> Email: derek.andr...@kcl.ac.uk >>>>> >>>>> >>>>> >>&
Re: [Freesurfer] mapping ROI to surface space
Hi Bruce, As always thank you for your prompt reply. For the morphological close operation, would you suggest using mris_fill on the surface ROI I created and then running mri_vol2surf again on the volume output by mris_fill? Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 28/10/2016 14:54, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >p.s. you could remove many/most of these holes using a morphological >close operation >On Fri, 28 Oct 2016, Andrews, Derek wrote: > >> Hello Freesurfer Developers and Community, >> >> I am looking to map a ROI.nii based on the MNI152 template to the >>fsaverage >> pial surface. >> >> I have used the following commands >> >> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl ‹12 >>‹t1 >> >> Then >> >> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >> >> The ROI appears to be in the right place however is very blotchy. Have I >> missed a step? Or is this correct? >> >> See bellow a picture of the ROI highlighted in FSL and in tksurfer after >> mapped using the above. >> >> Thank you for your support, >> >> Best, Derek >> >> [IMAGE] >> >> >> >> >>_ >>___ >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> >> Department of Forensic and Neurodevelopmental Sciences >> >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >>___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm >r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek.a >ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b8 >3c724071654356%7C0=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D >served=0 > > >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://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part >ners.org%2Fcomplianceline=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65ef7 >af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0=% >2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=0 . 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] FA/MD.nii to fsaverage space
Dear Freesurfer developers, I would like to perform an analysis that requires me to have all of my subjects surface based and diffusion data in the same space. I have performed recon-all -qcache so that all my surface based measures are in fsaverage space. I now would like to register the FA.nii and MD.nii images to fsaverage space as well. Could you please provide me some command line examples to perform this? I am unsure if I should be using mri_vol2vol or mri_cvs_register. Thank you for your support. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk ___ 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] longitudinal qdec tables
Hi Martin, Thank you for the tip. Indeed there is some issue with the character spacing in my qdec file. I usually generate subject text files like this in excel and save them as csv .txt files. Do you have any suggestions for easily writing the qdec file without going line by line, space by space? Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk From: Martin Reuter <mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Mon, 11 Jul 2016 13:59:53 +0200 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] longitudinal qdec tables Hi Derek, For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows. Best Martin On Jul 11, 2016 12:58 PM, "Andrews, Derek" <derek.andr...@kcl.ac.uk<mailto:derek.andr...@kcl.ac.uk>> wrote: Dear FreeSurfer Developers and Community, I have been trying to run some commands using the -qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the -fsgd flag but am unsure of how to go about this with longitudinal data, therefore I am using the qdec.dat file structure. I believe something must be wrong with the format of my qdec file. I'm working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See these qdec files attached. I receive the following errors: asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 514, in subj_listoftuples = assemble_inputs(options) File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs for row in reader: File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next self.fieldnames File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames self._fieldnames = self.reader.next() _csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode? And mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh ERROR: no subjects specified I imagine something silly with the qdec file must be going on. Any advice would be very appreciated. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk<mailto:derek.andr...@kcl.ac.uk> ___ 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.
[Freesurfer] longitudinal qdec tables
Dear FreeSurfer Developers and Community, I have been trying to run some commands using the -qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the -fsgd flag but am unsure of how to go about this with longitudinal data, therefore I am using the qdec.dat file structure. I believe something must be wrong with the format of my qdec file. I'm working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See these qdec files attached. I receive the following errors: asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 514, in subj_listoftuples = assemble_inputs(options) File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs for row in reader: File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next self.fieldnames File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames self._fieldnames = self.reader.next() _csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode? And mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh ERROR: no subjects specified I imagine something silly with the qdec file must be going on. Any advice would be very appreciated. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk 1.long.qdec.table.dat Description: 1.long.qdec.table.dat 2.long.qdec.table.dat Description: 2.long.qdec.table.dat fsidfsid-base years 0008Y1 00080 0011Y1 00110 0011Y2 00110.490410959 0012Y1 00120 0012Y2 00120.490410959 0033Y1 00330 0033Y2 00330 0093Y1 00930 0095Y1 00950 0095Y2 00950.95890411 0097Y2 00970 0098Y1 00980 0101Y1 01010 0101Y2 01010.989041096 0101Y3 01011.980821918 0104Y1 01040 0105Y3 01050 0106Y1 01060 0106Y2 01061.208219178 0107Y3 01070 0108Y2 01080 0110Y1 01100 0110Y3 01102.169863014 0112Y1 01120 0112Y2 01121.054794521 0114Y1 01140 0114Y2 01141.315068493 0116Y1 01160 0116Y2 01160.989041096 0117Y1 01170 0120Y1 01200 0127Y1 01270 0128Y1 01280 0134Y1 01340 0135Y1 01350 0135Y2 01350 0136Y1 01360 0136Y2 01361.002739726 0136Y3 01362 0137Y3 01370 0138Y1 01380 0139Y1 01390 0139Y3 01390.978082192 0146Y3 01460 0153Y1 01530 0153Y2 01530.95890411 0153Y3 01531.994520548 0158Y1 01580 0158Y2 01581.169863014 0160Y2 01600 0160Y3 01601.035616438 0175Y1 01750 0175Y2 01750 0180Y1 01800 1004Y2 10040 1005Y1 10050 1005Y2 10051.178082192 1005Y3 10052.301369863 1006Y2 10060 1006Y3 10060.997260274 1007Y1 10070 1009Y1 10090 1016Y2 10160 1017Y1 10170 1017Y2 10171.054794521 1017Y3 10172.123287671 1022Y1 10220 1023Y1 10230 1023Y2 10231.476712329 1027Y1 10270 1027Y2 10270.961643836 1032Y2 10320 1032Y3 10321.054794521 1034Y1 10340 1034Y2 10341.112328767 1034Y3 10342.109589041 1041Y1 10410 1041Y3 10412.293150685 1042Y2 10420 1042Y3 10420.997260274 1044Y1 10440 1045Y2 10450 1046Y1 10460 1046Y2 10461.109589041 1046Y3 10462.068493151 1052Y1 10520 1052Y2 10521.156164384 1052Y3 10522.271232877 1054Y2 10540 1054Y3 10541.073972603 1057Y2 10570 1057Y3 10570.912328767 1071Y2 10710 1071Y3 10710 1073Y3 10730 1075Y2 10750 1075Y3 10750.978082192 1077Y1 10770 1091Y1 10910 1091Y2 10910 1091Y3 10911.994520548 1096Y2 10960 Y1 0 Y3 2.473972603 1121Y1 11210 1121Y2 11211.22739726 1141Y1 11410 1144Y3 11440 1151Y1 11510 1159Y1 11590 1159Y2 11590.989041096 1159Y3 11592.024657534 1161Y1 11610 1161Y2 1161-0.115068493 1164Y1 11640 1164Y2 11641.035616438___ 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
[Freesurfer] g-w.pct vs. g-w. ratio
>Dear FreeSurfer Support team, > >Thank you for your quick response. > >Is it fair to present both g-w.pct (100*(w-g)/((w+g)/2)) and g-w.ratio >(g/w) as GWR? I have seen the pct calculation presented as GWR in an >abstract that cited Salat (2009) in its introduction text. >Also, is it fair to say that decreases in in g-w.pct indicate less >definition between >the g/w matter boundary as a decrease in g-w.ratio would indicate? If I >want to make a statement about reduced definition between the g/w matter >boundary, what calculation would you suggest? > >Thank you very much for your clarifications on this. > >Best, Derek > > > > > >Derek Sayre Andrews, MSc >PhD Candidate > >The Sackler Institute for Translational Neurodevelopment >Department of Forensic and Neurodevelopmental Sciences >Institute of Psychiatry, Psychology & Neuroscience, King's College London > >Telephone: +44 (0)20 7848 5701 >Email: derek.andr...@kcl.ac.uk > > > > > >On 03/12/2015 17:26, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >>g-w.pct is computed as >> >>pct = 100*(w-g)/((w+g)/2) >> >>in the pctsurfcon script >> >> >>On 12/03/2015 12:18 PM, Andrews, Derek wrote: >>> Dear FreeSurfer Support team and Community >>> >>> I am wondering if someone can give me an explanation of the difference >>> between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div >>> lh.wm.mgh -o lh.ratio.mgh) >>> Will both these measures essentially measure the relationship between >>> grey and white matter signal intensity but in a different way? >>> >>> >>> Best, Derek >>> >>> >>> >>> >>> >>> *Derek Sayre Andrews, MSc* >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: derek.andr...@kcl.ac.uk >>> >>> >>> >>> >>> ___ >>> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] g-w.pct vs. g-w. ratio
Dear FreeSurfer Support team and Community I am wondering if someone can give me an explanation of the difference between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div lh.wm.mgh -o lh.ratio.mgh) Will both these measures essentially measure the relationship between grey and white matter signal intensity but in a different way? Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk ___ 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] SOLVED Re: zcat issue, lGI processing
Dear FreeSurfer support team, It appears that ‘zcat’ appears in line 126 of the load.mgh script, I have changed this to gzcat which appears to have solved the issue. Again, thank you for your support. It is very appreciated! Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 04/11/2015 11:33, "Andrews, Derek" <derek.andr...@kcl.ac.uk> wrote: >Dear Douglas, > >Thank you for response. To clarify, I need to find out where in the lGI >scripts zcat is being called so that I can change the code to use >something like gunzip. > >Best, Derek > > > >Derek Sayre Andrews, MSc >PhD Candidate > >The Sackler Institute for Translational Neurodevelopment >Department of Forensic and Neurodevelopmental Sciences >Institute of Psychiatry, Psychology & Neuroscience, King's College London > >Telephone: +44 (0)20 7848 5701 >Email: derek.andr...@kcl.ac.uk > > > > > >On 03/11/2015 17:41, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >> >>you can find out where it is with >> which zcat >> >>On 11/03/2015 07:42 AM, Andrews, Derek wrote: >>> Hello Freesurfer Support Team, >>> >>> I have encountered an issue running recon-all lgi that I believe is >>> due to a zcat issue on mac OSx where a .Z is added to the end of the >>> file name the resulting error looks like thisŠ >>> >>> >> reading filled volume... >>> >>> zcat: can't stat: >>> >>>/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia >>>l >>>.filled.mgz >>> >>>(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pi >>>a >>>l.filled.mgz.Z): >>> No such file or directory >>> >>> >>> Upon reading through some message boards it appears replacing zcat >>> with gzcat can solve this issue, however I am unsure where this >>> troublesome zcat command is (it does not appear in the mriscomputelgi >>> script). >>> >>> >>> Any suggestions or work throughs would be appreciated. >>> >>> >>> Best, Derek >>> >>> >>> >>> >>> >>> >>> *Derek Sayre Andrews, MSc* >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> >>> Department of Forensic and Neurodevelopmental Sciences >>> >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: derek.andr...@kcl.ac.uk >>> >>> >>> >>> >>> ___ >>> 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 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
Re: [Freesurfer] zcat issue, lGI processing
Dear Douglas, Thank you for response. To clarify, I need to find out where in the lGI scripts zcat is being called so that I can change the code to use something like gunzip. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 03/11/2015 17:41, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > >you can find out where it is with > which zcat > >On 11/03/2015 07:42 AM, Andrews, Derek wrote: >> Hello Freesurfer Support Team, >> >> I have encountered an issue running recon-all lgi that I believe is >> due to a zcat issue on mac OSx where a .Z is added to the end of the >> file name the resulting error looks like thisŠ >> >> >> reading filled volume... >> >> zcat: can't stat: >> >>/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial >>.filled.mgz >> >>(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia >>l.filled.mgz.Z): >> No such file or directory >> >> >> Upon reading through some message boards it appears replacing zcat >> with gzcat can solve this issue, however I am unsure where this >> troublesome zcat command is (it does not appear in the mriscomputelgi >> script). >> >> >> Any suggestions or work throughs would be appreciated. >> >> >> Best, Derek >> >> >> >> >> >> *Derek Sayre Andrews, MSc* >> PhD Candidate >> >> The Sackler Institute for Translational Neurodevelopment >> >> Department of Forensic and Neurodevelopmental Sciences >> >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> ___ >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] zcat issue, lGI processing
Hello Freesurfer Support Team, I have encountered an issue running recon-all -lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this... >> reading filled volume... zcat: can't stat: /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz.Z): No such file or directory Upon reading through some message boards it appears replacing zcat with gzcat can solve this issue, however I am unsure where this troublesome zcat command is (it does not appear in the mriscomputelgi script). Any suggestions or work throughs would be appreciated. Best, Derek Derek Sayre Andrews, MSc PhD Candidate The Sackler Institute for Translational Neurodevelopment Department of Forensic and Neurodevelopmental Sciences Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk ___ 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] high area.pial values
Dear Bruce, Thank you for your response regarding high area values. I have indeed observed high values (I.e. >20) in both the white and pial surfaces of my subjects, albeit only at a few vertices. The vertices indices that contain the highest values in these surface appear around ~258,000-324,000. Would you consider this the end of the array? And if not, what could cause a value of ~80 in the ~258,000 vertex of a pial surface reconstruction? As a background to what I¹m hoping to accomplish: I am using Freesurfer features (arrays) as inputs for pattern classification, therefore I am interested in potential impact on my models due to these outliers. Smoothing reduces the effect of these outliers, however also raises the values of surrounding vertices. I am thinking of replacing these high values with an average area measure taken across all participants prior to smoothing. Again, thank you for your insights in this topic. Best, Derek Derek Sayre Andrews, MSc PhD Candidate & IoPPN Student Forum Chair Department of Forensic and Neurodevelopmental Sciences & The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk On 25/09/2015 17:00, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >are they only high on the pial and not on the white? I would have guessed >that they would be high on both, and further that it is due to the >topology >correction and the quirks of the way we retesselate. One easy way to find >out if this is true is if the vertex index is near the end of the list >(i.e. close to the total number of vertices, since the vertices added >during the correction are at the end of the array) > >cheers >Bruce > >On Fri, 25 Sep 2015, Andrews, Derek wrote: > >> Dear FreeSurfer Support Team >> >> First of all, I must thank you for your excellent software! >> >> I have been looking at distributions of various free surfer features >> (histograms of the vertex wise measures). I have noticed some high >>values >> among the pial and white matter surfaces, these values range from 20-85. >> Again, this in only in a handful of vertices (out of millions of >>measures). >> I am wondering what could account for such a high value? >> >> Thank you for your help in clarifying this. >> >> Best, Derek >> >> >> >>_ >>___ >> >> Derek Sayre Andrews, MSc >> PhD Candidate >> >> Department of Forensic and Neurodevelopmental Sciences & >> >> The Sackler Institute for Translational Neurodevelopment >> Institute of Psychiatry, Psychology & Neuroscience, King's College >>London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >>___ >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
[Freesurfer] high area.pial values
Dear FreeSurfer Support Team First of all, I must thank you for your excellent software! I have been looking at distributions of various free surfer features (histograms of the vertex wise measures). I have noticed some high values among the pial and white matter surfaces, these values range from 20-85. Again, this in only in a handful of vertices (out of millions of measures). I am wondering what could account for such a high value? Thank you for your help in clarifying this. Best, Derek Derek Sayre Andrews, MSc PhD Candidate Department of Forensic and Neurodevelopmental Sciences & The Sackler Institute for Translational Neurodevelopment Institute of Psychiatry, Psychology & Neuroscience, King's College London Telephone: +44 (0)20 7848 5701 Email: derek.andr...@kcl.ac.uk ___ 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.
