[Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).
External Email - Use Caution Dear all, I am trying to run recon-all command for a subject ben. Before I perform this command, I have exported SUBJECTS_DIR to a folder with only T1 data for this subject ben in it. However after I entered the command "recon-all -s ben -i T1.nii -all", this error showed up: ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. I have tried all the suggestions listed in the error information, but none worked. Does anyone have any suggestion? I would really appreciated it. Many Thanks Peng -------- Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng@med.ovgu.de/peng@dzne.de Phone: +49 391 67 25074 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).
External Email - Use Caution Hi Andrew, Thank you for your reply. I have tried this command you sent me rm -rf $SUBJECTS_DIR/ben It indeed deleted the ben folder under the subject directory, but when I try to run recon-all for this participant under another name, it still responds with the same error. I have also tried the same data in another laptop. Also showed up the error. Would you say it might be something wrong with the data itself? (Although I am quite certain this is the raw T1 data which has never been performed any analysis). Many Thanks Peng Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng@med.ovgu.de/peng@dzne.de Phone: +49 391 67 25074 On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew wrote: > Hi Peng, > > > > Are you sure you’re deleting the subject folder from within the > SUBJECTS_DIR? > > > > rm -rf $SUBJECTS_DIR/ben > > > > Should clear the issue. > > > > best > > Andrew > > > > > > *From: * on behalf of Peng Liu < > claudialiu1...@gmail.com> > *Reply-To: *FS Help > *Date: *Friday, March 20, 2020 at 6:39 AM > *To: *FS Help > *Subject: *[Freesurfer] Error with recon-all: You are trying to re-run an > existing subject with (possibly) new input data (-i). > > > > *External Email - Use Caution* > > Dear all, > > > > I am trying to run recon-all command for a subject ben. Before I perform > this command, I have exported SUBJECTS_DIR to a folder with only T1 data > for this subject ben in it. However after I entered the command "recon-all > -s ben -i T1.nii -all", this error showed up: > > > > ERROR: You are trying to re-run an existing subject with (possibly) > > new input data (-i). If this is truly new input data, you should delete > > the subject folder and re-run, or specify a different subject name. > > If you are just continuing an analysis of an existing subject, then > > omit all -i flags. > > > > I have tried all the suggestions listed in the error information, but none > worked. > > > > Does anyone have any suggestion? I would really appreciated it. > > > > Many Thanks > > > > Peng > > > > Peng Liu, PhD Candidate > > > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > > Otto-von-Guericke Universität Magdeburg > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > > > Leipziger Str. 44| Haus 64| Raum 217 > > 39120 Magdeburg, Deutschland > > > > Email: peng@med.ovgu.de/peng@dzne.de > > Phone: +49 391 67 25074 > ___ > 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] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).
External Email - Use Caution Hello Douglas, If I do ls $SUBJECTS_DIR/ben, the T1 image will show up as predicted. However if I tried to recon-all, the error will pop up. Many Thanks Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng@med.ovgu.de/peng@dzne.de Phone: +49 391 67 25074 On Fri, 20 Mar 2020 at 15:54, Douglas N. Greve wrote: > What is your SUBJECTS_DIR set to? What do you get if you > ls $SUBJECTS_DIR/ben > > On 3/20/2020 9:48 AM, Peng Liu wrote: > > External Email - Use Caution > Hi Andrew, > > Thank you for your reply. I have tried this command you sent me > > rm -rf $SUBJECTS_DIR/ben > > It indeed deleted the ben folder under the subject directory, but when I > try to run recon-all for this participant under another name, it still > responds with the same error. > > I have also tried the same data in another laptop. Also showed up the > error. Would you say it might be something wrong with the data itself? > (Although I am quite certain this is the raw T1 data which has never been > performed any analysis). > > Many Thanks > > Peng > > > Peng Liu, PhD Candidate > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > Otto-von-Guericke Universität Magdeburg > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > Leipziger Str. 44| Haus 64| Raum 217 > 39120 Magdeburg, Deutschland > > Email: peng@med.ovgu.de/peng@dzne.de > Phone: +49 391 67 25074 > > > On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew > wrote: > >> Hi Peng, >> >> >> >> Are you sure you’re deleting the subject folder from within the >> SUBJECTS_DIR? >> >> >> >> rm -rf $SUBJECTS_DIR/ben >> >> >> >> Should clear the issue. >> >> >> >> best >> >> Andrew >> >> >> >> >> >> *From: * on behalf of Peng Liu < >> claudialiu1...@gmail.com> >> *Reply-To: *FS Help >> *Date: *Friday, March 20, 2020 at 6:39 AM >> *To: *FS Help >> *Subject: *[Freesurfer] Error with recon-all: You are trying to re-run >> an existing subject with (possibly) new input data (-i). >> >> >> >> *External Email - Use Caution* >> >> Dear all, >> >> >> >> I am trying to run recon-all command for a subject ben. Before I perform >> this command, I have exported SUBJECTS_DIR to a folder with only T1 data >> for this subject ben in it. However after I entered the command "recon-all >> -s ben -i T1.nii -all", this error showed up: >> >> >> >> ERROR: You are trying to re-run an existing subject with (possibly) >> >> new input data (-i). If this is truly new input data, you should delete >> >> the subject folder and re-run, or specify a different subject name. >> >> If you are just continuing an analysis of an existing subject, then >> >> omit all -i flags. >> >> >> >> I have tried all the suggestions listed in the error information, but >> none worked. >> >> >> >> Does anyone have any suggestion? I would really appreciated it. >> >> >> >> Many Thanks >> >> >> >> Peng >> >> >> >> Peng Liu, PhD Candidate >> >> >> >> Institut für Kognitive Neurologie und Demenzforschung (IKND) >> >> Otto-von-Guericke Universität Magdeburg >> >> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) >> >> >> >> Leipziger Str. 44| Haus 64| Raum 217 >> >> 39120 Magdeburg, Deutschland >> >> >> >> Email: peng@med.ovgu.de/peng@dzne.de >> >> Phone: +49 391 67 25074 >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
External Email - Use Caution Dear Freesurfer experts, I am trying to customize a colour map of my own, with five colours and scale from -12.5 to 12.5, since when using Heat (with default options), the scale is correct but it is shown in only four colours. However after I created the .lut file (attached below), when loading it into freeview, the colour scale is from 0 to 6. [image: image.png] Does this mean I should also include scale information in the .lut file? Any help would be much appreciated. Peng Liu Map.lut Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Customizing colour map
External Email - Use Caution Dear Freesurfer experts, I am trying to customize a colour map of my own, with five colours and scale from -12.5 to 12.5, since when using Heat (with default options), the scale is correct but it is shown in only four colours. However after I created the .lut file (attached below), when loading it into freeview, the colour scale is from 0 to 6. [image: image.png] Does this mean I should also include scale information in the .lut file? Any help would be much appreciated. Peng Liu Map.lut Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
External Email - Use Caution Hi Ruopeng, Thank you for your reply. I have also tried NIH and JET, but with negative scale, the entire image will turn into one same color as if there is some error. Meanwhile the reason of me trying to create .lut map is because I want five colours and five colours only... Is there any specific reason to not display negative scales with look up table? Will it cause any error or jeopardize the results displayed? Many Thanks Peng On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang wrote: > Hi Peng, > > Your lookup table only contains indices between 0 to 6. In any case I > would not use look up table to display negative scales. Have you tried any > other color maps like JET or NIH which has more colors? > > Best, > Ruopeng > > On Apr 6, 2020, at 6:30 AM, Peng Liu wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I am trying to customize a colour map of my own, with five colours and > scale from -12.5 to 12.5, since when using Heat (with default options), the > scale is correct but it is shown in only four colours. > > However after I created the .lut file (attached below), when loading it > into freeview, the colour scale is from 0 to 6. > > > > Does this mean I should also include scale information in the .lut file? > > Any help would be much appreciated. > > Peng Liu > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
External Email - Use Caution Thank you so much. I shall modify my other scripts then. Peng On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang wrote: > I don’t think look up table works with negative indices. It was mainly > designed for label volumes. > > Ruopeng > > On Apr 6, 2020, at 10:35 AM, Peng Liu wrote: > > External Email - Use Caution > > Hi Ruopeng, > > Thank you for your reply. > > I have also tried NIH and JET, but with negative scale, the entire image > will turn into one same color as if there is some error. > > Meanwhile the reason of me trying to create .lut map is because I want > five colours and five colours only... > > Is there any specific reason to not display negative scales with look up > table? Will it cause any error or jeopardize the results displayed? > > Many Thanks > > Peng > > > On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang > wrote: > >> Hi Peng, >> >> Your lookup table only contains indices between 0 to 6. In any case I >> would not use look up table to display negative scales. Have you tried any >> other color maps like JET or NIH which has more colors? >> >> Best, >> Ruopeng >> >> On Apr 6, 2020, at 6:30 AM, Peng Liu wrote: >> >> External Email - Use Caution >> >> Dear Freesurfer experts, >> >> I am trying to customize a colour map of my own, with five colours and >> scale from -12.5 to 12.5, since when using Heat (with default options), the >> scale is correct but it is shown in only four colours. >> >> However after I created the .lut file (attached below), when loading it >> into freeview, the colour scale is from 0 to 6. >> >> >> >> Does this mean I should also include scale information in the .lut file? >> >> Any help would be much appreciated. >> >> Peng Liu >> ___ >> 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 > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon-all Talairach failed error
External Email - Use Caution Dear Freesurfer experts, I am trying to run recon-all for a new subject, however I came across with this error 'Talairach failed'. The error log is as following: *talairach done\n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n##@# Talairach Failure Detection Thu May 14 15:11:47 CEST 2020/Users/pliu/Documents/DataAnalysis0512/subjects/Pilot03/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0153, pval=0. < threshold=0.0050)\nManual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See:\nhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>\nERROR: Talairach failed!\n* I have read online that I might need to perform a rough coregistration for the input image before running recon-all. But I am a bit lost by which image should it be registered to... Would 'mni305.cor.mgz' be okay as reference image? Any help would be much appreciated. Kindly Regards Peng Liu [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng@med.ovgu.de/peng@dzne.de Phone: +49 391 67 25074 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Brodmann area labels
External Email - Use Caution Dear Freesurfer experts, I was trying to perform some ROI analysis with results obtained from recon-all. However I noticed that after recon-all, the labels created were like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create are like 'lh.BA3b.label'. I have tried mri_annotation2label command, but the results I got were not as wanted either. Does anyone know how to create labels like 'lh.BA3b.label'? Any help would be appreciated a lot! Many Thanks PL [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng@med.ovgu.de/peng@dzne.de Phone: +49 391 67 25074 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Brodmann area labels
External Email - Use Caution Hi Douglas, Previously, after I ran recon-all, I would get multiple labels for the same brain area. For example, for BA3b, I have BA3b.label, BA3b.hmap.label and BA3b.thresh.label for each hemisphere. However this time I only have BA3b_exvivo.label, I wonder how would I get other labels, which command should I run? Many Thanks PL On Wed, 24 Jun 2020 at 16:09, Douglas N. Greve wrote: > I'm not sure what you mean by "like lh.BA3b.label". Are you just talking > about the file name or the actual label? > > On 6/24/2020 7:37 AM, Peng Liu wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I was trying to perform some ROI analysis with results obtained from > recon-all. However I noticed that after recon-all, the labels created were > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create > are like 'lh.BA3b.label'. > > I have tried mri_annotation2label command, but the results I got were not > as wanted either. > > Does anyone know how to create labels like 'lh.BA3b.label'? > > Any help would be appreciated a lot! > > Many Thanks > > PL > > [image: Otto-von-Guericke University Magdeburg] > > Peng Liu, PhD Candidate > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > Otto-von-Guericke Universität Magdeburg > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > Leipziger Str. 44| Haus 64| Raum 217 > 39120 Magdeburg, Deutschland > > Email: peng@med.ovgu.de/peng@dzne.de > Phone: +49 391 67 25074 > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Brodmann area labels
External Email - Use Caution Hi Bruce, I have tried this label, but it seems not working as it should be. That is why I wanted to create labels like before. Thank you so much! PL On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce wrote: > Hi Peng > > > > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo just > means that the data that went into the prediction was acquired on ex vivo > brains. > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > *Sent:* Wednesday, June 24, 2020 7:38 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Brodmann area labels > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > I was trying to perform some ROI analysis with results obtained from > recon-all. However I noticed that after recon-all, the labels created were > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create > are like 'lh.BA3b.label'. > > > > I have tried mri_annotation2label command, but the results I got were not > as wanted either. > > > > Does anyone know how to create labels like 'lh.BA3b.label'? > > > > Any help would be appreciated a lot! > > > > Many Thanks > > > > PL > > > > [image: Otto-von-Guericke University Magdeburg] > > > > Peng Liu, PhD Candidate > > > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > > Otto-von-Guericke Universität Magdeburg > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > > > Leipziger Str. 44| Haus 64| Raum 217 > > 39120 Magdeburg, Deutschland > > > > Email: peng@med.ovgu.de/peng@dzne.de > > Phone: +49 391 67 25074 > ___ > 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] Brodmann area labels
External Email - Use Caution I usually convert BA3b.label to a nifti mask with SPM to perform ROI analysis. But with exvivo label, the mask seems not working. Many Thanks PL On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce wrote: > Can you elaborate? What do you mean it is not working as it should be? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > *Sent:* Thursday, June 25, 2020 7:23 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Brodmann area labels > > > > *External Email - Use Caution* > > Hi Bruce, > > > > I have tried this label, but it seems not working as it should be. That is > why I wanted to create labels like before. > > > > Thank you so much! > > > > PL > > > > On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce > wrote: > > Hi Peng > > > > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo just > means that the data that went into the prediction was acquired on ex vivo > brains. > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > *Sent:* Wednesday, June 24, 2020 7:38 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Brodmann area labels > > > > *External Email - Use Caution* > > Dear Freesurfer experts, > > > > I was trying to perform some ROI analysis with results obtained from > recon-all. However I noticed that after recon-all, the labels created were > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create > are like 'lh.BA3b.label'. > > > > I have tried mri_annotation2label command, but the results I got were not > as wanted either. > > > > Does anyone know how to create labels like 'lh.BA3b.label'? > > > > Any help would be appreciated a lot! > > > > Many Thanks > > > > PL > > > > [image: Otto-von-Guericke University Magdeburg] > > > > Peng Liu, PhD Candidate > > > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > > Otto-von-Guericke Universität Magdeburg > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > > > Leipziger Str. 44| Haus 64| Raum 217 > > 39120 Magdeburg, Deutschland > > > > Email: peng@med.ovgu.de/peng@dzne.de > > Phone: +49 391 67 25074 > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Brodmann area labels
External Email - Use Caution Not exactly. I can successfully create a nifti mask with this exvivo label, and the brain area it highlighted is correct from observation. But when I try to employ this mask to ROI analysis. The results I got are exactly the same, with and without this mask. That is why I said it seems not working. If exvivo label is the same label as I used before, I will further look into the script and parameter setups. Thank you for all your help PL On Thu, 25 Jun 2020 at 19:20, Tim Schäfer wrote: > External Email - Use Caution > > What do you mean with 'not working'? Is an incorrect area highlighted on > the brain? Does some command you are using respond with an error message? > > Tim > > > On June 25, 2020 at 5:33 PM Peng Liu wrote: > > > > > > External Email - Use Caution > > > > I usually convert BA3b.label to a nifti mask with SPM to perform ROI > > analysis. But with exvivo label, the mask seems not working. > > > > Many Thanks > > > > PL > > > > On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce > wrote: > > > > > Can you elaborate? What do you mean it is not working as it should be? > > > > > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > > > *Sent:* Thursday, June 25, 2020 7:23 AM > > > *To:* Freesurfer support list > > > *Subject:* Re: [Freesurfer] Brodmann area labels > > > > > > > > > > > > *External Email - Use Caution* > > > > > > Hi Bruce, > > > > > > > > > > > > I have tried this label, but it seems not working as it should be. > That is > > > why I wanted to create labels like before. > > > > > > > > > > > > Thank you so much! > > > > > > > > > > > > PL > > > > > > > > > > > > On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce > > > wrote: > > > > > > Hi Peng > > > > > > > > > > > > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo > just > > > means that the data that went into the prediction was acquired on ex > vivo > > > brains. > > > > > > Cheers > > > > > > Bruce > > > > > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > > > *Sent:* Wednesday, June 24, 2020 7:38 AM > > > *To:* Freesurfer support list > > > *Subject:* [Freesurfer] Brodmann area labels > > > > > > > > > > > > *External Email - Use Caution* > > > > > > Dear Freesurfer experts, > > > > > > > > > > > > I was trying to perform some ROI analysis with results obtained from > > > recon-all. However I noticed that after recon-all, the labels created > were > > > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to > create > > > are like 'lh.BA3b.label'. > > > > > > > > > > > > I have tried mri_annotation2label command, but the results I got were > not > > > as wanted either. > > > > > > > > > > > > Does anyone know how to create labels like 'lh.BA3b.label'? > > > > > > > > > > > > Any help would be appreciated a lot! > > > > > > > > > > > > Many Thanks > > > > > > > > > > > > PL > > > > > > > > > > > > [image: Otto-von-Guericke University Magdeburg] > > > > > > > > > > > > Peng Liu, PhD Candidate > > > > > > > > > > > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > > > > > > Otto-von-Guericke Universität Magdeburg > > > > > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > > > > > > > > > > > Leipziger Str. 44| Haus 64| Raum 217 > > > > > > 39120 Magdeburg, Deutschland > > > > > > > > > > > > Email: peng@med.ovgu.de/peng@dzne.de > > > > > > Phone: +49 391 67 25074 > > > > > > ___ > > > 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 > > ___ > > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
