Re: [Freesurfer] TRACULA mask error
Hi Anastasia, Thanks for your response. I have sent over a zip file via the filedrop portal, it seemed to fail each time I tried to send it to freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email address - hopefully you have received this. I've had a look at the segmentations and they look ok, so I think there may be an issue with registrating between the T1 and diffusion. Anyway I have sent an example over, hopefully this will give you some idea of what has gone wrong. Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 11 December 2014 19:37 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error Hi Amanda - The final masks used by tracula are derived from the structural and not the diffusion data, i.e., they are the whole-brain FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion space and dilated slightly. It may be that there was something wrong with the FreeSurfer reconstructions of those subjects (if, for example, the T1 contrast was poorer in part of the brain and the part was not included in the brain mask), or that there was misregistration between the T1 and diffusion. You can troubleshoot this by looking at the aparc+aseg in diffusion space (from the dlabel/diff directory, over the FA map (from the dmri directory). If you still have trouble deciding what went wrong, you can upload a zip file for me with all the directories created by trac-all (dmri, dlabel, etc) for one of these subjects, here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Best, a.y On Thu, 27 Nov 2014, Worker, Amanda wrote: > > Dear All, > > > I have run all of the pre-processing steps on my DTI data and as I am > checking my nodif_brain_mask I have realised that some of the masks have > become distorted and twisted in some way. I have attached screenshots of > both the raw data (which looks fine) and the white mask (which is > distorted). In addition, as I have read that it is important to check the > dtifit_V1 and dtifit_FA I have also included these in the word document, > incase this helps. > > > This distortion has occured for approximately a quarter of the subjects that > I have processed and the rest look good. Please can you let me know if you > have any ideas about what has gone wrong and how to fix this? > > > Thanks in advance for your help, > > > Amanda > > > ___ 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
Re: [Freesurfer] Meninges labelled as cortex
Hi Michael and Bruce, Thanks for your help. This does look a lot better when I look at the aparc+aseg.mgz. Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Harms, Michael Sent: 07 January 2015 15:43 To: Freesurfer support list Subject: Re: [Freesurfer] Meninges labelled as cortex Make sure that you are looking at the surfaces though. It looks like the image you attached was the aseg.mgz, and you should not be using the "cortex" as defined in the aseg.mgz because that is based on the volume-stream segmentation. Either overlay the surfaces, or take a look at the aparc+aseg.mgz instead to see if you really have dura included within the pial surface. (The aparc+aseg.mgz uses the pial surface to "mask out" any cortex in the aseg.mgz that was outside the pial surface). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 1/7/15 9:12 AM, "Bruce Fischl" wrote: >Hi Amanda > >it depends what you are doing. They will certainly distort thickness >estimates in those regions. It is really, really hard to get rid of dura >unless you acquire data for that purpose. If you have a highres FLAIR or >T2 >or a multi-echo mprage we have tools for automatically avoiding it. > >cheers >Bruce > > >On Wed, 7 Jan 2015, Worker, Amanda wrote: > >> >> Hi All, >> >> >> I have noticed that almost all of my data has some voxels of dura that >>have >> incorrectly been labelled as cortex. It doesn't look like a severe >>problem >> and I've attached a screen shot to show you. >> >> >> I'm just wondering whether this is something that will affect my >>results? I >> have tried using -gcut and adjusting the watershed parameters to a >>height of >> 24, but nothing seems to work. As I have many subjects it would be very >>time >> consuming to manually adjust all of these voxels. >> >> >> Do you think this poses a problem or can I leave it as it is? >> >> >> Best wishes, >> >> >> Amanda >> >> The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA mask error
Hi Anastasia, Thank you for your response. I have made the changes that you recommended and attempted to run trac-all -prep on one of the subjects with errors. I am now getting the following error: Writing output files to /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* Writing spline volumes to /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz Segmentation fault trac-preproc-edit exited with ERRORS at Fri Jan Do you have any idea what the problem could be now? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: 07 January 2015 17:11 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error Hi Amanda - See attached screenshot of your data, there is a gross misregistration (~45 degree angle rotation) between the diffusion and anatomical. You can check if this is the case for the rest of your bad cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii). According to bbregister czar Doug, a big error like this in bbregister happens when the initialization of the registration fails. If the diffusion and T1 were acquired in the same session, you can try initializing the registration from the headers of the images, by running bbregister with "--init-header" instead of "--init-fsl". You can try it on one of your subjects first. Search for the bbregister command line in trac-all.log of this subject and rerun bbregister with the changed option. Follow the instructions that bbregister prints out when it's done to check the registration. To change how tracula does this, you'll have to edit the script $FREESURFER_HOME/bin/trac-preproc Search for "bbregister" and edit the --init-fsl option. Then rerun trac-all for the subjects that had this problem. You can skip the first 2 steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa. Hope this helps, a.y PS: Yes, when you send something with filedrop that I should look at, give my email address as the recipient. On Wed, 7 Jan 2015, Worker, Amanda wrote: > Hi Anastasia, > > Thanks for your response. I have sent over a zip file via the filedrop > portal, it seemed to fail each time I tried to send it to > freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email > address - hopefully you have received this. > > I've had a look at the segmentations and they look ok, so I think there > may be an issue with registrating between the T1 and diffusion. Anyway I > have sent an example over, hopefully this will give you some idea of > what has gone wrong. > > Thanks, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 11 December 2014 19:37 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Hi Amanda - The final masks used by tracula are derived from the > structural and not the diffusion data, i.e., they are the whole-brain > FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion > space and dilated slightly. It may be that there was something wrong with > the FreeSurfer reconstructions of those subjects (if, for example, the T1 > contrast was poorer in part of the brain and the part was not included in > the brain mask), or that there was misregistration between the T1 and > diffusion. You can troubleshoot this by looking at the aparc+aseg in > diffusion space (from the dlabel/diff directory, over the FA map (from the > dmri directory). > > If you still have trouble deciding what went wrong, you can upload a zip > file for me with all the directories created by trac-all (dmri, dlabel, > etc) for one of these subjects, here: >https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Best, > a.y > > On Thu, 27 Nov 2014, Worker, Amanda wrote: > >> >> Dear All, >> >> >> I have run all of the pre-processing steps on my DTI data and as I am >> checking my nodif_brain_mask I have realised that some of the masks have >> become distorted and twisted in some way. I have attached screenshots of >> both the raw data (which looks fine) and the white mask (which is >> distorted). In addition, as I have read that it is important to check the >> dtifit_V1 and dtifit_FA I have also included these in the word document, >> incase this helps. >> >> >> This distortion has occured for approximately a quarter of the subjects that >> I have processed and the rest look good. Please can you let me know if you >> have any
Re: [Freesurfer] TRACULA mask error
I have edited the trac-preproc script to "--init-header" instead of "--init-fsl" - hoping that this would fix the registration problem. Perhaps this hasn't helped? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 12 January 2015 19:58 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error Have you checked that the registration has been fixed? It looks like it might not. On Mon, 12 Jan 2015, Worker, Amanda wrote: > Yes of course. Please find attached. > > Thanks, > > Amanda > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 12 January 2015 16:39 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Can you please attach the entire trac-all.log file? It's hard to tell just > from the last few lines, the initial error may have happened much earlier. > > On Mon, 12 Jan 2015, Worker, Amanda wrote: > >> Hi Anastasia, >> >> Thank you for your response. I have made the changes that you recommended >> and attempted to run trac-all -prep on one of the subjects with errors. I am >> now getting the following error: >> >> Writing output files to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* >> Writing spline volumes to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz >> Segmentation fault >> >> trac-preproc-edit exited with ERRORS at Fri Jan >> >> >> Do you have any idea what the problem could be now? >> >> Thanks, >> >> Amanda >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: 07 January 2015 17:11 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA mask error >> >> Hi Amanda - See attached screenshot of your data, there is a gross >> misregistration (~45 degree angle rotation) between the diffusion and >> anatomical. You can check if this is the case for the rest of your bad >> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical >> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii). >> >> According to bbregister czar Doug, a big error like this in bbregister >> happens when the initialization of the registration fails. If the >> diffusion and T1 were acquired in the same session, you can try >> initializing the registration from the headers of the images, by running >> bbregister with "--init-header" instead of "--init-fsl". >> >> You can try it on one of your subjects first. Search for the bbregister >> command line in trac-all.log of this subject and rerun bbregister with the >> changed option. Follow the instructions that bbregister prints out when >> it's done to check the registration. >> >> To change how tracula does this, you'll have to edit the script >>$FREESURFER_HOME/bin/trac-preproc >> Search for "bbregister" and edit the --init-fsl option. Then rerun >> trac-all for the subjects that had this problem. You can skip the first 2 >> steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa. >> >> Hope this helps, >> a.y >> >> PS: Yes, when you send something with filedrop that I should look at, give >> my email address as the recipient. >> >> >> On Wed, 7 Jan 2015, Worker, Amanda wrote: >> >>> Hi Anastasia, >>> >>> Thanks for your response. I have sent over a zip file via the filedrop >>> portal, it seemed to fail each time I tried to send it to >>> freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email >>> address - hopefully you have received this. >>> >>> I've had a look at the segmentations and they look ok, so I think there >>> may be an issue with registrating between the T1 and diffusion. Anyway I >>> have sent an example over, hopefully this will give you some idea of >>> what has gone wrong. >>> >>> Thanks, >>> >>> Amanda >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Anastasia Yendiki >>> >>> Sent: 11 December 2014 19:37 >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA mask error &
[Freesurfer] Viewing QDEC results in tksurfer
Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying "could not open file */mri/transforms/talairach.xfm ..no such file or directory" . Is this a file that is not created with qdec? I'm also trying to visualise group mean thickness' in different colours to allow difference between groups, that are not significant in the analysis to be visualised. I cannot find any advice on how to do this, is this something it's possible to do using either freeview of tksurfer? Thanks, Amanda ___ 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] TRACULA mask error
Sorry, I misunderstood. I've attached a screenshot of what I can see, it does look like there is probably a different problem now as both the dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre. Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 13 January 2015 17:52 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error It's impossible to know unless you actually check the registration. See my previous email below on how to do that. On Tue, 13 Jan 2015, Worker, Amanda wrote: > I have edited the trac-preproc script to "--init-header" instead of > "--init-fsl" - hoping that this would fix the registration problem. Perhaps > this hasn't helped? > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 12 January 2015 19:58 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Have you checked that the registration has been fixed? It looks like it > might not. > > On Mon, 12 Jan 2015, Worker, Amanda wrote: > >> Yes of course. Please find attached. >> >> Thanks, >> >> Amanda >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Anastasia Yendiki >> >> Sent: 12 January 2015 16:39 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA mask error >> >> Can you please attach the entire trac-all.log file? It's hard to tell just >> from the last few lines, the initial error may have happened much earlier. >> >> On Mon, 12 Jan 2015, Worker, Amanda wrote: >> >>> Hi Anastasia, >>> >>> Thank you for your response. I have made the changes that you recommended >>> and attempted to run trac-all -prep on one of the subjects with errors. I >>> am now getting the following error: >>> >>> Writing output files to >>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* >>> Writing spline volumes to >>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz >>> Segmentation fault >>> >>> trac-preproc-edit exited with ERRORS at Fri Jan >>> >>> >>> Do you have any idea what the problem could be now? >>> >>> Thanks, >>> >>> Amanda >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: 07 January 2015 17:11 >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA mask error >>> >>> Hi Amanda - See attached screenshot of your data, there is a gross >>> misregistration (~45 degree angle rotation) between the diffusion and >>> anatomical. You can check if this is the case for the rest of your bad >>> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical >>> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii). >>> >>> According to bbregister czar Doug, a big error like this in bbregister >>> happens when the initialization of the registration fails. If the >>> diffusion and T1 were acquired in the same session, you can try >>> initializing the registration from the headers of the images, by running >>> bbregister with "--init-header" instead of "--init-fsl". >>> >>> You can try it on one of your subjects first. Search for the bbregister >>> command line in trac-all.log of this subject and rerun bbregister with the >>> changed option. Follow the instructions that bbregister prints out when >>> it's done to check the registration. >>> >>> To change how tracula does this, you'll have to edit the script >>>$FREESURFER_HOME/bin/trac-preproc >>> Search for "bbregister" and edit the --init-fsl option. Then rerun >>> trac-all for the subjects that had this problem. You can skip the first 2 >>> steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa. >>> >>> Hope this helps, >>> a.y >>> >>> PS: Yes, when you send something with filedrop that I should look at, give >>> my email address as the recipient. >>> >>> >>> On Wed, 7 Jan 2015, Worker, Amanda wrote: >>> >>>> Hi Anastasia,
Re: [Freesurfer] Viewing QDEC results in tksurfer
Hi, I am currently only able to open a thickness map for a single subject using "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, but I'd really like to plot the mean thickness for a particular group to compare to others visually. Is this possible? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: 14 January 2015 23:46 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer what is your tksurfer command line? On 01/13/2015 07:12 AM, Worker, Amanda wrote: > > Hi, > > > Is it possible to view the results of a qdec analysis (correlation > with a single continuous group) in tksurfer? I am currently unable to > open it and I'm getting an error saying "could not open > file */mri/transforms/talairach.xfm ..no such file or directory" . Is > this a file that is not created with qdec? > > > I'm also trying to visualise group mean thickness' in different > colours to allow difference between groups, that are not significant > in the analysis to be visualised. I cannot find any advice on how to > do this, is this something it's possible to do using either freeview > of tksurfer? > > > Thanks, > > > Amanda > > > > ___ > 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
Re: [Freesurfer] Viewing QDEC results in tksurfer
Hi Doug, I have set up and run the usual Group Analysis through the command line. I have then run " mri_concat output-of-preproc.mgh --mean --o mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects included in the preprocessing. I'm now having a problem with visualising this with tksurfer, getting ERROR: could not read header info from T1 or orig in /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri Presumably this is because all of the T1/orig are stored in each subjects data file and I'm not trying to look at a specific subject. Is there a way to get around this problem? Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: 15 January 2015 16:56 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer QDEC will not produce mean maps for each group. If this is something you want to do, you will need to do it in the command-line group analysis stream. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 01/15/2015 05:25 AM, Worker, Amanda wrote: > Hi, > > I am currently only able to open a thickness map for a single subject using > "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, but > I'd really like to plot the mean thickness for a particular group to compare > to others visually. Is this possible? > > Thanks, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 14 January 2015 23:46 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > what is your tksurfer command line? > > On 01/13/2015 07:12 AM, Worker, Amanda wrote: >> Hi, >> >> >> Is it possible to view the results of a qdec analysis (correlation >> with a single continuous group) in tksurfer? I am currently unable to >> open it and I'm getting an error saying "could not open >> file */mri/transforms/talairach.xfm ..no such file or directory" . Is >> this a file that is not created with qdec? >> >> >> I'm also trying to visualise group mean thickness' in different >> colours to allow difference between groups, that are not significant >> in the analysis to be visualised. I cannot find any advice on how to >> do this, is this something it's possible to do using either freeview >> of tksurfer? >> >> >> Thanks, >> >> >> Amanda >> >> >> >> ___ >> 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 > > -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Viewing QDEC results in tksurfer
My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" d- which is when I got the error. I have now tried loading fsaverage first with "tksurfer fsaverage lh inflated" and it seems to be working fine. The problem now is changing the colour scale to display only positive values. I have played around with the Min, Max and Slope and can't seem to remove values below zero. What I'm after is a scale showing thickness in mm ranging from something like 1mm-3.5mm (or if it's easier whatever the min and max thickness' are for the group) Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve Sent: 16 January 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer what is your command line? On 01/16/2015 11:02 AM, Worker, Amanda wrote: > Hi Doug, > > I have set up and run the usual Group Analysis through the command line. I > have then run " mri_concat output-of-preproc.mgh --mean --o > mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects > included in the preprocessing. > > I'm now having a problem with visualising this with tksurfer, getting ERROR: > could not read header info from T1 or orig in > /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri > > Presumably this is because all of the T1/orig are stored in each subjects > data file and I'm not trying to look at a specific subject. Is there a way to > get around this problem? > > Best wishes, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 15 January 2015 16:56 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > QDEC will not produce mean maps for each group. If this is something you > want to do, you will need to do it in the command-line group analysis > stream. See > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > > > > On 01/15/2015 05:25 AM, Worker, Amanda wrote: >> Hi, >> >> I am currently only able to open a thickness map for a single subject using >> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, >> but I'd really like to plot the mean thickness for a particular group to >> compare to others visually. Is this possible? >> >> Thanks, >> >> Amanda >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Douglas N Greve >> >> Sent: 14 January 2015 23:46 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >> >> what is your tksurfer command line? >> >> On 01/13/2015 07:12 AM, Worker, Amanda wrote: >>> Hi, >>> >>> >>> Is it possible to view the results of a qdec analysis (correlation >>> with a single continuous group) in tksurfer? I am currently unable to >>> open it and I'm getting an error saying "could not open >>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is >>> this a file that is not created with qdec? >>> >>> >>> I'm also trying to visualise group mean thickness' in different >>> colours to allow difference between groups, that are not significant >>> in the analysis to be visualised. I cannot find any advice on how to >>> do this, is this something it's possible to do using either freeview >>> of tksurfer? >>> >>> >>> Thanks, >>> >>> >>> Amanda >>> >>> >>> >>> ___ >>> 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-ma
Re: [Freesurfer] Viewing QDEC results in tksurfer
Hi Bruce, Thanks for your help. Is there a way that I can now change the colour bar, it's currently red to yellow meaning pretty much the whole brain is red. I'd like several different colours to illustrate different thickness'. I don't seem to be able to edit Mid or Slope. Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 20 January 2015 12:47 To: Freesurfer support list Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer Hi Amanda, click the "truncate" button. cheers Bruce On Tue, 20 Jan 2015, Worker, Amanda wrote: > My command line was "tksurfer mean.lh.thick_age.thickness.10.mgh lh inflate" > d- which is when I got the error. > > I have now tried loading fsaverage first with "tksurfer fsaverage lh > inflated" and it seems to be working fine. > > The problem now is changing the colour scale to display only positive values. > I have played around with the Min, Max and Slope and can't seem to remove > values below zero. What I'm after is a scale showing thickness in mm ranging > from something like 1mm-3.5mm (or if it's easier whatever the min and max > thickness' are for the group) > > Best wishes, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 16 January 2015 19:52 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer > > what is your command line? > > On 01/16/2015 11:02 AM, Worker, Amanda wrote: >> Hi Doug, >> >> I have set up and run the usual Group Analysis through the command line. I >> have then run " mri_concat output-of-preproc.mgh --mean --o >> mean.output-of-preproc.mgh" to obtain a mean thickness for all subjects >> included in the preprocessing. >> >> I'm now having a problem with visualising this with tksurfer, getting >> ERROR: could not read header info from T1 or orig in >> /home/k1204763/images/BRCATLAS/FREESURFER.v5.3.0/GroupAnalysis/mri >> >> Presumably this is because all of the T1/orig are stored in each subjects >> data file and I'm not trying to look at a specific subject. Is there a way >> to get around this problem? >> >> Best wishes, >> >> Amanda >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Douglas N Greve >> >> Sent: 15 January 2015 16:56 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >> >> QDEC will not produce mean maps for each group. If this is something you >> want to do, you will need to do it in the command-line group analysis >> stream. See >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis >> >> >> >> >> On 01/15/2015 05:25 AM, Worker, Amanda wrote: >>> Hi, >>> >>> I am currently only able to open a thickness map for a single subject using >>> "tksurfer SUBJECT lh inflated". I can use the analysis figures from qdec, >>> but I'd really like to plot the mean thickness for a particular group to >>> compare to others visually. Is this possible? >>> >>> Thanks, >>> >>> Amanda >>> >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Douglas N Greve >>> >>> Sent: 14 January 2015 23:46 >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Viewing QDEC results in tksurfer >>> >>> what is your tksurfer command line? >>> >>> On 01/13/2015 07:12 AM, Worker, Amanda wrote: >>>> Hi, >>>> >>>> >>>> Is it possible to view the results of a qdec analysis (correlation >>>> with a single continuous group) in tksurfer? I am currently unable to >>>> open it and I'm getting an error saying "could not open >>>> file */mri/transforms/talairach.xfm ..no such file or directory" . Is >>>> this a file that is not created with qdec? >>>> >>>> >>>> I'm also trying to visualise group mean thickness' in different >>>> colours to allow difference between groups, that are not significant >>>> in the analysis to be visualised. I cannot find any advice on how to >>>> do this, is this something it's possible to do using either freeview >>
Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Anastasia, Apologies this looks like an error on my part. I had edited the script to specify --init-spm instead of --init-fsl but forgot to specify that this script was to be used. It all seems to be looking good now which is fantastic- thanks very much for all of your help!! One last question, when using the command: freeview -tv $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \ -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & I am able to see all of the tracts clearly, except in some of the subjects the Forceps Major seems to be missing. Changing the threshold doesn't seem to make a difference. Do you have any ideas what the issue could be with this? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 11 February 2015 16:21 To: Freesurfer support list Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] Hi Amanda - It doesn't look like the new registration was applied to the aparc+aseg. Can you tell us the exact sequence of steps that you followed, including your bbregister command line and the trac-all command lines that you ran after running bbregister? Thanks, a.y On Wed, 11 Feb 2015, Worker, Amanda wrote: > Hi, > > Thanks for this. --init-spm does appear to work and when checking the > registration using the instructions bbregister gives it all looks good to me. > However, when I check the dtifit_FA and aparc+aseg.bbr.nii it still doesn't > look too good. I've continued on with the next steps for reconstructing the > pathways just to see what happens, but they don't come out well. > > I've attached a screenshot of the registration using --init-spm and then also > a screenshot of the dmri/dtfit_FA.nii.gz alone and with aparc+aseg.bbri.nii > overlayed. > > Best wishes, > > Amanda > > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: 06 February 2015 19:15 > To: Bruce Fischl; Freesurfer support list > Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] > > or --init-rr if you don't have matlab/spm > > On 02/06/2015 01:49 PM, Bruce Fischl wrote: >> try --init-spm >> On Fri, 6 Feb 2015, Anastasia Yendiki wrote: >> >>> >>> Hi Amanda - So it looks like --init-header didn't work, and neither does >>> --init-fsl. I'll defer to the father of bbregister, Doug, for clues >>> about >>> how to proceed. >>> >>> a.y >>> >>> On Wed, 21 Jan 2015, Worker, Amanda wrote: >>> >>>> Hi Anastasia, >>>> >>>> Yes I have done that. My command line was... " bbregister --s >>>> PDPLUS010 --init-header --dti --mov >>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz >>>> --reg >>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat >>>> --fslmat >>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat >>>> " >>>> >>>> Following the instructions printed I can only see a tiny bit of the >>>> dwi.nii.gz, as attached. >>>> >>>> I've also tried substituting --dti for --t1 in the command line and >>>> that doesn't make much difference. >>>> >>>> Do you have any other ideas? >>>> >>>> Thanks, >>>> >>>> Amanda >>>> >>>> >>>> >>>> >>>> ________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> on behalf of Anastasia >>>> Yendiki >>>> Sent: 15 January 2015 15:36 >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] TRACULA mask error >>>> >>>> Did you follow the instructions and the end of the output of the >>>> bbregister command? What does that look like? See what I wrote below >>>> about >>>> looking for the bbregister command in trac-all.log, running it >>>> separately >>>> on one subject after changing that one option and looking at its >>>> output. >>>> >>>> On Wed, 14 Jan 2015, Worker, Amanda wrote: >>>> >>>>> Sorry, I misunderstood. >>>>> >>>>> I've attached a screenshot of what I can see, it does look like >>>>> there is probably a diff
Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Anastasia, Yes that seems to work! Thank you very much for all your help. Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki Sent: 12 February 2015 20:02 To: Freesurfer support list Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] Hi Amanda - Glad to hear the registration issue got fixed! If the tract looks like a single line in the volume (in which case you wouldn't be able to see it 3D in view), it's probably a case where the initialization failed for that specific tract and subject. This happens sometimes with the forceps major when there are enlarged ventricles or something like that. You can reinitialize by including "set reinit = 1" in your config file, setting the pathlist and subjlist to only the specific tract/subject that needs to be reinitialized, and then rerunning the -prior and -path steps in that order. Hope this helps, a.y On Thu, 12 Feb 2015, Worker, Amanda wrote: > Hi Anastasia, > > Apologies this looks like an error on my part. I had edited the script to > specify --init-spm instead of --init-fsl but forgot to specify that this > script was to be used. It all seems to be looking good now which is > fantastic- thanks very much for all of your help!! > > One last question, when using the command: > > freeview -tv > $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \ > -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & > > I am able to see all of the tracts clearly, except in some of the subjects > the Forceps Major seems to be missing. Changing the threshold doesn't seem to > make a difference. Do you have any ideas what the issue could be with this? > > Thanks, > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: 11 February 2015 16:21 > To: Freesurfer support list > Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] > > Hi Amanda - It doesn't look like the new registration was applied to the > aparc+aseg. Can you tell us the exact sequence of steps that you followed, > including your bbregister command line and the trac-all command lines that > you ran after running bbregister? > > Thanks, > a.y > > On Wed, 11 Feb 2015, Worker, Amanda wrote: > >> Hi, >> >> Thanks for this. --init-spm does appear to work and when checking the >> registration using the instructions bbregister gives it all looks good to >> me. However, when I check the dtifit_FA and aparc+aseg.bbr.nii it still >> doesn't look too good. I've continued on with the next steps for >> reconstructing the pathways just to see what happens, but they don't come >> out well. >> >> I've attached a screenshot of the registration using --init-spm and then >> also a screenshot of the dmri/dtfit_FA.nii.gz alone and with >> aparc+aseg.bbri.nii overlayed. >> >> Best wishes, >> >> Amanda >> >> >> >> >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Douglas N Greve >> >> Sent: 06 February 2015 19:15 >> To: Bruce Fischl; Freesurfer support list >> Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] >> >> or --init-rr if you don't have matlab/spm >> >> On 02/06/2015 01:49 PM, Bruce Fischl wrote: >>> try --init-spm >>> On Fri, 6 Feb 2015, Anastasia Yendiki wrote: >>> >>>> >>>> Hi Amanda - So it looks like --init-header didn't work, and neither does >>>> --init-fsl. I'll defer to the father of bbregister, Doug, for clues >>>> about >>>> how to proceed. >>>> >>>> a.y >>>> >>>> On Wed, 21 Jan 2015, Worker, Amanda wrote: >>>> >>>>> Hi Anastasia, >>>>> >>>>> Yes I have done that. My command line was... " bbregister --s >>>>> PDPLUS010 --init-header --dti --mov >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz >>>>> --reg >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat >>>>> --fslmat >>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat >>>>> " >>>>> >>>>> Following the instructions printed I can only see a tiny bit of the >>>>> dwi.nii.
[Freesurfer] Overlaying .nii
Hi, I am trying to find a way to overlay a .nii file for a single blob of activation - simply to visualise the region of the blob with the cortical surface. Is there a way to do this in either freeview or tksurfer? The blob is in nifti format and the surface is in the usual .mgh format. Thanks, Amanda ___ 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] extracting subcortical volumes from longitudinal processed data
Hi all, I am trying to extract subcortical volumes from data that has been processed longitudinally, but I am getting the following error. [k1204763@nanlnx9 SAGA]0% asegstats2table --qdec-long long.qdec.table.dat --stats aseg.stats --tablefile aseg.table.txt SUBJECTS_DIR : /home/k1204763/images/SAGA Traceback (most recent call last): File "/software/system/freesurfer/freesurfer-5.3.0/bin/asegstats2table", line 514, in subj_listoftuples = assemble_inputs(options) File "/software/system/freesurfer/freesurfer-5.3.0/bin/asegstats2table", line 323, in assemble_inputs o.subjects.append(fsid+'.long.'+row['fsid-base'].strip()) KeyError: 'fsid-base' Do you have any ideas as to what the issue is here? Thanks, Amanda ___ 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] qdec error
Hi Lena, Have you changed your Group.levels file to include the two groups you are currently looking at? If this doesn't match your qdec table it will not work. Best wishes, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lim, Lena Sent: 29 September 2015 12:42 To: 'Freesurfer support list' Subject: Re: [Freesurfer] qdec error Thanks, Doug. I used the qdec table attached. L -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 28 September 2015 21:54 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec error Can you send the FSGD file? On 09/28/2015 02:06 PM, Lim, Lena wrote: > Sorry, please see error below: > > > > Reading > /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl > > Using > /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot.tcl > > Loading data table > /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat...Number of > columns: 5 > fsid column:1 > Number of factors: 4 > Number of subjects: 46 > > Data table /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat loaded. > Verifying subject data..Subject > verification complete. > Input table: > /home/spjwker/PAC/Lena/CT_SA/FSL/PCHC3/qdec.table_PCHC.dat > Subj#, SubjID, Data... > 1 PAC01 HC Male 110.00 16.17 > 2 PAC02 HC Male 108.00 16.17 > 3 PAC03 HC Male 118.00 14.50 > 4 PAC04 HC Male 113.00 17.25 > 5 PAC05 HC Male 125.00 17.33 > 6 PAC06 HC Male 102.00 15.42 > 7 PAC09 HC Female 115.00 16.42 > 8 PAC12 HC Female 106.00 16.50 > 9 PAC14 HC Male 106.00 19.08 > 10 PAC18 HC Male 106.00 19.08 > 11 PAC19 HC Male 91.00 18.33 > 12 PAC23 HC Male 109.00 16.67 > 13 PAC24 PC Female 94.00 20.33 > 14 PAC26B PC Female 96.00 14.50 > 15 PAC27 PC Male 88.00 17.75 > 16 PAC28 PC Male 76.00 17.08 > 17 PAC33 PC Female 95.00 13.92 > 18 PAC37 PC Female 79.00 17.42 > 19 PAC38 HC Male 96.00 16.25 > 20 PAC39 PC Male 112.00 19.50 > 21 PAC40 HC Male 119.00 18.25 > 22 PAC41 PC Male 92.00 18.42 > 23 PAC42 PC Female 78.00 13.17 > 24 PAC43 PC Male 96.00 19.25 > 25 PAC44 PC Male 78.00 15.00 > 26 PAC45 PC Female 84.00 17.92 > 27 PAC46 HC Female 94.00 19.83 > 28 PAC47 HC Male 107.00 15.17 > 29 PAC48 PC Female 117.00 20.50 > 30 PAC51 HC Male 112.00 20.17 > 31 PAC52 PC Female 105.00 12.42 > 32 PAC53 HC Male 88.00 18.83 > 33 PAC54 HC Male 82.00 18.25 > 34 PAC56 HC Male 97.00 17.92 > 35 PAC58 HC Male 109.00 18.42 > 36 PAC59 PC Male 106.00 17.75 > 37 PAC60B HC Male 104.00 19.33 > 38 PAC61 HC Female 108.00 18.33 > 39 PAC62 HC Male 93.00 19.33 > 40 PAC63 PC Male 110.00 12.42 > 41 PAC65 HC Female 100.00 19.33 > 42 PAC66 PC Male 78.00 18.92 > 43 PAC67 HC Male 114.00 14.50 > 44 PAC68 HC Female 113.00 16.67 > 45 PAC69 PC Female 89.00 15.83 > 46 PAC70 PC Female 103.00 17.92 > 1 Group discrete 2 > 1 HC > 2 PC > 2 Gender discrete 2 > 1 Male > 2 Female > 3 IQ continuous 0 > 4 Age continuous 0 > Continuous Factors: Mean: StdDev: > --- - --- > IQ 100.45712.631 > Age17.250 2.083 > > Number of subjects: 46 > Number of factors:4 (2 discrete, 2 continuous) > Number of classes:4 > Number of regressors: 12 > > Data table loading completed successfully. > SUBJECTS_DIR is '/home/spjwker_PAC/Lena/CT_SA/FSL' > lh-Avg-Intercept-thickness --- Does the average > thickness differ from zero? > Nuisance factors: IQ Age > 1.000 1.000 1.000 1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000; > > lh-Diff-HC-PC-Intercept-thickness --- Does the > average thickness, accounting for Gender, differ between HC and PC? > Nuisance factors: IQ Age > 1.000 -1.000 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000; > > lh-Diff-Male-Female-Intercept-thickness --- Does > the average thickness, accounting for Group, differ between Male and Female? > Nuisance factors: IQ Age > 1.000 1.000 -1.000 -1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000; > > lh-X-Group-Gender-Intercep
[Freesurfer] Group Analysis with fsgd
Dear all, I am trying to run a group analysis through the terminal using an .fsgd file, with no additional covariates. GroupDescriptorFile 1 Title PDPLUS2 Class PD Class MSA Class PSP Input PDPLUS007/ PD Input PDPLUS005/ MSA Input PDPLUS004/ PSP etc... When I try to run a command similar to the example fsgd analysis on the freesurfer wiki: mri_glmfit \ --glmdir pdplus \ --y y.mgh \ --fsgd g3v0.fsgd \ --C PD-MSA.mtx \ --C PD-PSP.mtx \ --C MSA-PSP.mtx \ --C group.effect.mtx \ --C PD+MSA-vs-ad.mtx I have received the following error message: Creating output directory pdplus2 Loading y from /home/k1204763/images/PDPLUS/y.mgh mghRead(/home/k1204763/images/PDPLUS/y.mgh, -1): could not open file ERROR: loading y /home/k1204763/images/PDPLUS/y.mgh I am not too sure whether y.mgh actually exists, is there a way that I can create this file for the three groups? Any other thoughts on this error would very much be appreciated. Thanks in advance, Amanda ___ 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] DESPOT T1 map
Hi All, I have a T1 map which has been synthesised from a DESPOT imaging sequence and I am hoping to use this as input to recon-all. Do you know if this will be possible at all, or if there is anything I can do to prepare the T1 map to run through recon-all? Thanks in advance, Amanda ___ 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] Viewing nifti file in freeview
Hi All, I was hoping someone could help with an issue that I'm having that I'm sure has a simple explanation. I have a proton density map in nifti format that I am trying to convert to mgz using mri_convert. However, when I load the original nifti file into freeview, I get a blank screen and the same when I try to load the converted .mgz - but I have no issue with loading this file into fslview. Other nifti and .mgz files are also loading fine into freeview. Has anyone seen this problem before? Thanks, Amanda ___ 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] Viewing nifti file in freeview
Hi, Changing the min and max fields doesn't make it visible, however changing the color map to Lookup Table makes the volume all red. But I can't seem to do much else. Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of dgw Sent: 04 February 2016 12:17 To: Freesurfer support list Subject: Re: [Freesurfer] Viewing nifti file in freeview Amanda, Is there a progress bar still running? Have you tried changing the window min max fields? hth d Sent from my Phone On Feb 4, 2016, at 06:46, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>> wrote: Hi All, I was hoping someone could help with an issue that I'm having that I'm sure has a simple explanation. I have a proton density map in nifti format that I am trying to convert to mgz using mri_convert. However, when I load the original nifti file into freeview, I get a blank screen and the same when I try to load the converted .mgz - but I have no issue with loading this file into fslview. Other nifti and .mgz files are also loading fine into freeview. Has anyone seen this problem before? Thanks, Amanda ___ 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] mri_annotation2label
Hi All, I am trying to run a vertex-wise analysis on a pre-defined ROI - the caudal anterior cingulate label as defined by the Desikan atlas. I have used mri_annotation2label to get these labels for each subjects ./label directory. I assumed that as these labels were created in fsaverage space, it would be ok to get these labels for each subject without further sampling to fsaverage? If not, how can I do this? I have also tried to run mri_glmfit, using --label instead of --cortex, but I don't have the label 'lh.caudalanteriorcingulate.label' in standardised space, only in each subjects directory. How can I specify that this is the label I'd like to confine my analysis to (this might be answered by the first question). Thanks in advance, Amanda ___ 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] Group thickness means
Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by QDEC I can see individual subjects mean thickness but I'm not sure how to get the group mean? If you could help with this it would be much appreciated. Thank you in advance. Amanda ___ 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] Group thickness means
Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by QDEC I can see individual subjects mean thickness but I'm not sure how to get the group mean? If you could help with this it would be much appreciated. Thank you in advance. Amanda ___ 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] deformation fields
Hi All, I am trying to use the subcortical segmentation of regions from the longitudinal template to propogate to each time point using deformation fields. Does anyone know how if this is possible and if so, how can I do it? Thanks in advance, Amanda ___ 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 hippocampal subfield registered to base
Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using: mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest --out_type mgz TP.long/mri/lh.hippoSfLabels-T1.v10.mgz TP.long/lh.hipp.base.mgz Firstly, when I try to overlay lh.hipp.base.mgz for each timepoint onto BASE/mri/T1.mgz they do not align. Do you have any idea why this is? Secondly, the output seems to be for the whole hippocampus, is there a way to do this for each subfield individually? Any advice would be much appreciated, Amanda ___ 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 hippocampal subfield registered to base
Hi Eugenio, Thanks for your quick response. It would be great to get the probabilistic segmentations for each subfield, it's fine if we have to run the segmentation again. I have only just realised that you now have a longitudinal subfield segmentation pipeline - is this what I'll need to use? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 01 March 2017 13:30:05 To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Longitudinal hippocampal subfield registered to base Dear Amanda The longitudinally processed time points are already in base space. Those transforms you used map base to the original, cross sectionally processed volumes. Regarding individual subfields: you can use mri_extract_label to extract individual labels. You can also obtain probabilistic segmentations, but it requires some extra work (and rerunning your subfield segmentation). Let me know if you are interested. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Worker, Amanda Sent: Wednesday, March 1, 2017 12:14:50 PM To: Freesurfer support list Subject: [Freesurfer] Longitudinal hippocampal subfield registered to base Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using: mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest --out_type mgz TP.long/mri/lh.hippoSfLabels-T1.v10.mgz TP.long/lh.hipp.base.mgz Firstly, when I try to overlay lh.hipp.base.mgz for each timepoint onto BASE/mri/T1.mgz they do not align. Do you have any idea why this is? Secondly, the output seems to be for the whole hippocampus, is there a way to do this for each subfield individually? Any advice would be much appreciated, Amanda ___ 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] Cortical thickness repeated measures
Hi all, I have a repeated measures design with two groups (drug and placebo) and two time points (baseline and follow-up). The groups are not very well matched so I'd like to control for age and gender. The data was also acquired across three sites which I'll need to control for. I do not have any drop outs. Essentially, I want to know if there is a significant effect of drug on cortical thickness. I've tried this out in qdec, but because I have site (with three levels) qdec isn't appropriate, so I'm trying to set up my own fsgd and contrast matrix. Because I have already created the percent change and symmetrized percent change files (as part of qdec prep) I thought I might be able to simply run a t-test on those. Which would answer the question...'is there a significant difference in percent change for the drug and placebo groups'. Does this seem like a sensible approach? If the above does seem sensible, I am not quite sure how to set up my contrast matrix. As I have three categorical variables to include (Treatment, Gender, Site) and only one continuous variable (age). This would leave me with 12 classes (DrugFemaleSite1, DrugMaleSite1, DrugFemaleSite2, DrugMaleSite2 etc etc) and one variable. Would it look something like this? Or is this absurd? 0.333 0.333 0.333 0.333 0.333 0.333 -0.333 -0.333 -0.333 -0.333 -0.333 -0.333 0 0 0 0 0 0 0 0 0 0 0 0 Thanks in advance, Amanda ___ 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] Univariate Linear Mixed Effects
Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could you explain why that is please? And also what hypotheses these three different contrasts are testing? C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]; At the moment I have a simple design with two groups, 4-5 time points so I have a design matrix with 4 columns (intercept, weeks, group, group*time) and the contrast I am using is [0 0 0 1] to test the interaction term. If I were to add covariates such as age and gender would I simply add two more columns to my design matrix and contrast to look like this...[0 0 0 1 0 0]? Thanks in advance for your help. Amanda ___ 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] Univariate Linear Mixed Effects {Disarmed}
Hi Martin, Thank you that makes sense now. I don't seem to be able to read a file into matlab containing hippocampal subfield volumes instead of the standard aseg using fast_ldtable. I haven't changed anything other than substituting hippocampal volume for dentate gyrus volumes. So the file consists of columns fsid, fsid-base, weeks, group, left_GC-ML-DG, right_GC-ML-DG, EstimatedICV. 276 rows. The error I am getting in matlab is: 'Subscripted assignment dimension mismatch. Error in fast_ldtable (line 84) tbl(nthrow-1,nthcol-1) = sscanf(char(s(nth)),'%f'); ' Do you have any idea what the problem is? Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter Sent: 03 August 2017 08:15:29 To: Freesurfer support list Subject: Re: [Freesurfer] Univariate Linear Mixed Effects Hi Amanda, the C matrix below has 14 columns ( 3 + 5 + 6 ). To find out what hypothesis are tested, look at the corresponding columns. column 4 for example is the MCIs slope delta with respect to controls (so slope difference MCIs and CN) the next test is slope difference between MCIs and MCIc and finally slope difference between MCIc and AD. Your test 0 0 0 1 similarly tests slope difference between your two groups. And yes, the remaining columns would be control variables . Best, Martin On 31. Jul 2017, at 13:38, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>> wrote: Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could you explain why that is please? And also what hypotheses these three different contrasts are testing? C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]; At the moment I have a simple design with two groups, 4-5 time points so I have a design matrix with 4 columns (intercept, weeks, group, group*time) and the contrast I am using is [0 0 0 1] to test the interaction term. If I were to add covariates such as age and gender would I simply add two more columns to my design matrix and contrast to look like this...[0 0 0 1 0 0]? Thanks in advance for your help. Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C049bca7456e94483779f08d4da3f9caa%7C8370cf1416f34c16b83c724071654356%7C0&sdata=GzYIFLnX13bO6fZYl5A%2FkGtLAX26AvflmOPvT2wXZDQ%3D&reserved=0> ___ 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] Test-retest reliability in longitudinal data
Hi all, I have a longitudinal dataset that I'd like to calculate test-retest reliability for. However, I am not sure whether to calculate this for the cross-sectionally processed data or longitudinal data? It would seem to make sense to use the cross-sectional data, as the time points are independent, but then it means that the test-retest results would not be applicable in a dataset processed longitudinally. On the other hand, calculating reliability metrics for data processed in the exact same way as will be used in further studies seems to make sense also, but would calculating test-retest on the longitudinally processed data bias the results, as the data points are not fully independent? Does anyone have any idea of the best way forward? Thanks, A ___ 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] Test-retest reliability in longitudinal data
Hi, Thank you very much for your fast response. I had thought that it would make sense to use the exact same pipeline, as I would be using in a longitudinal study in future. If I could just be a bit more specific about the details, as I have a publication under review at the moment and one of the reviewers isn't happy about this approach. I just wanted to check that we haven't misunderstood how the algorithm works if that is ok? Reviewer's comment “It is unclear to me what is the value of establishing test-retest reliability of applying FreeSurfer subfield segmentation to a within-subject template constructed by the Reuter algorithm. Once this template is constructed and mapped to the different time point images, test-retest measures become meaningless because the segmentations are not independent, but instead, highly dependent on each other.” Our response "our understanding is that the use of a within-subject’s template to initialise the segmentation will minimise potential bias or inaccuracy in segmentation in multi-session data. The segmentations are themselves run independently, but with the template being used to initialise (provide a starting point) for the nonlinear parameter fitting. We don’t believe that this would be expected to, and does not appear to, constrain the segmentation to the degree that it would produce “identical” values, as the reviewer suggested in a previous review. The alternative is to risk a biased segmentation which could potentially give a false impression of poor reliability and increased risk of false positive results. " Any thoughts appreciated. Thanks, Amanda From: Jovicich, Jorge Sent: 20 September 2017 15:51:40 To: Worker, Amanda Cc: Freesurfer support list Subject: Re: [Freesurfer] Test-retest reliability in longitudinal data Hi Amanda, I would recommend you to quantify reliability using the same processing pipeline you will use to test for longitudinal effects in your sample. Relevant literature include those listed below. For reliability you would want to evaluate subjects over a time period in which you do not expect the main effects of your study (e.g., disease related or learning related morphometric effects), but rather standard physiological and MRI system variability. Ideally this group also has the same age/gender representation of the group in which you later want to test for longitudinal effects. Cheers, Jorge https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F22430496&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0&sdata=5Zna%2FnZpaN62IpZVdWf%2FUE7MTSEjA0ygXQCUIIQP%2BuA%3D&reserved=0 https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F23668971&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0&sdata=yQaldU8xwFyenqpdPlZ%2FLDVu2aH7zpeWPVxfd5YqccQ%3D&reserved=0 On 20/09/2017 15:00, Worker, Amanda wrote: > > Hi all, > > > I have a longitudinal dataset that I'd like to calculate test-retest > reliability for. However, I am not sure whether to calculate this for > the cross-sectionally processed data or longitudinal data? It would > seem to make sense to use the cross-sectional data, as the time points > are independent, but then it means that the test-retest results would > not be applicable in a dataset processed longitudinally. On the other > hand, calculating reliability metrics for data processed in the exact > same way as will be used in further studies seems to make sense also, > but would calculating test-retest on the longitudinally processed data > bias the results, as the data points are not fully independent? > > > Does anyone have any idea of the best way forward? > > > Thanks, > > > A > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0&sdata=KvaIAsox9nAxI1YQATw%2FAPoTe71b1QploiDCPR158Ls%3D&reserved=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.partners.org%2Fcomplianceline&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0&
[Freesurfer] TRACULA bedpost error
Hello, I am trying to run the second step of the TRACULA processing which is: trac-all -bedp -c /home/... I am currently using freesurfer v5.3.0 and I get the following error: WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri subjectdir is /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage Unable to read script file because of error: error opening bedpostx: No such file or directory Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Exiting. I have read that this may be a bedpostx FSL problem, however I am not familiar with this. Do you have any advice on how to overcome this problem? Thanks in advance, Amanda ___ 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] QDEC cluster stats
Hi All, I am using QDEC to run a correlation analysis and I have a lot of large significant clusters that encompass various different cortical regions. I am hoping to extract mean thickness' from the significant clusters in order to create a plot to display the correlations. Can anyone tell me where to find or how to generate stats (e.g. mean thickness/SD) for each significant cluster? At the moment I am only able to visualise the regions or plot correlations for regional thickness' but this doesn't reflect the significant clusters. Do I need to draw an ROI around the cluster and generate the stats? Best wishes, Amanda ___ 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] Visualise QDEC results
Hi, I have run a correlation in QDEC and I have quite a lot of results, some of which pass monte simulation correction at p=0.05 and some of which remain at p=0.0001. Ideally, I'd like a single figure that will display all significant results regardless of their p-value. However, I would need this figure to clearly show the difference between those with a low p value and those with a high pvalue i.e. different shades of blue. I've tried playing around with the thresholds, which kind of gives me what I need however these maps are uncorrected. Do you have any advice on how best to display these results? I'm really having trouble getting anything other than the basic one shade, significant clusters at each p-value that I set. Thanks in advance for your help, Amanda ___ 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] Using a .asc file as overlay in freeview/tksurfer
External Email - Use Caution Hello, I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck. As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command: % mris_convert -c lh.thickness lh.white lh.thickness.asc I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message: % mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New Interestingly, I can load the file as a curvature file, but then can't play around with the threshold. Do you have any idea what I'm doing wrong? Any help would be appreciated! Thanks, Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
External Email - Use Caution How would I do that? mris_convert doesn't seem to take .asc as an input? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Not sure. Can you use mris_convert to convert the asc back to a curv file? On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > External Email - Use Caution > > Hello, > > > I am trying to overlay a .asc file in either freeview or tksurfer, but > so far having no luck. > > > As practice and to determine the right format, I am simply using > lh.thickness, which I've converted to .asc using the following command: > > > % mris_convert -c lh.thickness lh.white lh.thickness.asc > > > I am trying to overlay this onto lh.pial for one subject, however I > cannot load the file and I get the following error message: > > > % mri_read(): couldn't determine type of file > /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc > surfer: couldn't load > /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. > If you were trying to load a functional volume, make sure > you selected the right registration method, and if necessary, > that the registration file exists. > If you were trying to load a volume-encoded value file, > make sure it has the same number of values as this surface > does vertices (128970). > sclv_read_from_volume: error in FunD_New > > Interestingly, I can load the file as a curvature file, but then can't > play around with the threshold. > > > Do you have any idea what I'm doing wrong? Any help would be appreciated! > > > Thanks, > > > Amanda > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d632b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz8%3D&reserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d632b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz8%3D&reserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
External Email - Use Caution Thank you! So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being corrupt? Cheers, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 15 October 2018 17:06:26 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Hi Amanda mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote: > > External Email - Use Caution > > How would I do that? mris_convert doesn't seem to take .asc as an input? > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of > Greve, Douglas N.,Ph.D. > Sent: 15 October 2018 16:25:51 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer > Not sure. Can you use mris_convert to convert the asc back to a curv file? > > On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > > > External Email - Use Caution > > > > Hello, > > > > > > I am trying to overlay a .asc file in either freeview or tksurfer, but > > so far having no luck. > > > > > > As practice and to determine the right format, I am simply using > > lh.thickness, which I've converted to .asc using the following command: > > > > > > % mris_convert -c lh.thickness lh.white lh.thickness.asc > > > > > > I am trying to overlay this onto lh.pial for one subject, however I > > cannot load the file and I get the following error message: > > > > > > % mri_read(): couldn't determine type of file > >/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne > ss.asc > > surfer: couldn't load > >/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne > ss.asc. > > If you were trying to load a functional volume, make sure > > you selected the right registration method, and if necessary, > > that the registration file exists. > > If you were trying to load a volume-encoded value file, > > make sure it has the same number of values as this surface > > does vertices (128970). > > sclv_read_from_volume: error in FunD_New > > > > Interestingly, I can load the file as a curvature file, but then can't > > play around with the threshold. > > > > > > Do you have any idea what I'm doing wrong? Any help would be appreciated! > > > > > > Thanks, > > > > > > Amanda > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailm > an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63 > 2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz > 8%3D&reserved=0 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailm > an%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63 > 2b28e63%7C8370cf1416f34c16b83c724071654356%7C0&sdata=p6poNQ0vBOYwWAjR4Ujk5lfKTtIcbEDR6icoWCJ2mz > 8%3D&reserved=0 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
External Email - Use Caution Hi Bruce, I have the same issue in freeview. The error is: ERROR: could not determine type of /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc ERROR: could not determine type of /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc could not read overlay data from /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc Thanks, Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 16 October 2018 18:13:18 To: Freesurfer support list Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer Hi Amanda can you try it in freeview? tksurfer has been deprecated for a while now cheers Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote: > > External Email - Use Caution > > Thank you! > > > So the answer to the first question is that yes I can convert it back to a > curvature file and that curvature file can be loaded as an overlay. So this > must mean that the problem is with reading the .asc file rather than the > file being corrupt? > > > Cheers, > > > Amanda > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: 15 October 2018 17:06:26 > To: Freesurfer support list > Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer > > Hi Amanda > > mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz > > should do the trick > cheers > Bruce > On Mon, 15 Oct > 2018, Worker, Amanda wrote: > > > > > External Email - Use Caution > > > > How would I do that? mris_convert doesn't seem to take .asc as an input? > > > > > > > >___ > _ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of > > Greve, Douglas N.,Ph.D. > > Sent: 15 October 2018 16:25:51 > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Using a .asc file as overlay in > freeview/tksurfer > > Not sure. Can you use mris_convert to convert the asc back to a curv file? > > > > On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > > > > > External Email - Use Caution > > > > > > Hello, > > > > > > > > > I am trying to overlay a .asc file in either freeview or tksurfer, but > > > so far having no luck. > > > > > > > > > As practice and to determine the right format, I am simply using > > > lh.thickness, which I've converted to .asc using the following command: > > > > > > > > > % mris_convert -c lh.thickness lh.white lh.thickness.asc > > > > > > > > > I am trying to overlay this onto lh.pial for one subject, however I > > > cannot load the file and I get the following error message: > > > > > > > > > % mri_read(): couldn't determine type of file > >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70 > 62a631d19/surf/lh.thickne > > ss.asc > > > surfer: couldn't load > >>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70 > 62a631d19/surf/lh.thickne > > ss.asc. > > > If you were trying to load a functional volume, make sure > > > you selected the right registration method, and if necessary, > > > that the registration file exists. > > > If you were trying to load a volume-encoded value file, > > > make sure it has the same number of values as this surface > > > does vertices (128970). > > > sclv_read_from_volume: error in FunD_New > > > > > > Interestingly, I can load the file as a curvature file, but then can't > > > play around with the threshold. > > > > > > > > > Do you have any idea what I'm doing wrong? Any help would be > appreciated! > > > > > > > > > Thanks, > > > > > > > > > Amanda > > > > > > > > > > > > __
[Freesurfer] Multivariable linear regression with binary variables
External Email - Use Caution Hi, I am trying to run a multivariable GLM with mri_glmfit and I am currently setting up my fsgd file. I have 9 binary variables and 1 continuous variable. My understanding is that in the fsgd file, my "class" would be every possible combination of these binary variables - which is a lot (hundreds) and setting this up manually doesn't seem reasonable. Is this correct and if so could you recommend another way to run this analysis? Thanks, Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Multivariable linear regression with binary variables
External Email - Use Caution Yes. I just want to use 7 of those variables as predictors and 2 as covariates of no interest in a linear regression model From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 08 November 2018 18:03:16 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Multivariable linear regression with binary variables You'd have 512 groups total, which is probably way too many regardless of whether you do so manually or automatically. You need to think about how you want to model all those variables since modeling all possible interactions is not going to be possible. On 11/08/2018 12:45 PM, Worker, Amanda wrote: > > External Email - Use Caution > > Hi, > > > I am trying to run a multivariable GLM with mri_glmfit and I am > currently setting up my fsgd file. I have 9 binary variables and 1 > continuous variable. My understanding is that in the fsgd file, my > "class" would be every possible combination of these binary variables > - which is a lot (hundreds) and setting this up manually doesn't seem > reasonable. Is this correct and if so could you recommend another way > to run this analysis? > > > Thanks, > > > Amanda > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb26b267c9ba949a22f6508d645a49d14%7C8370cf1416f34c16b83c724071654356%7C0&sdata=yfksDn8zNZc3nNAT6nqtfCSvECUdmNciUI91AnUtjOE%3D&reserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb26b267c9ba949a22f6508d645a49d14%7C8370cf1416f34c16b83c724071654356%7C0&sdata=yfksDn8zNZc3nNAT6nqtfCSvECUdmNciUI91AnUtjOE%3D&reserved=0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] statistical map in matlab
External Email - Use Caution Hi, I am working with cortical thickness data in matlab and I have a t-statistic map that I'd like to firstly write to .mgh/mgz format so that I can overlay it in freeview. And secondly, convert it to MNI space and write it out as a volume (preferably nifti). I think that save_mgh might be what I need but I don't understand what M is and how I would get that info for a statistical map in fsaverage space. Any ideas would be much appreciated. Thanks in advance, Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Customising overlay
External Email - Use Caution Dear FreeSurfer Developers, I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients and healthy controls. In total there will be four independent figures. The problem I am having is that the range of values is different for each overlay e.g. overlay 1 regional value range from 0-3, overlay 2 regional values range from 0-8, which means that the colour scales are on different scales. I would like to find a way to manually set the scale to 0-10 for each overlay, regardless of the actual values that exist within the overlay file. I am currently using the below command to load the overlay and then manually configuring the colour scale via the custom option, but I cannot add a point that is outside the range of values that exist in that overlay. I hope this makes sense and I would appreciate any advice you can give on how to achieve consistent colour scales for different overlays. freeview -f /software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10 Kind regards, Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Customising overlay
External Email - Use Caution Hi, I was using version 6.0.0 but I have just tried 7.1.1 and it works fine. Thank you! Amanda From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng Sent: 23 September 2021 16:56 To: Freesurfer support list Subject: Re: [Freesurfer] Customising overlay You don't often get email from rwa...@mgh.harvard.edu. Learn why this is important<http://secure-web.cisco.com/1s9Gk6oIUjBZIyl-B7jw8KdllSqDTnZKvoMebAeIJpJHh0DbJJy9BVCZWPbO6za6RArW63BQ5I96zvGvWmRqzrEQgEFwOzP5lx1T7TR8QjWxtrG_h5NX2CIx-XM1PXC33oPcEb9bik8J--B3msp_PsKLMZbLJsRm_2zkYNkHmfZKcZwJMU2fsHGeQVEkvXwuzHUMdZ6O2tdnSDxS4GBjwYx24uPjSC_xbaCqbv3zo43xZoRAu4KD5WAPRj-bGil13h2Kvv6A5fkEbEeDfDLEcWw/http%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> What version of freesurfer are you using? I tried the latest freeview build and had no problem inserting colors at arbitrary value for customized color option. Best, Ruopeng On Sep 23, 2021, at 9:00 AM, Worker, Amanda mailto:amanda.wor...@kcl.ac.uk>> wrote: External Email - Use Caution External Email - Use Caution Dear FreeSurfer Developers, I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients and healthy controls. In total there will be four independent figures. The problem I am having is that the range of values is different for each overlay e.g. overlay 1 regional value range from 0-3, overlay 2 regional values range from 0-8, which means that the colour scales are on different scales. I would like to find a way to manually set the scale to 0-10 for each overlay, regardless of the actual values that exist within the overlay file. I am currently using the below command to load the overlay and then manually configuring the colour scale via the custom option, but I cannot add a point that is outside the range of values that exist in that overlay. I hope this makes sense and I would appreciate any advice you can give on how to achieve consistent colour scales for different overlays. freeview -f /software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10 Kind regards, Amanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1Mvs087uVuGMwQ43VKbZ4KQUC8sXdfwJ_HJN63344pj1RZdNgj3LOa62UZoVaTOMEheuzBeobIvsoNbJzkpmwsNXB3DmaDQRXq-UoMpQne6KYNlErDKFALpp4l65DOiL-RIqtoF016NEtQcI4xMfhkoCwiqN1yQyLfj7FDvAr25wnulgZji0vaisuA3BQRRUOb9RrgT34Od8lnN8pQIrZ2hI4AVwNLOt5C9dW5wpcYDB6AzstorI-BKRO5XtKjdjYGhTtp1erj5NqQefOeqHKNA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1nDkoAYU1WruFiFbF_xvio3zzurFit9BM4T2Yzgm7K2PhqpKKaUlxx7Zy-xnMPhSReix36V8H-D71vNkkBjWu-6jPGTR0sc2pKrctM-RtIISobtl94VVaBZX1ofAyT2SMekf9ICklz2fjlIEPzVMndE9NDk3J2l8TOApSGW8Iy7ZVQZ9WGJ6f6ZRfotgWxQUWNQR1OfvO-XbHd4taI1gBTYCFsDZzPd6e5GqrE2b97K-t3mu_rE4rQ4CFTmlVo_O2E0Rq5kQ6NE-WviJJ9etPcw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1Mvs087uVuGMwQ43VKbZ4KQUC8sXdfwJ_HJN63344pj1RZdNgj3LOa62UZoVaTOMEheuzBeobIvsoNbJzkpmwsNXB3DmaDQRXq-UoMpQne6KYNlErDKFALpp4l65DOiL-RIqtoF016NEtQcI4xMfhkoCwiqN1yQyLfj7FDvAr25wnulgZji0vaisuA3BQRRUOb9RrgT34Od8lnN8pQIrZ2hI4AVwNLOt5C9dW5wpcYDB6AzstorI-BKRO5XtKjdjYGhTtp1erj5NqQefOeqHKNA%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257Camanda.worker%2540kcl.ac.uk%257C63041bed3a8e46bb874908d97eaadfaa%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C637680094657111886%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D5IJHJuK8JLgs%252BaZhZ1ISMdww2kboWizZnR1Mbjkx%252F5s%253D%26reserved%3D0> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
