[Freesurfer] qcache error
Hi FreeSurfer team, I am trying to run qcache but it is exiting with errors because it is not able to find files in the fsaverage/surf directory. I looked in $FREESURFER_HOME/subjects/fsaverage and there is indeed not a surf folder. Should I use one of the other directories like fsaverage3? Thanks, Lily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all exited with errors
Hi Bruce, I re-ran it without running anything else on the machine. Took almost three times as long as my recons usually take but it finished without error. Thank you for your help! Best, Lily From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Monday, March 30, 2020 5:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Recon-all exited with errors Hi Lily that looks ok I think, although it's hard to tell for sure. The cerebellum shouldn't be included in the surface. Are you sure you have enough ram on your machine? It looked like half of it was in use when you ran recon-all. If you want you can tar and gzip the whole subject dir and ftp it to us and we will take a look, but I would try rerunning when nothing else is taking up significant chunks of memory on your machine and see if that fixes it cheers Bruce On Mon, 30 Mar 2020, Wang, Lily wrote: > Hi Dr. Greve, > > I'm not seeing any glaring issues with inclusion of cerebellum or skull in > the surfaces or the mgz. There is a bit of inclusion of the cerebellum in > the wm.mgz. However, two things that do seem strange are 1. a portion of the > subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it > looks like the ventricles are supposed to be white, but a big portion of > this subject's ventricles are not included and it seems that it's messing up > the lh.orig.nofix surface as well. Could this possibly be an issue? Please > see attached screenshot. > > Thank you, > Lily > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N. Greve > > Sent: Monday, March 30, 2020 11:55 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Recon-all exited with errors > It looks like there might be a very large defect. Try looking at the wm.mgz > and brainmask.mgz and the lh.orig.nofix surface to see if there is a large > part of skull or cerebellum that is encompassed in the orig.nofix surface > > On 3/30/2020 11:26 AM, Wang, Lily wrote: > Hi All, > > I have a subject whose T1 quality is quite good but reconstruction > exited with errors so I am not sure what the issue could be. Attached > is the recon-all.log. Could it be that the subject is very old and has > a lot of degeneration? > > Thank you, > Lily > > ___ > 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] Recon-all exited with errors
Hi Dr. Greve, I'm not seeing any glaring issues with inclusion of cerebellum or skull in the surfaces or the mgz. There is a bit of inclusion of the cerebellum in the wm.mgz. However, two things that do seem strange are 1. a portion of the subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it looks like the ventricles are supposed to be white, but a big portion of this subject's ventricles are not included and it seems that it's messing up the lh.orig.nofix surface as well. Could this possibly be an issue? Please see attached screenshot. Thank you, Lily From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, March 30, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all exited with errors It looks like there might be a very large defect. Try looking at the wm.mgz and brainmask.mgz and the lh.orig.nofix surface to see if there is a large part of skull or cerebellum that is encompassed in the orig.nofix surface On 3/30/2020 11:26 AM, Wang, Lily wrote: Hi All, I have a subject whose T1 quality is quite good but reconstruction exited with errors so I am not sure what the issue could be. Attached is the recon-all.log. Could it be that the subject is very old and has a lot of degeneration? Thank you, Lily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dmri_pathstats segment
Hi, I am trying to get voxel by voxel stats for fmajor on a threshold that's not the 0.2 default because when I looked at merged nii, fmajor is constructed correctly but on a different threshold. This is the command I used: dmri_pathstats --intrk fmajor_PP_avg33_mni_bbr/path.pd.trk --dtbase ../dmri/dtifit --outvox new_fmajor --pthr 0.4 And I am getting in the terminal: INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 940 streamlines as length outliers INFO: Have 1460 total streamlines (min/mean/max length: 75/101/117) INFO: Have 1460 non-truncated streamlines (min/mean/max length: 75/101/117) Segmentation fault (core dumped) Am I running the command incorrectly? Thank you, Lily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Three qdec analyses, different results
Hi Freesurfer Team, I made a qdec table with columns fsid, disease status (control and diseased), age, df, db, dtotal (which are three continuous psychological test scores). I performed one analysis in qdec with disease status as the discrete factor and each of the three test scores as the continuous factor with no nuisance factor chosen, for a total of three analyses. All three analyses ran successfully but when I choose "Does the average thickness differ between Control and Diseased?", which should ignore the test scores (right?), and applied an FDR = 0.05, I get wildly different results among the three analyses even though I believe I should get the same results since it is the same pool of subjects in all three analyses. Did I do something wrong? Thank you, Lily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Corresponding structures to an ROI
I think I'm confused about what the inputs and outputs of the bbregister command are. Should the input volume --mov be my FLAIR? I thought that would register the FLAIR to the T1--or is there no difference between registering FLAIR to T1 and T1 to FLAIR? Best, Lily From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wang, Lily Sent: Thursday, August 29, 2019 11:17 AM To: Freesurfer support list Subject: Re: [Freesurfer] Corresponding structures to an ROI Sorry, I meant the masks were made using FLAIR. Does bbregister work on registering T1 to FLAIR? I was considering using mri_binarize but because I have 20+ subjects each with multiple ROI's that can span several brain structures, I would have to go through every single subject and manually find the corresponding segmentation code numbers? Thank you, Lily From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, August 29, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corresponding structures to an ROI Use bbregister instead of mri_robust_register You can then use mri_label2vol with the --seg option to map into either direction. Once they are in register, I would isolate each of your ROIs by creating a binary volume for each with mri_binarize --i yourrois.mgz --match SegId --o segid.mgz where SegId is your segmentation code number. Then run mri_segstats --seg wmparc.mgz --i segid.mgz --ctab-default --sum sum.segid.dat The values in the "Mean" field of sum.segid.dat (6th column I think) will be the fraction of the ROI in that wmparc segment. On 8/29/19 10:25 AM, Wang, Lily wrote: > Hi All, > > I have several white matter ROI masks unique to each subject that were > made using the subjects' T2 scans and I would like to use wmparc to > find out what brain structures those ROI's correspond to. I'm guessing > that I will need to either register T1 to T2 or T2 to T1 at one point, > which I have done by using mri_robust_register to register T1 to T2 > (and it seemed to turn out ok, but how do I check other than by eye? > And is there a better way to register?), and apply that transformation > to wmparc. But other than figuring out the registration, what else do > I do? > > Thank you, > > Lily > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Corresponding structures to an ROI
Sorry, I meant the masks were made using FLAIR. Does bbregister work on registering T1 to FLAIR? I was considering using mri_binarize but because I have 20+ subjects each with multiple ROI's that can span several brain structures, I would have to go through every single subject and manually find the corresponding segmentation code numbers? Thank you, Lily From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, August 29, 2019 10:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corresponding structures to an ROI Use bbregister instead of mri_robust_register You can then use mri_label2vol with the --seg option to map into either direction. Once they are in register, I would isolate each of your ROIs by creating a binary volume for each with mri_binarize --i yourrois.mgz --match SegId --o segid.mgz where SegId is your segmentation code number. Then run mri_segstats --seg wmparc.mgz --i segid.mgz --ctab-default --sum sum.segid.dat The values in the "Mean" field of sum.segid.dat (6th column I think) will be the fraction of the ROI in that wmparc segment. On 8/29/19 10:25 AM, Wang, Lily wrote: > Hi All, > > I have several white matter ROI masks unique to each subject that were > made using the subjects' T2 scans and I would like to use wmparc to > find out what brain structures those ROI's correspond to. I'm guessing > that I will need to either register T1 to T2 or T2 to T1 at one point, > which I have done by using mri_robust_register to register T1 to T2 > (and it seemed to turn out ok, but how do I check other than by eye? > And is there a better way to register?), and apply that transformation > to wmparc. But other than figuring out the registration, what else do > I do? > > Thank you, > > Lily > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Corresponding structures to an ROI
Hi All, I have several white matter ROI masks unique to each subject that were made using the subjects' T2 scans and I would like to use wmparc to find out what brain structures those ROI's correspond to. I'm guessing that I will need to either register T1 to T2 or T2 to T1 at one point, which I have done by using mri_robust_register to register T1 to T2 (and it seemed to turn out ok, but how do I check other than by eye? And is there a better way to register?), and apply that transformation to wmparc. But other than figuring out the registration, what else do I do? Thank you, Lily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
