[Freesurfer] RAM per CPU for running Freesurfer 7.1
External Email - Use Caution Hi Freesurfer Experts, I am designing some new hardware for a mini-cluster running Freesurfer and other neuroimaging toolboxes and wanted to better understand requirements from Freesurfer. 1) Is there a minimum amount of ram per core that is needed/recommended or is the amount of ram only defined per subject. Most of the threads I found say you need a minimum of 4 GB ram but these were from a long time ago and may not apply to the OPENMP code. Our compute node will have between 52-64 cores so I wanted to know what is the ratio for Ram to CPU (multithreading turned off) that is recommended as opposed to Ram per subject. 2) AMD vs Intel We will run jobs on an existing cluster that has Dual Intel Xeon 6230R and for our new minicluster we are debating between AMD and Intel. While AMD offers higher core-count per CPU, I am worried that results could potentially differ based on the CPU/underlying libraries. We plan on using docker images so from your perspective do you have a recommendation ? Best, Ajay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Multiple Comparison Question for surface-based analyses
Hi Doug, I had some additional questions regarding multiple comparisons in Freesurfer. 1) Do you correct the left and right hemispheres separately or combine both together for muliple comparison correction? 2) Say you are testing multiple contrasts in your model: A > B, A< B etc. Do you correct for multiple contrasts and if not, is there any particular reason why not. Thanks, Ajay On Wed, Aug 3, 2016 at 2:45 AM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >Thank you very much for your update regarding this issue. > > 1)Just curious, will LGI be included in this report as this is another > analysis of interest? > > 2)As for the cortical thickness I originally used 15mm in the analysis so > based on your email I think using 5-10mm may be more prudent in order to > minimize FPR. From your email, I understand that mris_surf2surf (command I > use to convert individual subject to fsaverage or template and smooth to > 10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into > account the long tail distribution. Does this mean that when using > mri_mcsim on my own template, the cluster extents for a given smoothness > will be undersampled due to the fact that the "true" smoothness is more > than what is estimated in the simulation, correct? For instance, when I > select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm > estimate), and I would select a given cluster extent for p=0.05. However, > in this case, 15mm may translate to a larger FWHM than the estimated 21mm, > correct? > > 3)You mentioned that I can use mri_glmfit-sim which is permutation testing > based. I am struggling a bit in understanding how this differs from the > simulation ran with mri_mcsim/qdec? Does qdec monte carlo simulation > option run mri_glmfit-sim in the background to estimate the smoothness > which looks up the cluster extent within the mri_mcsim based on the > estimated FWHM? If so, is this estimate incorrect due to the fact that the > long tails are not taken into account? > > > Thanks, > Ajay > > On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hello Freesurfer Experts, >>Recently there were two article published regarding clusterwise >> simulations for volumetric fmri analyses and potential errors for >> underestimating clusterwise extent thresholds. >> >> 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes >> 2) biorxiv.org/content/early/2016/07/26/065862 >> >> One issue pointed out from these articles seems software specific, >> however the second issue is determining the proper clustersize. The >> heavy-tail nature of spatial smoothness seems to be ignored and a gaussian >> shape is generally assumed, leading to an underestimation of the spatial >> smoothness which can affect cluster size calculations. The issues are >> highlighted in the second article above. >> >> I created my own monte carlo simulation in Freesurfer for a specific >> brain template and I wanted to find out if these concerns also apply to my >> surface based simulations? I am not sure if it does since the monte carlo >> tool is a GRF simulation as opposed to an analytic equation, however given >> that these articles were highlighted very recently, I wanted to ensure I am >> running things appropriately for surface based cortical thickness/dti >> analyses. >> >> Thanks, >> Ajay >> > > ___ 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] Display FSL PALM(permutation) stats in freeview
Hi Anderson, My full design contrasts are below: /ContrastName1 HC > Grp1 /ContrastName2 HC < Grp1 /ContrastName3 HC > Grp2 /ContrastName4 HC < Grp2 /ContrastName5 Grp1 > Grp2 /ContrastName6 Grp1 < Grp2 /ContrastName7 M > F /ContrastName8 M < F /ContrastName9 HC/Grp1 M/F Interaction /ContrastName10 HC/Grp2 M/F Interaction /ContrastName11 Grp1/Grp2 M/F Interaction /NumWaves 9 /NumPoints 11 /Matrix 1 1 -1 -1 0 0 0 0 0 -1 -1 1 1 0 0 0 0 0 1 1 0 0 -1 -1 0 0 0 -1 -1 0 0 1 1 0 0 0 0 0 1 1 -1 -1 0 0 0 0 0 -1 -1 1 1 0 0 0 1 -1 1 -1 1 -1 0 0 0 -1 1 -1 1 -1 1 0 0 0 1 -1 -1 1 0 0 0 0 0 1 -1 0 0 -1 1 0 0 0 0 0 1 -1 -1 1 0 0 0 My colums correspond to the following: EV1:HC-M EV2:HC-F EV3:Grp1-M EV4:Grp1-F EV5:Grp2-M EV6:Grp2-F EV7:Age EV8:Education EV9:Disease Severity In the folder I was running the analysis I put the lh.thickness.10mm.mgz, rh.thickness.10mm.mgz, lh.white (fsaverage), rh.white (fsaverage), lh.mask.mgh (taken from running qdec initially), rh.mask.mgh (taken from running qdec initially). I initially ran palm_hemimerge lh* within matlab Then from a terminal I ran the following command: palm -i bh.thickness.10mm.mgz -d design.mat -t design.con -o bh.thickness -n 500 -approx tail -corrcon -s bh.white -T -tfce2D -logp -m bh.mask.mgz -nouncorrected The command ran fully. When I loaded contrast 6 I found no results on the pial surface, however the white matter surface (where the mask was) was speckled all over with no cluster. If there is a location,I can upload the stats file if that is easier. Thanks, Ajay On Sat, Sep 17, 2016 at 10:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Anderson, >Thanks for the help. When viewing my results they looked very > strange. Upon further investigation it looks as though the mask I supplied > to PALM was a white matter mask (mask.mgh from running qdec initially) > created when I ran qdec. I assumed this would be the whole cortex but I > was wrong. Therefore it seems to only run permutation testing on the > surface of the white matter. Due to the fact that it is unsmoothed white > matter, I think this is why we see some speckling bleeding through near the > boundaries > > In order to do permutation testing accurately for surface based cortical > thickness, would the mask need to be a volume file which is between the > pial and white matter surfaces or would it just need to be the pial surface > (lh.pial / rh.pial), or something else? Any suggestions on the best way to > create this? > > Thanks, > Ajay > > On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Anderson, >>Thanks for the help. When viewing my results they looked very >> strange. Upon further investigation it looks as though the mask I supplied >> to PALM was a white matter mask (mask.mgh from running qdec initially) >> created when I ran qdec. I assumed this would be the whole cortex but I >> was wrong. Therefore it seems to only run permutation testing on the >> surface of the white matter as seen in the attached photo. Due to the fact >> that it is unsmoothed white matter, I think this is why we see some >> speckling bleeding through near the boundaries >> >> In order to do permutation testing accurately for surface based cortical >> thickness, would the mask need to be a volume file which is between the >> pial and white matter surfaces or would it just need to be the pial surface >> (lh.pial / rh.pial), or something else? Any suggestions on the best way to >> create this? >> >> Thanks, >> Ajay >> >> >> >> >> On Thu, Sep 15, 2016 at 1:46 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hello Freesurfer Experts, >>>I was running permutation simulations on cortical thickness data and >>> I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I >>> then tried FSL's PALM which is an extension of randomize to calculate >>> threshold free stats. I saved the output as logp(which is similar to qdec >>> I believe), however I have not been able to load the stats files >>> correctly. The output of palm is lh.thickness_tfce.mgz for my various >>> contrasts. >>> >>> 1) Is .mgz the proper format for the stats files or do I need to convert >>> this to another type like .mgh etc? >>> >>> 2) Can I display this in freeview or is another program needed? I also >>> tried tksurfer but when I loaded the stats file as an overlay nothing >>> displayed. I want to make sure that the stats is loaded as an overlay in >>> freeview/tksurfer and if so, do I need to select anything special so that >>> it scales th
Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview
Hi Anderson, Thanks for the help. When viewing my results they looked very strange. Upon further investigation it looks as though the mask I supplied to PALM was a white matter mask (mask.mgh from running qdec initially) created when I ran qdec. I assumed this would be the whole cortex but I was wrong. Therefore it seems to only run permutation testing on the surface of the white matter. Due to the fact that it is unsmoothed white matter, I think this is why we see some speckling bleeding through near the boundaries In order to do permutation testing accurately for surface based cortical thickness, would the mask need to be a volume file which is between the pial and white matter surfaces or would it just need to be the pial surface (lh.pial / rh.pial), or something else? Any suggestions on the best way to create this? Thanks, Ajay On Sat, Sep 17, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Anderson, >Thanks for the help. When viewing my results they looked very > strange. Upon further investigation it looks as though the mask I supplied > to PALM was a white matter mask (mask.mgh from running qdec initially) > created when I ran qdec. I assumed this would be the whole cortex but I > was wrong. Therefore it seems to only run permutation testing on the > surface of the white matter as seen in the attached photo. Due to the fact > that it is unsmoothed white matter, I think this is why we see some > speckling bleeding through near the boundaries > > In order to do permutation testing accurately for surface based cortical > thickness, would the mask need to be a volume file which is between the > pial and white matter surfaces or would it just need to be the pial surface > (lh.pial / rh.pial), or something else? Any suggestions on the best way to > create this? > > Thanks, > Ajay > > > > > On Thu, Sep 15, 2016 at 1:46 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hello Freesurfer Experts, >>I was running permutation simulations on cortical thickness data and I >> had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I >> then tried FSL's PALM which is an extension of randomize to calculate >> threshold free stats. I saved the output as logp(which is similar to qdec >> I believe), however I have not been able to load the stats files >> correctly. The output of palm is lh.thickness_tfce.mgz for my various >> contrasts. >> >> 1) Is .mgz the proper format for the stats files or do I need to convert >> this to another type like .mgh etc? >> >> 2) Can I display this in freeview or is another program needed? I also >> tried tksurfer but when I loaded the stats file as an overlay nothing >> displayed. I want to make sure that the stats is loaded as an overlay in >> freeview/tksurfer and if so, do I need to select anything special so that >> it scales the logp values correctly? >> >> Thanks, >> Ajay >> > > ___ 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] Display FSL PALM(permutation) stats in freeview
Hello Freesurfer Experts, I was running permutation simulations on cortical thickness data and I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I then tried FSL's PALM which is an extension of randomize to calculate threshold free stats. I saved the output as logp(which is similar to qdec I believe), however I have not been able to load the stats files correctly. The output of palm is lh.thickness_tfce.mgz for my various contrasts. 1) Is .mgz the proper format for the stats files or do I need to convert this to another type like .mgh etc? 2) Can I display this in freeview or is another program needed? I also tried tksurfer but when I loaded the stats file as an overlay nothing displayed. I want to make sure that the stats is loaded as an overlay in freeview/tksurfer and if so, do I need to select anything special so that it scales the logp values correctly? Thanks, Ajay ___ 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] Covariates for cortical Thickness and LGI
Hi Doug, Thanks for the follow up. Do you recommend using a covariate such as mean thickness or is a covariate not necessary for cortical thickness analysis? Thanks, Ajay On Thu, Sep 8, 2016 at 2:00 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer Experts, >I am comparing a control group and 2 patient groups (HC vs Group1, HC > vs Group2, Group1 vs Group2). I am interested in seeing what is the most > appropriate covariate to use for both a cortical thickness analysis and LGI > analysis. I do not expect major changes in brain shape etc, and at most > maybe some more cortical atrophy in one of the groups) > > > I have seen several papers using ICV for cortical thickness analyses, > however I am not sure if this makes the most sense. Does ICV really scale > with thickness as a global measure to account for brain differences? To me > something like left mean thickness and right mean thickness may make more > sense, however, I am new to CT analyses and would like to get your feedback. > > Along with CT, I was interested in what covariate makes most sense in an > LGI analysis. Since LGI may change depending on the location within the > brain, does a global measure such as total surface area (or other measure) > make sense? Is there a suggested covariate to use for this type of > analysis? > > Are there any publications from your group regarind this issue? > > Thanks, > Ajay > ___ 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] Covariates for cortical Thickness and LGI
Hi Freesurfer Experts, I am comparing a control group and 2 patient groups (HC vs Group1, HC vs Group2, Group1 vs Group2). I am interested in seeing what is the most appropriate covariate to use for both a cortical thickness analysis and LGI analysis. I do not expect major changes in brain shape etc, and at most maybe some more cortical atrophy in one of the groups) I have seen several papers using ICV for cortical thickness analyses, however I am not sure if this makes the most sense. Does ICV really scale with thickness as a global measure to account for brain differences? To me something like left mean thickness and right mean thickness may make more sense, however, I am new to CT analyses and would like to get your feedback. Along with CT, I was interested in what covariate makes most sense in an LGI analysis. Since LGI may change depending on the location within the brain, does a global measure such as total surface area (or other measure) make sense? Is there a suggested covariate to use for this type of analysis? Are there any publications from your group regarind this issue? Thanks, Ajay ___ 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_glmfit-sim permutation testing running after 3 days!
Hi Freesurfer Experts, I am trying to use freesurfer's mri_glmfit-sim tool to run permutation testing on cortical thickness data (as recommended by Doug in my previous post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html ) Most of the tutorials I found were not related to permutation testing so the subsequent steps may be incorrect. Please let me know where I go wrong... 1) I first ran QDec to generate a folder for the analysis which would create the subsequent fsgd and y files needed my mri_glmfit-sim. I am running both left and right hemisphere cortical thickness analysis with 10mm smoothing. The following is for just the left hemisphere. Note I am doing a 3 group comparison, but for this 2 group ttest I manually centered the data based on the 3 group mean for age and education. 2) I ran the following command: /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 1 2 perm.abs.2 --sim-sign abs --bg 16 Prior to running the command above, from the y.fsdg file I deleted the fwhm estimate of 13mm since this was not correctly estimated (ACF with long tails). I assumed that by removing this estimate, it would force the permutation test to calculate based on the data but when looking at the log output I see the following which says fwhm 0: cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-Gender-Group-Intercept-thickness.mtx --sim perm 625 2 ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0 --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013 3)I started this a few days ago on a 16 core machine and it is still running in the terminal. I have 150 subjects in the analysis and specified 1 iterations. In the terminal I assumed when I reach Poll 1 it would be complete but currently I am at : Poll 13341 job 1 Thu Aug 25 12:03:51 CDT 2016 Questions: a) I am curious, is this going to run 10,000 simulations X 150 patients or does the Poll number not have anything to do with the number of iterations it is on? b) Did I run this procedure correctly? Was I incorrect in deleting the fwhm estimate from y.fsgd file generated by Qdec even though we know the estimate is incorrect since smoothness assumed a gaussian distribution as opposed to gaussian with heavy tails c) I noticed in the logfile the following warning: INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 5.65727 Matrix condition is 935.597 Found 136777 voxels in mask Reshaping mriglm->mask... search space = 89675.729228 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016 I am not sure if this means my simulation is incorrect? Thanks, Ajay ___ 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] Multiple Comparison Question for surface-based analyses
Hi Doug, Thank you very much for your update regarding this issue. 1)Just curious, will LGI be included in this report as this is another analysis of interest? 2)As for the cortical thickness I originally used 15mm in the analysis so based on your email I think using 5-10mm may be more prudent in order to minimize FPR. From your email, I understand that mris_surf2surf (command I use to convert individual subject to fsaverage or template and smooth to 10-15mm) assumes an ACF estimation of smoothness which DOES NOT take into account the long tail distribution. Does this mean that when using mri_mcsim on my own template, the cluster extents for a given smoothness will be undersampled due to the fact that the "true" smoothness is more than what is estimated in the simulation, correct? For instance, when I select 15mm in qdec, it would point to the 21mm folder (fwhm.dat=20.8mm estimate), and I would select a given cluster extent for p=0.05. However, in this case, 15mm may translate to a larger FWHM than the estimated 21mm, correct? 3)You mentioned that I can use mri_glmfit-sim which is permutation testing based. I am struggling a bit in understanding how this differs from the simulation ran with mri_mcsim/qdec? Does qdec monte carlo simulation option run mri_glmfit-sim in the background to estimate the smoothness which looks up the cluster extent within the mri_mcsim based on the estimated FWHM? If so, is this estimate incorrect due to the fact that the long tails are not taken into account? Thanks, Ajay On Mon, Aug 1, 2016 at 11:43 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hello Freesurfer Experts, >Recently there were two article published regarding clusterwise > simulations for volumetric fmri analyses and potential errors for > underestimating clusterwise extent thresholds. > > 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes > 2) biorxiv.org/content/early/2016/07/26/065862 > > One issue pointed out from these articles seems software specific, however > the second issue is determining the proper clustersize. The heavy-tail > nature of spatial smoothness seems to be ignored and a gaussian shape is > generally assumed, leading to an underestimation of the spatial smoothness > which can affect cluster size calculations. The issues are highlighted in > the second article above. > > I created my own monte carlo simulation in Freesurfer for a specific brain > template and I wanted to find out if these concerns also apply to my > surface based simulations? I am not sure if it does since the monte carlo > tool is a GRF simulation as opposed to an analytic equation, however given > that these articles were highlighted very recently, I wanted to ensure I am > running things appropriately for surface based cortical thickness/dti > analyses. > > Thanks, > Ajay > ___ 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] Multiple Comparison Question for surface-based analyses
Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay ___ 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] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, Ok this makes more sense now. In my case if I choose abs I would look at the max cdf < 0.05 for the corresponding cluster extent in the TH13 folder. In terms of the |a-b|<0,05 does this mean that if I got results in blue it just means significant but with no directionality as to if A > B or B>A? I guess with the blue and red color bars I thought directionality was implied. Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in order to determine directionality of thickness results? Thanks, Ajay On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >Thanks for the explanation. In using p=0.05 with my thickness files > (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf > file. > > In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the > overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail > (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size > of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the > first question of if 0.05 relates to the overall probability or per tail. > > Also is there a T/Z threshold applied? I initially thought that T or > Z=1.3 is the threshold but in looking at tutorials I see that may be > related to the color scale -log(0.05), so I am not sure if there is a > minimum T/Z value to be included in the cluster or if I was correct at 1.3 > is the threshold value (T or Z score or something else)?. > > Thanks, > Ajay > > On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Doug, >>Thanks for the explanation. In using p=0.05 with my thickness files >> (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf >> file. >> >> In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean >> the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per >> tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster >> size of 1302 or would I look at max cdf <0.1 which is 1109? This relates >> to the first question of if 0.05 relates to the overall probability or per >> tail. >> >> Also is there a T/Z threshold applied to these clusters or just >> cluster-extent is used? In looking at the tutorials I see that 1.3 really >> is -log(0.05) so I do not think this relates to any sort of T or Z >> threshold but I just wanted to verify. >> >> Thanks, >> Ajay >> >> >> >> Also, when smoothed at 15mm the estimated smoothness was around 21mm. >> When lo >> >> >> On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: >> >>> Hi Doug, >>>I wanted to figure out what is the minimum cluster extent for a given >>> monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the >>> following tutorial : >>> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so >>> I wanted to know if freesurfer estimates the smoothness for each subject's >>> cortical thickness for a hemisphere and then chooses the corresponding fwhm >>> folder or if by choosing lh 15mm in qdec the clusterwise values are taken >>> from the 15mm folder? Is the smoothness based on the smoothing kernel used >>> or the inherent smoothness of that particular measure (ie measuring the >>> smoothness of the input thicknesss image)? Is there a way to see what >>> cluster minimum is used? >>> >>> Thanks, >>> Ajay >>> >>> >>> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hi Doug, >>>>Thanks for the clarification. So in the case of cortical thickness, >>>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I >>>> should be getting similar results if everything is entered in the same >>>> fashion. This would be the approriate choice compared to mri_smooth. >>>> >>>> For mri_surf2surf I used the following command for smoothing LGI and >>>> cortical thickness and converting to .gii files. >>>> >>>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval >>>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex >>>> mris_convert -c rh.thickness.fwhm15.mgz >>>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii >>>> >>>> >>>> 1) For cortical thickness does it m
Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?. Thanks, Ajay On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >Thanks for the explanation. In using p=0.05 with my thickness files > (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf > file. > > In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the > overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail > (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size > of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the > first question of if 0.05 relates to the overall probability or per tail. > > Also is there a T/Z threshold applied to these clusters or just > cluster-extent is used? In looking at the tutorials I see that 1.3 really > is -log(0.05) so I do not think this relates to any sort of T or Z > threshold but I just wanted to verify. > > Thanks, > Ajay > > > > Also, when smoothed at 15mm the estimated smoothness was around 21mm. > When lo > > > On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > >> Hi Doug, >>I wanted to figure out what is the minimum cluster extent for a given >> monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the >> following tutorial : >> https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so >> I wanted to know if freesurfer estimates the smoothness for each subject's >> cortical thickness for a hemisphere and then chooses the corresponding fwhm >> folder or if by choosing lh 15mm in qdec the clusterwise values are taken >> from the 15mm folder? Is the smoothness based on the smoothing kernel used >> or the inherent smoothness of that particular measure (ie measuring the >> smoothness of the input thicknesss image)? Is there a way to see what >> cluster minimum is used? >> >> Thanks, >> Ajay >> >> >> On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hi Doug, >>>Thanks for the clarification. So in the case of cortical thickness, >>> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I >>> should be getting similar results if everything is entered in the same >>> fashion. This would be the approriate choice compared to mri_smooth. >>> >>> For mri_surf2surf I used the following command for smoothing LGI and >>> cortical thickness and converting to .gii files. >>> >>> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval >>> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex >>> mris_convert -c rh.thickness.fwhm15.mgz >>> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii >>> >>> >>> 1) For cortical thickness does it make sense to use the --cortex option >>> or should I specify a mask of some type (if so which) in mris_surf2surf? >>> >>> 2) For converting files to .gii should I be using rh.white as the option >>> or should it be rh.pial? >>> >>> >>> Best, >>> Ajay >>> >>> >>> >>> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hi Doug, >>>>Thanks for the quick reply. >>>> >>>> Is there a difference from qcache/mris_fwhm with mris_smooth and >>>> mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness >>>> analysis? >>>> >>>> Thanks, >>>> Ajay >>>> >>>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>>> wrote: >>>> >>>>
Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify. Thanks, Ajay Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >I wanted to figure out what is the minimum cluster extent for a given > monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the > following tutorial : > https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I > wanted to know if freesurfer estimates the smoothness for each subject's > cortical thickness for a hemisphere and then chooses the corresponding fwhm > folder or if by choosing lh 15mm in qdec the clusterwise values are taken > from the 15mm folder? Is the smoothness based on the smoothing kernel used > or the inherent smoothness of that particular measure (ie measuring the > smoothness of the input thicknesss image)? Is there a way to see what > cluster minimum is used? > > Thanks, > Ajay > > > On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Doug, >>Thanks for the clarification. So in the case of cortical thickness, >> qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I >> should be getting similar results if everything is entered in the same >> fashion. This would be the approriate choice compared to mri_smooth. >> >> For mri_surf2surf I used the following command for smoothing LGI and >> cortical thickness and converting to .gii files. >> >> mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval >> rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex >> mris_convert -c rh.thickness.fwhm15.mgz >> $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii >> >> >> 1) For cortical thickness does it make sense to use the --cortex option >> or should I specify a mask of some type (if so which) in mris_surf2surf? >> >> 2) For converting files to .gii should I be using rh.white as the option >> or should it be rh.pial? >> >> >> Best, >> Ajay >> >> >> >> On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hi Doug, >>>Thanks for the quick reply. >>> >>> Is there a difference from qcache/mris_fwhm with mris_smooth and >>> mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness >>> analysis? >>> >>> Thanks, >>> Ajay >>> >>> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hi Freesurfer Experts, >>>>Just as a followup through my reading i've come across posts which >>>> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my >>>> cortical thickness analysis I would like to smooth all of my >>>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a >>>> group analysis. After finding regions of difference, I would then like to >>>> use the ROI to extract each individual's mean thickness in the ROI in order >>>> to run a correlation with other measures. Based on this, I assume it would >>>> make sense to use smoothed data to identify the ROI and then use unsmoothed >>>> data for extracting actual thickness measures (does lh.thickness.fsaverage >>>> contain the original thickness or warped thickness values). >>>> >>>> I am unsure which smoothing is the most accurate or preferred. In >>>> using qcache the smoothness of the images do not seem to reach the filter >>>> level (based on the earlier email) so I am not sure if there is a >>>> freesurfer tool to check the smoothness level or if the qcache smoothness >>>> levels make sense for cortical thickness. >>>> >>>> Thanks,
Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used? Thanks, Ajay On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >Thanks for the clarification. So in the case of cortical thickness, > qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I > should be getting similar results if everything is entered in the same > fashion. This would be the approriate choice compared to mri_smooth. > > For mri_surf2surf I used the following command for smoothing LGI and > cortical thickness and converting to .gii files. > > mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval > rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex > mris_convert -c rh.thickness.fwhm15.mgz > $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii > > > 1) For cortical thickness does it make sense to use the --cortex option or > should I specify a mask of some type (if so which) in mris_surf2surf? > > 2) For converting files to .gii should I be using rh.white as the option > or should it be rh.pial? > > > Best, > Ajay > > > > On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Doug, >>Thanks for the quick reply. >> >> Is there a difference from qcache/mris_fwhm with mris_smooth and >> mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness >> analysis? >> >> Thanks, >> Ajay >> >> On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hi Freesurfer Experts, >>>Just as a followup through my reading i've come across posts which >>> use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my >>> cortical thickness analysis I would like to smooth all of my >>> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a >>> group analysis. After finding regions of difference, I would then like to >>> use the ROI to extract each individual's mean thickness in the ROI in order >>> to run a correlation with other measures. Based on this, I assume it would >>> make sense to use smoothed data to identify the ROI and then use unsmoothed >>> data for extracting actual thickness measures (does lh.thickness.fsaverage >>> contain the original thickness or warped thickness values). >>> >>> I am unsure which smoothing is the most accurate or preferred. In using >>> qcache the smoothness of the images do not seem to reach the filter level >>> (based on the earlier email) so I am not sure if there is a freesurfer tool >>> to check the smoothness level or if the qcache smoothness levels make sense >>> for cortical thickness. >>> >>> Thanks, >>> Ajay >>> >>> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >>> wrote: >>> >>>> Hi Freesurfer Experts, >>>>I am trying to understand the difference between qcache option and >>>> mris_fwhm and which is appropriate for a cortical thickness analysis. I >>>> processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii >>>> (converted) files. I used an afni tool SurfFWHM to estimate the smoothness >>>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 >>>> and 20mm it was approximately 9.3-9.9 smoothness level. >>>> >>>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i >>>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when >>>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25. >>>> >>>> >>>> 1) I am not sure if the qcache or the mris_fwhm file is more >>>> appropriate to use for a cortical thickness analysis. >>>> >>>> 2) For qdec if I select the 15mm option does it assume the smoothness >>>> is
Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth. For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files. mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii 1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf? 2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial? Best, Ajay On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >Thanks for the quick reply. > > Is there a difference from qcache/mris_fwhm with mris_smooth and > mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness > analysis? > > Thanks, > Ajay > > On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Freesurfer Experts, >>Just as a followup through my reading i've come across posts which use >> qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my >> cortical thickness analysis I would like to smooth all of my >> rh/lh.thickness.fsaverage.mgh files for each subject in order to run a >> group analysis. After finding regions of difference, I would then like to >> use the ROI to extract each individual's mean thickness in the ROI in order >> to run a correlation with other measures. Based on this, I assume it would >> make sense to use smoothed data to identify the ROI and then use unsmoothed >> data for extracting actual thickness measures (does lh.thickness.fsaverage >> contain the original thickness or warped thickness values). >> >> I am unsure which smoothing is the most accurate or preferred. In using >> qcache the smoothness of the images do not seem to reach the filter level >> (based on the earlier email) so I am not sure if there is a freesurfer tool >> to check the smoothness level or if the qcache smoothness levels make sense >> for cortical thickness. >> >> Thanks, >> Ajay >> >> On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hi Freesurfer Experts, >>>I am trying to understand the difference between qcache option and >>> mris_fwhm and which is appropriate for a cortical thickness analysis. I >>> processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii >>> (converted) files. I used an afni tool SurfFWHM to estimate the smoothness >>> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 >>> and 20mm it was approximately 9.3-9.9 smoothness level. >>> >>> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i >>> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when >>> using SurfFWHM on the smae subject the smoothness was estimated at 11.25. >>> >>> >>> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate >>> to use for a cortical thickness analysis. >>> >>> 2) For qdec if I select the 15mm option does it assume the smoothness >>> is 15mm when calculating monte carlo corrections? Would there be a >>> different way to estimate this since my smoothness at 15mm is closer to >>> 10mm? >>> >>> Thanks, >>> Ajay >>> >> >> > ___ 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] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Doug, Thanks for the quick reply. Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis? Thanks, Ajay On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer Experts, >Just as a followup through my reading i've come across posts which use > qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my > cortical thickness analysis I would like to smooth all of my > rh/lh.thickness.fsaverage.mgh files for each subject in order to run a > group analysis. After finding regions of difference, I would then like to > use the ROI to extract each individual's mean thickness in the ROI in order > to run a correlation with other measures. Based on this, I assume it would > make sense to use smoothed data to identify the ROI and then use unsmoothed > data for extracting actual thickness measures (does lh.thickness.fsaverage > contain the original thickness or warped thickness values). > > I am unsure which smoothing is the most accurate or preferred. In using > qcache the smoothness of the images do not seem to reach the filter level > (based on the earlier email) so I am not sure if there is a freesurfer tool > to check the smoothness level or if the qcache smoothness levels make sense > for cortical thickness. > > Thanks, > Ajay > > On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Freesurfer Experts, >>I am trying to understand the difference between qcache option and >> mris_fwhm and which is appropriate for a cortical thickness analysis. I >> processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii >> (converted) files. I used an afni tool SurfFWHM to estimate the smoothness >> of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 >> and 20mm it was approximately 9.3-9.9 smoothness level. >> >> I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i >> lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when >> using SurfFWHM on the smae subject the smoothness was estimated at 11.25. >> >> >> 1) I am not sure if the qcache or the mris_fwhm file is more appropriate >> to use for a cortical thickness analysis. >> >> 2) For qdec if I select the 15mm option does it assume the smoothness is >> 15mm when calculating monte carlo corrections? Would there be a different >> way to estimate this since my smoothness at 15mm is closer to 10mm? >> >> Thanks, >> Ajay >> > > ___ 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] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values). I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness. Thanks, Ajay On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer Experts, >I am trying to understand the difference between qcache option and > mris_fwhm and which is appropriate for a cortical thickness analysis. I > processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii > (converted) files. I used an afni tool SurfFWHM to estimate the smoothness > of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 > and 20mm it was approximately 9.3-9.9 smoothness level. > > I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i > lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when > using SurfFWHM on the smae subject the smoothness was estimated at 11.25. > > > 1) I am not sure if the qcache or the mris_fwhm file is more appropriate > to use for a cortical thickness analysis. > > 2) For qdec if I select the 15mm option does it assume the smoothness is > 15mm when calculating monte carlo corrections? Would there be a different > way to estimate this since my smoothness at 15mm is closer to 10mm? > > Thanks, > Ajay > ___ 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] Freesurfer 6.0 -qcache vs mris_fwhm
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay ___ 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 stats question
Hello Freesurfer Experts, I wanted to see if I am setting up qdec correctly. I am using cortical thickness as my measure. When using the Qdec gui in Freesurfer 6.0 i supplied the following files: qdec.table.dat which contains the following: Subject Group Gender Age Site Yrs_Education For categorical variables I created the following Group.levels HC PAT Gender.levels Male Female Site.levels 1 5 6 For continuous variables such as Age and Years of Education here is a significant difference between both groups. 1) Should I demean age and Years of Education before creating the table? The tutorial uses the actual values (70 73 etc) but a previous user post said that we should deman the values for covariates. What is the preferred method for the qdec gui? 2) For nuisance variables in the design matrix I selected both age and years of education. For Discrete fixed factors, I only selected group as this is the independent variables I was interested in. For categorical nuisance variables such as Gender and Site, are these ignored by the model if they are not highlighted? Although they are not my independent variable are they accounted somehow if they are not highlighted as the independent variable? They do not appear in my nuissance variable box so I guess I am not sure if they are used in the model or not. 3) The dods / doss options are missing from the Qdec gui from Freesurfer v6.0. Which is the default used in this case? Is there a way I can change this? Thanks, Ajay On Thu, Apr 21, 2016 at 9:15 AM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer Experts, > > I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii) > to perform a cortical thickness analysis. I used qdec with a surface-based > morphometric analysis to compare two groups. As my discrete fixed factor I > used group membership. As Nuisance factors I used age (years), sex (0/1), > site(1-10) and years of education(years). I used Threshold min=2, max=5 > which I assume refers to a T-stat threshold. I see an FDR correction which > and the Monte Carlo Null-Z simulation. > > 1) Do I run both monte carlo and fdr or just one after my figure apprears? > Is the monte-carlo with threshold = 1.3(0.5) similar to a clusterwise > threshold with a fixed p value? > Are results valid when just setting the threshold min=2, max=5 but they > are just uncorrected results? > > > 2) When running Qdec with no nusiance factors and just a discrete fixed > factor of group membership, my results look almost identical to AFNI's > 3dttest++ output when the tmin=2. However, when I add the nuisance factors > the results between the two softare packages are different. > > When nuisances covariates are added does Qdec still use a ttest or switch > to some other method? > > > How is centering assumed between groups for covariances? Is the mean from > each covariate calculated and removed from each group separately based on > group membership or calculated together with all subjects and removed? > > Does the analysis assume to have pooled or unpooled variance across the > two groups? > > > 3) For the viewer it displaces a logarithmic scale from what I have read > in other papers. Is there a way to switch this to displace tvalue? > > 4) There was a previous post I saw yesterday saying qdec only uses 2 > nuisance covariates and so I wanted to see if this is the case or not so I > can try to understand why my afni and freesurfer results match with no > covariates added but are very different once covariates are added. > > > Thanks, > Ajay > ___ 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] mris_fix_topology with ROI surface
Thanks for clarifying Bruce. Just curious is there any freesurfer commands to convert this internal surface file into a .mgh file for external use? For example mri_surf2vol or mri_surf2label etc? Thanks, Ajay On Wed, Apr 6, 2016 at 5:17 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hello Freesurfer Experts, > > I ran the following commands (from recon-all devtable) to create a surface > model of the ROI's that I am interested in (they start off as a binary 1 > mask): > > 1) mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix > 2) mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix > 3) mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix > 4) mris_inflate > 5) mris_sphere > 6) mri_fixtopology > > When I use freeview the lh.smooth.nofix looks great. I wanted to use this > file to create a surface and volume file, however mri_info lh.smooth.nofix > comes up with the error of unknown filetype. > > What is the lh.smooth.nofix filetype? > > How would i be able to convert this lh.smooth.nofix to be used as a > surface for surface-based analysis? Are there other files that need to be > created first in order to convert this file to a surface? Is this file a > label, annotation surface etc? > > Thanks, > Ajay > > > On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Freesurfer experts, >>I wanted to create a Freesurfer surface on some of the aseg ROIs. I >> was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere >> some of the subcortical volumes for creating a surface. >> >> The mri_sphere had a big chunk that was deleted and so I wanted to run >> mris_fix_topology to fix this issue. In trying to run this command it >> appears that mris_fix_topology tries to correct based off of a brain sphere >> (which this ROI is clearly not) and therefore it fails. I plan to then run >> subsequent steps such as mris_euler number and mris_remove_intersections >> >> 1) Is there any way to fix the topology of this ROI using freesurfer >> tools or a way to work around this issue? Do you feel the sphere is needed >> for a small subcortical surface (ie globus pallidus) or is this really more >> for complex structures such as cortical surfaces? >> >> 2) Is there a recommended set of steps to accomplish creating a surface >> from the ROI that is different from what I stated? >> >> >> Thanks, >> Ajay >> > > ___ 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] bbregister --init-spm with Freesurfer 6.0
Thanks for the follow up about the new tool you developed! I look forward to using it and I will remove the --init-spm option. Just as a follow up I did add the pathway for freesurfer/matlab and it ran properly for hippocampal subfields, so I do not think that is the issue. Thanks, Ajay On Wed, Apr 6, 2016 at 12:59 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hello Freesurfer Experts, >As a follow up question for bbregister, I used the --tmp and --epi-mask > options, but I did not see a mask in the directory. I wanted to see if > there is any way to output the B0/edge excluded epi-mask used in bbregister? > > Thanks, > Ajay > > On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Freesurfer Experts, >>I was running bbregister and came across an issue. I have used >> previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at >> it worked perfectly for a specific subject. >> >> I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm >> option with the same resting state scan, and it did not move at all. When >> looking at the terminal I saw that when matlab started up within >> bbregister, the command fs_spmreg was not found. I also installed spm8 and >> reran the subject with the same issue. When I changed the option to >> --init-fsl everything worked. I checked the matlab installation and >> everything looks fine, so I think the issue may be the fs_spmreg function >> not being found. I am not sure if there is an easy fix for this, but any >> help would be appreciated. >> >> Thanks, >> Ajay >> >> > ___ 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] mris_fix_topology with ROI surface
Hello Freesurfer Experts, I ran the following commands (from recon-all devtable) to create a surface model of the ROI's that I am interested in (they start off as a binary 1 mask): 1) mri_tesselate ../mri/lh.ROI.mgz 1 ../surf/lh.orig.nofix 2) mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 3) mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smooth.nofix 4) mris_inflate 5) mris_sphere 6) mri_fixtopology When I use freeview the lh.smooth.nofix looks great. I wanted to use this file to create a surface and volume file, however mri_info lh.smooth.nofix comes up with the error of unknown filetype. What is the lh.smooth.nofix filetype? How would i be able to convert this lh.smooth.nofix to be used as a surface for surface-based analysis? Are there other files that need to be created first in order to convert this file to a surface? Is this file a label, annotation surface etc? Thanks, Ajay On Mon, Mar 21, 2016 at 1:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer experts, >I wanted to create a Freesurfer surface on some of the aseg ROIs. I > was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere > some of the subcortical volumes for creating a surface. > > The mri_sphere had a big chunk that was deleted and so I wanted to run > mris_fix_topology to fix this issue. In trying to run this command it > appears that mris_fix_topology tries to correct based off of a brain sphere > (which this ROI is clearly not) and therefore it fails. I plan to then run > subsequent steps such as mris_euler number and mris_remove_intersections > > 1) Is there any way to fix the topology of this ROI using freesurfer tools > or a way to work around this issue? Do you feel the sphere is needed for a > small subcortical surface (ie globus pallidus) or is this really more for > complex structures such as cortical surfaces? > > 2) Is there a recommended set of steps to accomplish creating a surface > from the ROI that is different from what I stated? > > > Thanks, > Ajay > ___ 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] bbregister --init-spm with Freesurfer 6.0
Hello Freesurfer Experts, As a follow up question for bbregister, I used the --tmp and --epi-mask options, but I did not see a mask in the directory. I wanted to see if there is any way to output the B0/edge excluded epi-mask used in bbregister? Thanks, Ajay On Tue, Apr 5, 2016 at 11:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Freesurfer Experts, >I was running bbregister and came across an issue. I have used > previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at > it worked perfectly for a specific subject. > > I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm > option with the same resting state scan, and it did not move at all. When > looking at the terminal I saw that when matlab started up within > bbregister, the command fs_spmreg was not found. I also installed spm8 and > reran the subject with the same issue. When I changed the option to > --init-fsl everything worked. I checked the matlab installation and > everything looks fine, so I think the issue may be the fs_spmreg function > not being found. I am not sure if there is an easy fix for this, but any > help would be appreciated. > > Thanks, > Ajay > > ___ 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] bbregister --init-spm with Freesurfer 6.0
Hi Freesurfer Experts, I was running bbregister and came across an issue. I have used previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it worked perfectly for a specific subject. I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm option with the same resting state scan, and it did not move at all. When looking at the terminal I saw that when matlab started up within bbregister, the command fs_spmreg was not found. I also installed spm8 and reran the subject with the same issue. When I changed the option to --init-fsl everything worked. I checked the matlab installation and everything looks fine, so I think the issue may be the fs_spmreg function not being found. I am not sure if there is an easy fix for this, but any help would be appreciated. Thanks, Ajay ___ 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] Left right flip surfaces
Hi Doug, I used the caudate surface I created as an example as I was testing the command out. I do not plan to use this command for the caudate. It just happened to show the same issue as the earlier post ( https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22%5C[Freesurfer%5C]+R+L+flipping%22=newest=1>) and so I thought it would be the clearest way of showing you the issue I was referring to. I want to flip the lh.thickness.fwhm10.fsaverage.gii files to the right hemisphere for certain subjects and I was worried about having a similar voxel shift if I used mris_reverse. I found posts using xhemireg and surfreg along with mris_reverse, and so I am trying to figure out what is the best way to flip these thickness files to the opposite hemisphere (files already warped to symmetric space) Thanks, Ajay On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hi Doug, >I attached a .png file to show an example. The Yellow outline is the > right and left caudate surface. The right surface (yellow) was created by > using 3dLRflip (Afni program) to symmetrically flip the volumetric ROI so > that I can create the right caudate surface from scratch again. The blue > outline is the same right caudate surface created when I used mris_reverse > on the left hemisphere surface. As you can see the blue surface outline is > not exactly symmetrical, but rather it is shifted to the left by one > voxel. This was noted in some earlier posts regarding mris_reverse from > 2004 as an issue ( > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1 > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22%5C[Freesurfer%5C]+R+L+flipping%22=newest=1>). > > > I was curious to see if xhemireg or the surfreg methods alleviate this > issue, or if there is another set of preferred commands to symmetrically > L-R flip the brain? > > Thanks, > Ajay > > On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> > wrote: > >> Hi Freesurfer Experts, >>In testing mris_reverse, there seems to be a voxel shift. In looking >> up other freesurfer utitlites I came across xhemireg and surfreg. >> >> >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html >> >> Does xhemireg or surfreg call out mris_reverse, causing the same pixel >> shift issue??? >> >> Based on what I can find is it best to run the following: >> >> surfreg --s sub001 --t fsaverage_sym --lh --xhemi >> Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other >> hemisphere? >> >> Thanks, >> >> Ajay >> >> >> On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> >> wrote: >> >>> Hello Freesurfer Experts, >>> >>>I processed all of my brains through freesurfer 6.0 dev for Linux and >>> warped the surfaces to standardized space. For a handful of subjects I >>> want to perform a left right flip of the cortical thickness files >>> (standardized space) for a group analysis. What is the best way to perform >>> this in freesurfer? I have found a previous post referencing mris_reverse >>> but there was a mention of it being off by a voxel when flipped. I wanted >>> to see if this is still a concern with the latest version? >>> >>> Is there a better way to achieve this goal without rerunning all of >>> freesurfer such as a newer took, or is this the preferred method? >>> >>> >>> >>> Thanks, >>> Ajay >>> >> >> > ___ 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] Left right flip surfaces
Hi Freesurfer Experts, In testing mris_reverse, there seems to be a voxel shift. In looking up other freesurfer utitlites I came across xhemireg and surfreg. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html Does xhemireg or surfreg call out mris_reverse, causing the same pixel shift issue??? Based on what I can find is it best to run the following: surfreg --s sub001 --t fsaverage_sym --lh --xhemi Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other hemisphere? Thanks, Ajay On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> wrote: > Hello Freesurfer Experts, > >I processed all of my brains through freesurfer 6.0 dev for Linux and > warped the surfaces to standardized space. For a handful of subjects I > want to perform a left right flip of the cortical thickness files > (standardized space) for a group analysis. What is the best way to perform > this in freesurfer? I have found a previous post referencing mris_reverse > but there was a mention of it being off by a voxel when flipped. I wanted > to see if this is still a concern with the latest version? > > Is there a better way to achieve this goal without rerunning all of > freesurfer such as a newer took, or is this the preferred method? > > > > Thanks, > Ajay > ___ 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] Left right flip surfaces
Hello Freesurfer Experts, I processed all of my brains through freesurfer 6.0 dev for Linux and warped the surfaces to standardized space. For a handful of subjects I want to perform a left right flip of the cortical thickness files (standardized space) for a group analysis. What is the best way to perform this in freesurfer? I have found a previous post referencing mris_reverse but there was a mention of it being off by a voxel when flipped. I wanted to see if this is still a concern with the latest version? Is there a better way to achieve this goal without rerunning all of freesurfer such as a newer took, or is this the preferred method? Thanks, Ajay ___ 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] mris_fix_topology with ROI surface
Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface. The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections 1) Is there any way to fix the topology of this ROI using freesurfer tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces? 2) Is there a recommended set of steps to accomplish creating a surface from the ROI that is different from what I stated? Thanks, Ajay ___ 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] Freesurfer 6.0 -hires mri_segment potential issue
Hello Freesurfer experts, I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu 14.04 with a high resolution image (0.5mm isotropic). I set OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags in my autorecon 2 line command. Autorecon1 and the beginning parts of Autorecon2 ran in a reasonable amount of time. Currently the program is running the mri_segment -keep -mprage brain.mgz wm.seg.mgz line command however it has been at this step for approximately 5 days! I used top line command to verify that the program is still running and it seems to be still running. I wasn't sure if this time for this step is typical for a high-res image (as this is my first time processing data higher than 1mm iso), or if there is a potential bug. I ran this same subject on another computer using the same version of Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been running for over a day so far. Any feedback would be appreciated as to if this amount of processing time is typical for this type of resolution, or if it could be a potential bug and that I should wait for a new beta release? Thanks, Ajay ___ 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] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Bruce, If it isn't too much trouble could you send the program update? I have another set of images (2009c template) which I can contrast enhance for GM/WM regions so I can try this set of images to process along with the images I sent you. Thanks, Ajay On Thursday, December 3, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu <javascript:_e(%7B%7D,'cvml','fis...@nmr.mgh.harvard.edu');>> wrote: > Hi Ajay > > I have found the problem that messed up the surfaces and fixed it. We can > get you an updated mris_fix_topology that will not generate corrupted > surfaces. However, the underlying problem is huge topological defects > caused by low gray/white contrast in this data. For example in the left > hemi, there is on in the insula (e.g. voxels around 362, 213, 200 and 364, > 229, 207 and in the temporal lobe (351, 286, 282, 283, 309, 258). > > > Basically the gray/white contrast isn't high enough for us to accurately > segment the wm with our default procedures. Control points may help a bit, > but you may also need to manually edit the wm.mgz to remove the largest > defects. The easiest way to do this is to visualize them on the > lh.inflated.nofix surface with the lh.defect_labels overlaid to show you > where the defects are, then go into the volume in the wm.mgz and either add > control points or erase wm to fix things. > > Let us know if you want a new mris_fix_topology. I'm not sure it is worth > the trouble since while it will now generate topologically correct surfaces > for this dataset, they will not be geometrically acccurate in the vicinity > of the huge (>200,000 vertices!) defects. > > cheers > Bruce > > > On Wed, 2 Dec 2015, Ajay Kurani wrote: > > Hi Bruce, >> >> The template is the ICBM 2009b nonlinear template (0.5mm isotropic) >> which I downloaded from the >> McGills site ( >> http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009). The >> template has a >> range of values from 0-100. Then I combined the csf/wm/gm masks (derived >> from the 2009c template >> which is 1mm isotropic) and resampled to 0.5 mm to mask the brain. >> Subsequently I rescaled the >> data to have a range of 0-255 and used this output as my input T1 for >> Freesurfer. Thank you very >> much for looking into this matter, it is much appreciated! I will look >> at the file as you >> suggested. >> >> Sincerely, >> Ajay >> >> On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Ajay >> >> can you explain your entire processing stream, including the >> details of the >> acquisition? What sequence/coil/scanner was used? You could fix >> your problem by looking >> at the defects on the inflated.nofix, overlaying >> lh.defect_labels on it to see where they are, then figuring out >> what caused them in the >> volume. However, there is a bug in mris_fix_topology that only >> comes up when it >> encounters a large enough defect (with nvertices>200,000). The code >> tries to avoid >> running it's normal genetic algorithm as it would take days (or >> weeks) to finish, since >> it scales with the square of the number of vertices. I haven't >> figured out what is >> going wrong yet, but hopefully will have a code fix soon. >> >> cheers >> Bruce >> >> >> On Tue, 1 Dec 2015, Ajay Kurani wrote: >> >> Hi Bruce, When looking at my top slices in brain ask I >> noticed that the >> gray/white matter shows but the darker areas surrounding it >> are not present >> (this usually goes to the edge of the brain). Could the >> large defects be a >> result of having masked this out on the input file? I >> multiplied the >> template with the GM/WM/CSF masks they provided to get the >> brain extracted >> so I only see this missing in the very top few slices of the >> brain. >> >> Thanks, >> Ajay >> >> On Tuesday, December 1, 2015, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Falk >> >> I don't think you need to rerun the qsphere. I'm pretty >> sure >> this is a bug in mris_fix_topology for giant defects, >> but >> haven't finished tracking it down yet >> >> cheers >> Bruce >> >> >>
Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Bruce, The template is the ICBM 2009b nonlinear template (0.5mm isotropic) which I downloaded from the McGills site ( http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009). The template has a range of values from 0-100. Then I combined the csf/wm/gm masks (derived from the 2009c template which is 1mm isotropic) and resampled to 0.5 mm to mask the brain. Subsequently I rescaled the data to have a range of 0-255 and used this output as my input T1 for Freesurfer. Thank you very much for looking into this matter, it is much appreciated! I will look at the file as you suggested. Sincerely, Ajay On Tue, Dec 1, 2015 at 7:55 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Ajay > > can you explain your entire processing stream, including the details of > the acquisition? What sequence/coil/scanner was used? You could fix your > problem by looking at the defects on the inflated.nofix, overlaying > lh.defect_labels on it to see where they are, then figuring out what > caused them in the volume. However, there is a bug in mris_fix_topology > that only comes up when it encounters a large enough defect (with > nvertices>200,000). The code tries to avoid running it's normal genetic > algorithm as it would take days (or weeks) to finish, since it scales with > the square of the number of vertices. I haven't figured out what is going > wrong yet, but hopefully will have a code fix soon. > > cheers > Bruce > > > > On Tue, 1 Dec 2015, Ajay Kurani wrote: > > Hi Bruce, When looking at my top slices in brain ask I noticed that the >> gray/white matter shows but the darker areas surrounding it are not >> present >> (this usually goes to the edge of the brain). Could the large defects be >> a >> result of having masked this out on the input file? I multiplied the >> template with the GM/WM/CSF masks they provided to get the brain extracted >> so I only see this missing in the very top few slices of the brain. >> >> Thanks, >> Ajay >> >> On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Falk >> >> I don't think you need to rerun the qsphere. I'm pretty sure >> this is a bug in mris_fix_topology for giant defects, but >> haven't finished tracking it down yet >> >> cheers >> Bruce >> >> >> On Tue, 1 Dec 2015, Falk Lüsebrink wrote: >> >> >> Hi Ajay, >> >> >> >> you should >> >> >> >> cp ?h.orig.nofix ?h.orig >> >> cp ?h.inflated.nofix ?h.inflated >> >> >> >> with ? being l or r depending your hemisphere. >> After the fixing stage the >> surfaces got damaged somehow, therefore you have to >> recreate it them. I’m >> not entirely sure about the qsphere. Probably you >> have to run the -qsphere >> stage again also. >> >> >> >> Best, >> >> Falk >> >> >> >> >> >> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] >> Gesendet: Montag, 30. November 2015 21:50 >> An: Falk Lüsebrink >> Cc: Freesurfer support list; Bruce Fischl >> Betreff: Re: [Freesurfer] Freesurfer 6.0 - >> Autorecon2 failure >> (mris_euler_number) using high res (0.5mm >> isotropic) T1 image >> >> >> >> Hi Falk, >> >>I used the command and got the following error: >> >> Command: ris_topo_fixer -mgz -warning -seed 1234 >> ICBM lh >> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading >> inputsurface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_n >> lin_sym >> _09b/ICBM/surf/lh.orig... >> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mn >> i_icbm152_nlin_sym >> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, >> but face 46196 not in >> vertex 24215 face list >> >> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading >> inputsurface/home/imuser/
Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Bruce, When looking at my top slices in brain ask I noticed that the gray/white matter shows but the darker areas surrounding it are not present (this usually goes to the edge of the brain). Could the large defects be a result of having masked this out on the input file? I multiplied the template with the GM/WM/CSF masks they provided to get the brain extracted so I only see this missing in the very top few slices of the brain. Thanks, Ajay On Tuesday, December 1, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Falk > > I don't think you need to rerun the qsphere. I'm pretty sure this is a bug > in mris_fix_topology for giant defects, but haven't finished tracking it > down yet > > cheers > Bruce > > > On Tue, 1 Dec 2015, Falk Lüsebrink wrote: > > >> Hi Ajay, >> >> >> >> you should >> >> >> >> cp ?h.orig.nofix ?h.orig >> >> cp ?h.inflated.nofix ?h.inflated >> >> >> >> with ? being l or r depending your hemisphere. After the fixing stage the >> surfaces got damaged somehow, therefore you have to recreate it them. I’m >> not entirely sure about the qsphere. Probably you have to run the -qsphere >> stage again also. >> >> >> >> Best, >> >> Falk >> >> >> >> >> >> Von: Ajay Kurani [mailto:dr.ajay.kur...@gmail.com] >> Gesendet: Montag, 30. November 2015 21:50 >> An: Falk Lüsebrink >> Cc: Freesurfer support list; Bruce Fischl >> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure >> (mris_euler_number) using high res (0.5mm isotropic) T1 image >> >> >> >> Hi Falk, >> >>I used the command and got the following error: >> >> Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh >> mris_topo_fixer -mgz -warning -seed 1234 ICBM lh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading input >> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/lh.orig... >> >> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in >> vertex 24215 face list >> >> mris_topo_fixer -mgz -warning -seed 1234 ICBM rh >> INFO: assuming .mgz format >> setting seed for random number genererator to 1234 >> reading input >> surface/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/rh.orig... >> >> mrisFindNeighbors:/home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym >> _09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in >> vertex 18903 face list >> >> Any suggestions would be appreciated. >> >> Thanks, >> >> Ajay >> >> >> >> On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de> >> wrote: >> >> Hi Ajay, >> >> I ran into the same error processing hires data a while ago using a >> nightly >> build of centos 6 with the hires flag only. Disk space or alike wasn't an >> issue. I ran mris_topo_fixer instead of mris_fix_topology to get working >> surfaces. >> >> Best, >> Falk >> >> -Ursprüngliche Nachricht- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce >> Fischl >> Gesendet: Sonntag, 29. November 2015 22:48 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure >> (mris_euler_number) using high res (0.5mm isotropic) T1 image >> >> Hi Ajay >> >> are you sure you didn't run out of disk space? That error is a sanity >> check >> on the surfaces that should never occur >> >> cheers >> Bruce >> >> On Sun, 29 Nov 2015, Ajay >> Kurani wrote: >> >> > Hello Freesurfer experts, >> >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 >> > version) with the -hires flag to process an MNI template image which >> > is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error >> > during >> > pocessing: >> > >> > Command run: >> > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts >> > >> > I supplied a skull stripped brain which was nu corrected and so I used >> > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 >> > stage. I then ran autore
Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Falk, Thank you very much for the suggestion! I will give it a try. Also Bruce I sent a separate email with a link to the original image for you to download. I can also move all of my processed files for that template there if you would like so you do not have to restart from scratch? Thanks, Ajay On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote: > Hi Ajay, > > I ran into the same error processing hires data a while ago using a > nightly build of centos 6 with the hires flag only. Disk space or alike > wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get > working surfaces. > > Best, > Falk > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl > Gesendet: Sonntag, 29. November 2015 22:48 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure > (mris_euler_number) using high res (0.5mm isotropic) T1 image > > Hi Ajay > > are you sure you didn't run out of disk space? That error is a sanity > check on the surfaces that should never occur > > cheers > Bruce > On Sun, 29 Nov 2015, Ajay > Kurani wrote: > > > Hello Freesurfer experts, > >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 > > version) with the -hires flag to process an MNI template image which > > is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error > > during > > pocessing: > > > > Command run: > > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts > > > > I supplied a skull stripped brain which was nu corrected and so I used > > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 > > stage. I then ran autorecon2 and it was working well until I was at > > the -fix stage and ran into the following error: > > > > > > Error: > > mris_euler_number ./surf/lh.orig > > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face > > 46196 not in vertex 24215 face list > > > > > > > > I am not sure if this is due to the fact that we have a very high > > resolution image (template) and if there are any modifications needed > > aside from the hires flag. Are there any suggestions you have? > > > > Thanks, > > Ajay > > > > > ___ 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] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hi Falk, I used the command and got the following error: Command: ris_topo_fixer -mgz -warning -seed 1234 ICBM lh mris_topo_fixer -mgz -warning -seed 1234 ICBM lh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list mris_topo_fixer -mgz -warning -seed 1234 ICBM rh INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig... mrisFindNeighbors: /home/imuser/Downloads/mni_icbm152_nlin_sym_09b_nifti/mni_icbm152_nlin_sym_09b/ICBM/surf/rh.orig: face[35822].v[2] = 18903, but face 35822 not in vertex 18903 face list Any suggestions would be appreciated. Thanks, Ajay On Mon, Nov 30, 2015 at 2:41 AM, Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote: > Hi Ajay, > > I ran into the same error processing hires data a while ago using a > nightly build of centos 6 with the hires flag only. Disk space or alike > wasn't an issue. I ran mris_topo_fixer instead of mris_fix_topology to get > working surfaces. > > Best, > Falk > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl > Gesendet: Sonntag, 29. November 2015 22:48 > An: Freesurfer support list > Betreff: Re: [Freesurfer] Freesurfer 6.0 - Autorecon2 failure > (mris_euler_number) using high res (0.5mm isotropic) T1 image > > Hi Ajay > > are you sure you didn't run out of disk space? That error is a sanity > check on the surfaces that should never occur > > cheers > Bruce > On Sun, 29 Nov 2015, Ajay > Kurani wrote: > > > Hello Freesurfer experts, > >I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 > > version) with the -hires flag to process an MNI template image which > > is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error > > during > > pocessing: > > > > Command run: > > recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts > > > > I supplied a skull stripped brain which was nu corrected and so I used > > the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 > > stage. I then ran autorecon2 and it was working well until I was at > > the -fix stage and ran into the following error: > > > > > > Error: > > mris_euler_number ./surf/lh.orig > > mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face > > 46196 not in vertex 24215 face list > > > > > > > > I am not sure if this is due to the fact that we have a very high > > resolution image (template) and if there are any modifications needed > > aside from the hires flag. Are there any suggestions you have? > > > > Thanks, > > Ajay > > > > > ___ 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] Freesurfer 6.0 - Autorecon2 failure (mris_euler_number) using high res (0.5mm isotropic) T1 image
Hello Freesurfer experts, I am trying to run Freesurfer 6.0 beta (downloaded 10/15/15 version) with the -hires flag to process an MNI template image which is 0.5mm isotropic. Stage 1 ran well and on stage 2 there is an error during pocessing: Command run: recon-all -s ICBM -autorecon2 -openmp 8 -3T -hires -expert expert.opts I supplied a skull stripped brain which was nu corrected and so I used the T1.mgz and copied it to brainmask.mgz and nu.mgz in autorecon1 stage. I then ran autorecon2 and it was working well until I was at the -fix stage and ran into the following error: Error: mris_euler_number ./surf/lh.orig mrisFindNeighbors: ./surf/lh.orig: face[46196].v[0] = 24215, but face 46196 not in vertex 24215 face list I am not sure if this is due to the fact that we have a very high resolution image (template) and if there are any modifications needed aside from the hires flag. Are there any suggestions you have? Thanks, Ajay ___ 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] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1
Hi Bruce, 1) I was also concerned 3mm may be too thick but I will try a few subjects to see how it goes. 2) Hi Eugenio I wanted to see if you can give a bit of insight into the hippocampal issue. 3) Bruce, sorry for the confusion. I was referring to sqrt(T1w*B1 x T2w*B1) ~ B1 bias field estimate not the T1/T2 myelin mapping. Do you see any forseeable issues of correcting the T1w and T2w image with the B1 estimate prior to running myelin mapping (T1/T2)? Essentially if we remove B1 already then there should not be any additional B1 cancellation when dividing the images. Do you see any issue with using the same B1 bias field to correct resting state data after motion correction is performed? Thanks, Ajay ___ 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] Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1
Hello Freesurfer experts, I am working with a database of pre-collected scans. Although the T1 images are collected at 1x1x1 mm^3 resolution, the T2 and proton density scans are .938x.938x3 mm^3. 1) I wanted to see if you think that using the T2 scans for recon-all would hurt or help the pial reconstruction/cortical thickness measurements based on it being much thicker of a volume? 2) Would the scans help with hippocampal subfield analysis based on this resolution? 3) I am interested in using T1/T2 scans for B1 bias field correction (similar to the HCP minimum pipeline paper). I think that using these scans would be ok since the bias field is supposed to be smooth, however I wanted to see your thoughts regarding using the T2 scans of this resolution for the B1 bias-field estimation. Any guidance to any of these questions would be much appreciated! Sincerely, Ajay Kurani ___ 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] Freesurfer v 6.0???
Hello Freesurfer experts, I wanted to see if the nightly dev builds of freesurfer are v6.0 with the new hippocampal subfields or if that download is in another section? If so can you send me the proper download location? Also is CUDA support still at 5.0 with this version or is there any updates to the cuda support? Thanks for your help. Sincerely, Ajay ___ 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] Freesurfer with whole brain T1 and partial coverage FLAIR
Hello Freesurfer experts, I have a question regarding the use of the -T2 and -FLAIR flags in freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR (bottom of cerebellum/brainstem gets cut off on some subjects). I wanted to see if freesurfer would still be able to run correctly if my FLAIR image is aligned, BUT DOES NOT COVER the exact same amount of the brain as my MPRAGE? I checked with autorecon1 and the mask seemed to cover the whole brain, however I am not sure if there are any subsequent steps that might not behave properly such lesion detection, surface creation etc. Thanks, Ajay ___ 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] bbregister / mri_vol2vol with nifti file header
Dear Freesurfer users,
I wanted to see if anyone knows what part of the file NIFIT header
mri_vol2vol or mri_convert uses to write transform information from
register.dat acquired from bbregister? I used the following commands to
register the anatiomcal brain.mgz to the last time point of my EPI scan:
bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat
--init-header --bold --frame $NP_last --nearest --template-out
${sub}.RS.template.nii
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
$SUBJECTS_DIR/${sub}_FS/mri/
brain.mgz --o $out_dir/brain_aligned.nii --inv --no-save-reg --reg
$out_dir/${sub}_RS_register.dat
When i view the images in Afni they look misaligned, but display perfectly
in freesurfer (tkregister2 --mov EP_001.RS.template.nii --reg
EP_001_RS_register.dat --surf) so I am assuming each program looks at a
different field in the nifti file header. I used mri_vol2vol to apply the
inverse transform of register.dat to brain.mgz so that it aligns with the
EPI but for some reason it is not showing up correctly in afni so I wanted
to get a better understanding of how freesurfer files write transformation
information in nifti format (sform, qform, another part of the header) and
if there is an easy way to get this into a format that afni reads correctly?
Thanks,
Ajay
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[Freesurfer] Combining multiple transforms into one register.dat file for oblique angle acquisitions
Dear Freesurfer users,
I had a question regarding how to combine multiple register.dat files
into one file. Essentially, I have a T1 image which I created masks for in
native space. I then import the T1 image into freesurfer and run through
the recon-all pipeline. Subsequently, I use bbregister in order to
register my last EPI timepoint to the T1 image and generate the
register.dat file and when viewing the files the overlap looked great.
1) mri_convert -i m${sub}.T1.nii --in_type nii -o ${sub}.T1.FS.mgz
--out_type mgz
2) bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat
--init-header --bold --frame $NP_last --nearest --template-out
${sub}.RS.template.nii
3) tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat
--surf
I wanted to take my brain (freesurfer) and masks(native space
pre-freesurfer) and the aseg file and then register this to the EPI scan
and used the following commands:
4) Convert mask to freesurfer format
mri_convert -i ${loc_dir}/spm/c1${sub}.T1.nii --in_type nii -o
${out_dir}/__c1${sub}.T1.mgz --out_type mgz
5) Take mask to brain freesurfer formatted space
mri_vol2vol --mov ${out_dir}/__c1${sub}.T1.mgz --targ
$SUBJECTS_DIR/${sub}_FS/mri/brainmask.mgz --regheader --o
${out_dir}/__c1${sub}.T1.FS.mgz --no-save-reg --nearest
6) Apply the inverse transforms of EPI to Anatomical so that the anatomical
scans and masks are now registered with the EPI scan in native space
(pre-freesurfer file).
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
$SUBJECTS_DIR/${sub}_FS/mri/brain.mgz --o $out_dir/__brain_FS2spm.nii --inv
--no-save-reg --reg $out_dir/${sub}_RS_register.dat
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
$SUBJECTS_DIR/${sub}_FS/mri/aseg.mgz --o $out_dir/__aseg_FS2spm.nii --inv
--reg $out_dir/${sub}_RS_register.dat --interp nearest
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
${out_dir}/__c1${sub}.T1.FS.mgz --o $out_dir/__c1${sub}.T1.FS2spm.nii --inv
--no-save-reg --reg $out_dir/${sub}_RS_register.dat --interp nearest
The steps above work great when the T1, generated masks and EPI were all
acquired plumb (no oblique angle). I tried using the steps for when the T1
(10.144 deg from plumb) and EPI (12.44 deg from plumb) were taken at 2
different oblique angles and the images did not register correctly when
going back to native space. I essentially would not be able to apply the
inverse register.dat directly to the aseg and mask files because when I did
they did not look oriented correctly in afni (I did also try 3dWarp
-deoblique on the resulting freesurfer files but this did not work for the
oblique images).
I wanted to see if I created two registration.dat files (One for EPI to
Freesurfer's brain.mgz and another for the masks to Freesurfers brain.mgz)
and combine these transforms into one file which I can pass to the native
space images via commands in 6) so that they transforms are correct. OR am
I wrong and there is a simpler way to achieve this. Please specify the
commands to use in either case.
Thanks,
Ajay
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[Freesurfer] bbregister and AFNI
Hi all,
I used freesurfer to process my anatomical scans, followed by BBregister
to align my resting state scan to the anatomical and finally afni to
process the resting state fmri scans. After recon-all I used bbregister:
*bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg $sub_RS_register.dat
--init-header --bold --frame $LAST --nearest --template-out
$sub.RS.template.nii*
I used the following for manual adjustments (although none were needed!)
*tkregister2 --mov $sub.RS.template.nii --reg $sub_RS_register.dat --surf*
The plan is to apply the reg file to the entire resting state timeseries
($sub.RS.nii).
My question is the following:
1) Does bbregister already move the last timepoint in $sub.RS.nii as well
as $sub.RS.template.nii or does it just store the rigid transformation in
the reg file (this is what I assume)? This is the reason I assume we
supply reg into tkregister2 as I assume the transform is not applied to the
nifti file header itself.
2) Assuming the transformations are not applied to the file itself, how
would I go about doing this? I used the following based on previous posts:
*mri_vol2vol --mov $sub.RS.nii --reg $sub_RS_register.dat --fstarg --interp
nearest --o $sub.RS.align.nii --precision short --no-resample *
I used no-resample as I do not want to put the data into orig space. The
plan is to align all of my timepoints to the last time point (same as
$sub.RS.template.nii).
Is --fstarg the best option (default orig.mgz vs --fstarg rawavg.mgz)?
Is the transform stored in the header of $sub.RS.align.nii and not in
the $sub.RS.template.nii file or $sub.RS.nii?
3) Using @SUMA_Make_Spec_FS did not correctly convert brain.mgz and
aseg.mgz correctly when overlaid with the original $sub.SPGR.FS.mgz as well
as $sub.RS.align.nii or $sub.RS.nii so I just used the following instead
/mri directory:
*mri_convert -ot nii brain.mgz brain.nii*
*mri_convert -ot nii aseg.mgz aseg.nii*
*4) Following relates to viewing images created in AFNI correctly if anyone
knows: *
When I tried to use AFNI to view the original anatomical scan
$sub.SPGR.FS.mgz and $sub.RS.align.nii it was not aligned (assume
anatomical is similar to rawavg.mgz).
When I load brain.nii and $sub.RS.align.nii into afni they are not
overlapped perfectly as in tkregister2. Additionally I get an error about
deobliquing the $sub.RS.align.nii file. Interestingly enough I do not get
this error with the $sub.RS.template.nii so I am not sure if there is an
error in applying the transform or if the template file has no transform
info stored while the aligned file does. How would I apply the reg file to
all timepoints without getting the oblique error or should I use the
following command and is this correct:
*3dWarp -deoblique -gridset $sub.RS.nii -prefix $sub.RS.align.deobl.nii
$sub.RS.align.nii*
Would i deoblique using the gridset of the original $sub.RS.nii, the
aligned file $sub.RS.align.nii or just the template file (or does it not
matter since the voxel dimensions are the same even though centers are
different).
Sorry for the long email but thanks in advance for any advice /
explanations.
Sincerely,
Ajay
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