[Freesurfer] Postdoctoral position
External Email - Use Caution Hi. We are looking for a postdoc to work with us on multimodal MRI and machine learning to predict Parkinson's disease dementia. An ideal candidate should be well versed and understand multi-shell diffusion MRI analysis and processing and have an interest in developing models for fusing across different MRI and non MRI modalities via deep learning or machine learning models. Contact me directly for more information or Apply here https://secure-web.cisco.com/1esZWcZk9kteVZxe-rcxz8vEdu1K9larHO-dBsWZn3e4QKm_OXqiJRkPp5BpGX8bti_JWaHuEV_p7UKGRkAywm4aRBGgoA0eb4b-1atL-nR0sQXBVWMTwYw4LHIWDmHM3-1UD1deDYH5xUteOzEj0nppvnTKGAC7UHUy3gS67IxOhBCln7OGLcn9TNnE1RFRtMjvZHFNy86WF9rZ2xPzbblkQZ0ubYDtwHSGYygn2P2ubzyFOmS3-YMGvIZpkAdHeSrk17uA-Yllooh1pjzv1tw/https%3A%2F%2Ft.co%2FEnVgKWQqRh Apologies for cross posting. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CNR of each surface
External Email - Use Caution Thank you, Drs. Fischl and Greve. I was able to compute the surface CNR following your suggestion. Regards --VM On Wed, Apr 3, 2019 at 3:25 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > or you can do it in matlab with read_annotation.m > You can read in the mgh file with MRIread.m > Make sure to account for the fact that the annotation vertices will be > 0-based and matlab is 1-based > > On 4/3/19 6:15 PM, Bruce Fischl wrote: > > actually, if you convert the aparc annotations to a bunch of labels, > > you can run: > > > > mri_cnr -label ... > > > > and it will limit the calculations to that label. FOr example: > > > > mri_cnr -label ~/links/subjects/bruce.dev//label/lh.cortex.label > > ~/links/subjects/bruce.dev//label/rh.cortex.label > > ~/links/subjects/bruce.dev/surf ~/links/subjects/bruce.dev/mri/norm.mgz > > reading lh and rh labels from > > /homes/4/fischl/links/subjects/bruce.dev//label/lh.cortex.label and > > /homes/4/fischl/links/subjects/bruce.dev//label/rh.cortex.label > > processing MRI volume > > /homes/4/fischl/links/subjects/bruce.dev/mri/norm.mgz... > > white = 91.0+-9.7, gray = 57.8+-20.2, csf = 33.6+-15.4 > > gray/white CNR = 2.204, gray/csf CNR = 0.910 > > lh CNR = 1.557 > > white = 90.4+-10.0, gray = 57.6+-19.7, csf = 34.6+-15.2 > > gray/white CNR = 2.196, gray/csf CNR = 0.851 > > rh CNR = 1.523 > > total CNR = 1.540 > > > > > > cheers > > Bruce > > > > On Wed, 3 Apr 2019, neuroimage analyst wrote: > > > >> > >> External Email - Use Caution > >> > >> Thanks, Dr. Greve. Where can I find the correspondence between the > >> vertices in ?h.w-g.pct.mgh and > >> the parcellations? > >> > >> On Wed, Apr 3, 2019 at 2:41 PM Greve, Douglas N.,Ph.D. > >> wrote: > >> you can get the contrast from surf/?h.w-g.pct.mgh, which you > >> can average > >> over each parcellation. Not sure where you would get the noise > >> term from. > >> > >> On 4/3/19 5:23 PM, neuroimage analyst wrote: > >> > > >> > External Email - Use Caution > >> > > >> > I apologize, Dr. Fischl, that I wasnt clear. > >> > > >> > We are using Desikan-Killany atlas that has 68 surfaces > >> defined on the > >> > atlas, 34 on each hemisphere. > >> > > >> > I might be wrong, but I was thinking that there should be a > >> way to > >> > define CNR of orbitofrontal cortex (OFC), for example. I know > >> that we > >> > can get CNR of the whole brain gray/white/CSF but is it > >> possible to > >> > get the gray/white/CSF CNR of OFC only? If no, then we report > >> the > >> > difference in cortical thickness as we observe. If yes, we > >> want to > >> > regress or potentially discard the worst CNR subjects and > >> recompute > >> > the statistics. the hope is we can get 68 CNRs for each > >> surface in the > >> > Desikan-Killany atlas.--Kindly let me know your suggestions > >> and thoughts. > >> > > >> > Thanks > >> > > >> > On Wed, Apr 3, 2019 at 2:11 PM Bruce Fischl > >> > >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > >> > > >> > can you clarify what you mean? What 68 surfaces do you > >> mean? And > >> > what do > >> > you mean by CNR of a surface? > >> > On Wed, 3 Apr 2019, neuroimage analyst wrote: > >> > > >> > > > >> > > External Email - Use Caution > >> > > > >> > > Hi, > >> > > We were interested in measuring CNR of each of the 68 > >> surfaces > >> > in Desikan-Killany atlas and compare > >> > > between the groups to verify if our results are being > >> biased by > >> > CNRs in the group? > >> > > > >> > > I came across mri_cnr and mris_ms_surface_cnr binaries > >> in the > >> > FreeSurfer tools and were wondering > >> > > how to loop it through each subject in the
Re: [Freesurfer] CNR of each surface
External Email - Use Caution Thanks, Dr. Greve. Where can I find the correspondence between the vertices in ?h.w-g.pct.mgh and the parcellations? On Wed, Apr 3, 2019 at 2:41 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > you can get the contrast from surf/?h.w-g.pct.mgh, which you can average > over each parcellation. Not sure where you would get the noise term from. > > On 4/3/19 5:23 PM, neuroimage analyst wrote: > > > > External Email - Use Caution > > > > I apologize, Dr. Fischl, that I wasnt clear. > > > > We are using Desikan-Killany atlas that has 68 surfaces defined on the > > atlas, 34 on each hemisphere. > > > > I might be wrong, but I was thinking that there should be a way to > > define CNR of orbitofrontal cortex (OFC), for example. I know that we > > can get CNR of the whole brain gray/white/CSF but is it possible to > > get the gray/white/CSF CNR of OFC only? If no, then we report the > > difference in cortical thickness as we observe. If yes, we want to > > regress or potentially discard the worst CNR subjects and recompute > > the statistics. the hope is we can get 68 CNRs for each surface in the > > Desikan-Killany atlas.--Kindly let me know your suggestions and thoughts. > > > > Thanks > > > > On Wed, Apr 3, 2019 at 2:11 PM Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > can you clarify what you mean? What 68 surfaces do you mean? And > > what do > > you mean by CNR of a surface? > > On Wed, 3 Apr 2019, neuroimage analyst wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi, > > > We were interested in measuring CNR of each of the 68 surfaces > > in Desikan-Killany atlas and compare > > > between the groups to verify if our results are being biased by > > CNRs in the group? > > > > > > I came across mri_cnr and mris_ms_surface_cnr binaries in the > > FreeSurfer tools and were wondering > > > how to loop it through each subject in the subject_list.txt file > > (each column in subject_list.txt is > > > the subject id) so that we get a text file (similar to ?cortical > > thickness txt file generated using > > > aparcstats2table) that has # of subjects * # of regions txt file > > and the entries within each matrix > > > cell is the CNR value corresponding to surface X of Subject Y. > > > > > > We will greatly appreciate any help or pointers regarding this. > > > > > > Thanks > > > > > > Regards > > > > > > --VM > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CNR of each surface
External Email - Use Caution I apologize, Dr. Fischl, that I wasnt clear. We are using Desikan-Killany atlas that has 68 surfaces defined on the atlas, 34 on each hemisphere. I might be wrong, but I was thinking that there should be a way to define CNR of orbitofrontal cortex (OFC), for example. I know that we can get CNR of the whole brain gray/white/CSF but is it possible to get the gray/white/CSF CNR of OFC only? If no, then we report the difference in cortical thickness as we observe. If yes, we want to regress or potentially discard the worst CNR subjects and recompute the statistics. the hope is we can get 68 CNRs for each surface in the Desikan-Killany atlas.--Kindly let me know your suggestions and thoughts. Thanks On Wed, Apr 3, 2019 at 2:11 PM Bruce Fischl wrote: > can you clarify what you mean? What 68 surfaces do you mean? And what do > you mean by CNR of a surface? > On Wed, 3 Apr 2019, neuroimage analyst wrote: > > > > > External Email - Use Caution > > > > Hi, > > We were interested in measuring CNR of each of the 68 surfaces in > Desikan-Killany atlas and compare > > between the groups to verify if our results are being biased by CNRs in > the group? > > > > I came across mri_cnr and mris_ms_surface_cnr binaries in the > FreeSurfer tools and were wondering > > how to loop it through each subject in the subject_list.txt file (each > column in subject_list.txt is > > the subject id) so that we get a text file (similar to ?cortical > thickness txt file generated using > > aparcstats2table) that has # of subjects * # of regions txt file and the > entries within each matrix > > cell is the CNR value corresponding to surface X of Subject Y. > > > > We will greatly appreciate any help or pointers regarding this. > > > > Thanks > > > > Regards > > > > --VM > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] CNR of each surface
External Email - Use Caution Hi, We were interested in measuring CNR of each of the 68 surfaces in Desikan-Killany atlas and compare between the groups to verify if our results are being biased by CNRs in the group? I came across mri_cnr and mris_ms_surface_cnr binaries in the FreeSurfer tools and were wondering how to loop it through each subject in the subject_list.txt file (each column in subject_list.txt is the subject id) so that we get a text file (similar to ?cortical thickness txt file generated using aparcstats2table) that has # of subjects * # of regions txt file and the entries within each matrix cell is the CNR value corresponding to surface X of Subject Y. We will greatly appreciate any help or pointers regarding this. Thanks Regards --VM ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal freesurfer
Hi, We are currently doing longitudinal FreeSurfer analysis on subjects some of whom are scanned over a period of 6 years. There were 2 groups. One was the control group and the other was mTBI group. The hypothesis was the control group would have a fairly stable cortical and sub-cortical volume (<1% change over time) while mTBI group would have a decreasing volume. Both the groups are relatively young (most participants between 22-30 years old). Unfortunately, we only have 7 controls that were scanned for over 3 years. What we have observed is there is no pattern in change in volume neither for controls nor for mTBI; with volume increasing from baseline to year1 and then decreasing and then for some increasing again. The delineation looks ok to us. There are a lot of subjects ~120 and hence manual delineation on every subject is not practical. The question is what is the expected measurement variance due to the longitudinal algorithm for healthy controls over time in both cortical and subcortical volumes? Since the effect that we were expecting to see is around 4% in mTBI participants and the delineation too looks okay then what is the best procedure to correct these? OR should we use cross-sectional data for our analysis? We have used longitudinal freesurfer v6 on a centos. I look forward to your thoughts. Thanks Regards Virendra ___ 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] Cuda 8, Centos 7, FreeSurfer 6
Hello. We recently installed Centos 7 with cuda 8 and tried to build the FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so. Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing to share the binaries with us or share their steps with us? We will greatly appreciate that. Thanks Regards V ___ 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
Thank you, Anderson. Regards. VM On Thu, Feb 2, 2017 at 11:06 PM, Anderson M. Winkler <wink...@fmrib.ox.ac.uk > wrote: > Hi VM, > > They can stay all in the same .csv file. The "fwep" files will have > p-values corrected across all columns of this input. > > All the best, > > Anderson > > > On 2 February 2017 at 12:09, neuroimage analyst < > neuroimage.anal...@gmail.com> wrote: > >> Thanks, Anderson. If there are several other measures such as volume, >> thickness, FA, can I then put them in a single csv file and run the >> command or I have to create 3 csv files, one each for volume, thickness,and >> FA and also invoke -corrmod? >> >> Thanks >> >> Regards >> VM >> >> On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" <wink...@fmrib.ox.ac.uk> >> wrote: >> >> Hi VM, >> >> Please see below: >> >> >> On 1 February 2017 at 02:38, neuroimage analyst < >> neuroimage.anal...@gmail.com> wrote: >> >>> Hi, >>> >>> We extracted volume measures from 7 ROIs in 2 groups and compared >>> a) Mean of each ROI volume between group, and compared independently >>> such as >>> i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 >>> ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 >>> and so on >>> >> >> This means 7 comparisons, or 14 if you test both directions (tails) >> separately. >> >> >>> >>> b) Plotted the mean ROI volume for 2 independent measures and compared >>> whether the slope between and within group is significantly different. such >>> as >>> i) Slope of ROI1 is positively associated with MoCA , age (grp1) ? >>> ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ? >>> iii) Slope of ROI1 vs MoCA (grp1) is significantly different >>> than slope of ROI1 vs MoCA (grp2) ? >>> iv) Slope of ROI1 vs MoCA (grp2) is significantly different >>> than slope of ROI2 vs MoCA (grp2) ? >>> >> >> These sound tests for main effects and interaction, with various >> combinations possible. >> >> >>> >>> Q1) Do we have to perform multiple comparisons for (a) and (b)? >>> >> >> Yes. >> >> >> >>> Q2) If yes, do we correct across 7 measurements for (a) and 2 >>> measurements for (b) or 7 measurements for both (a) and (b)? >>> >> >> You could put the values for the 7 ROIs in a table in .csv format, with >> one column per ROI and one row per subject. This would be the input data. >> Create a design matrix as: >> >> EV1: 0 or 1 coding for group 1 >> EV2: 0 or 1 coding for group 2 >> EV3: MoCA group 1 >> EV4: MoCA group 2 >> EV5: Age group 1 >> EV6: Age group 2 >> etc >> >> Then define a set of contrasts such as: >> >> C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2 >> C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2 >> C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 > >> slope for MoCA for group 2 >> C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 < >> slope for MoCA for group 2 >> C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0 >> C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0 >> etc >> >> You'd run this analysis in PALM with something as: >> >> *palm -i input.csv -d design.mat -t design.con -corrcon -o myresults >> -logp* >> >> >> Hope this helps! >> >> All the best, >> >> Anderson >> >> >> >>> There is evidence to both performing and nonperforming multiple >>> comparisons In the literature. >>> >>> Any response (hopefully pointing to a literature) will be greatly >>> appreciated. >>> >>> Thanks >>> >>> Regards >>> >>> --VM >>> >>> ___ >>> 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 >
[Freesurfer] Multiple comparison question
Hi, We extracted volume measures from 7 ROIs in 2 groups and compared a) Mean of each ROI volume between group, and compared independently such as i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 and so on b) Plotted the mean ROI volume for 2 independent measures and compared whether the slope between and within group is significantly different. such as i) Slope of ROI1 is positively associated with MoCA , age (grp1) ? ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ? iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of ROI1 vs MoCA (grp2) ? iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of ROI2 vs MoCA (grp2) ? Q1) Do we have to perform multiple comparisons for (a) and (b)? Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements for (b) or 7 measurements for both (a) and (b)? There is evidence to both performing and nonperforming multiple comparisons In the literature. Any response (hopefully pointing to a literature) will be greatly appreciated. Thanks Regards --VM ___ 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
Thanks, Anderson. If there are several other measures such as volume, thickness, FA, can I then put them in a single csv file and run the command or I have to create 3 csv files, one each for volume, thickness,and FA and also invoke -corrmod? Thanks Regards VM On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" <wink...@fmrib.ox.ac.uk> wrote: Hi VM, Please see below: On 1 February 2017 at 02:38, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > We extracted volume measures from 7 ROIs in 2 groups and compared > a) Mean of each ROI volume between group, and compared independently such > as > i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2 > ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2 > and so on > This means 7 comparisons, or 14 if you test both directions (tails) separately. > > b) Plotted the mean ROI volume for 2 independent measures and compared > whether the slope between and within group is significantly different. such > as > i) Slope of ROI1 is positively associated with MoCA , age (grp1) ? > ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ? > iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of > ROI1 vs MoCA (grp2) ? > iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of > ROI2 vs MoCA (grp2) ? > These sound tests for main effects and interaction, with various combinations possible. > > Q1) Do we have to perform multiple comparisons for (a) and (b)? > Yes. > Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements > for (b) or 7 measurements for both (a) and (b)? > You could put the values for the 7 ROIs in a table in .csv format, with one column per ROI and one row per subject. This would be the input data. Create a design matrix as: EV1: 0 or 1 coding for group 1 EV2: 0 or 1 coding for group 2 EV3: MoCA group 1 EV4: MoCA group 2 EV5: Age group 1 EV6: Age group 2 etc Then define a set of contrasts such as: C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2 C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2 C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 > slope for MoCA for group 2 C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 < slope for MoCA for group 2 C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0 C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0 etc You'd run this analysis in PALM with something as: *palm -i input.csv -d design.mat -t design.con -corrcon -o myresults -logp* Hope this helps! All the best, Anderson > There is evidence to both performing and nonperforming multiple > comparisons In the literature. > > Any response (hopefully pointing to a literature) will be greatly > appreciated. > > Thanks > > Regards > > --VM > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Multiple comparison correction on subcortical volume
Hi, I extracted thalamic, caudate, and putamen volume (left hemisphere), and cingulate thickness (right hemisphere) from freesurfer's parcellation. Then I compare these volumes and thickness across two groups using R and found significant differences in these measurements. Do I have to correct for multiple comparisons? If yes, how do I do that? Does this make sense to divide the p-value/4 and if the p-value < p-value/4 then the test is Bonferroni corrected? If no, what do I say in my results that the test statistic is not inflated? Thanks Regards --VM ___ 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] cortical label mask fro mri_glmfit
Ah, I see! thank you-- Regards --VM On Thu, Dec 22, 2016 at 11:42 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > It may change with the data set. Eg, in fMRI, the top of the head my be > cut off in one subject and so the top of the head will be out of the > mask. Also, there my be some differences in the definition of the medial > wall across subjects. This does not change with contrast. > > > On 12/22/2016 02:40 PM, neuroimage analyst wrote: > > Thanks, Doug for that quick response! > > > > Does mask.mgh varies between different set of subjects and (or) > > different set of contrasts for a given hemisphere? Since fsavearge > > doesnt change, the mask that is used for statistical comparisons > > should change neither unless I change --trgsubject to some other. Am i > > right? > > > > thanks > > > > regards > > > > VM > > > > On Thu, Dec 22, 2016 at 11:32 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > On 12/22/2016 01:33 PM, neuroimage analyst wrote: > > > Hi, > > > > > > I am just curious whether the mask.mgh file returned in glmdir > > folder > > > created from lh.cortex.label? > > In part. It will also include any voxels that have 0 values in any of > > the inputs (--y) > > > > > > If so, how can I create my own surface mask from the label file? > > > (mri_label2vol and mri_vol2surf ?) > > mri_label2label with the --mask option > > > > > > > > > Second: How can I compare the subcortical volumes between the 2 > > groups > > > using glm tools in freesurfer? Specifically, how do I call > > > mris_preproc and mri_glmfit? > > Run asegstats2table to create a table, then run mri_glmfit as > > before but > > with --table instead of --y > > > > > > I appreciate your response. > > > > > > Thank you > > > > > > Regards > > > > > > --VM > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <http://www.partners.org/complianceline> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu >
Re: [Freesurfer] cortical label mask fro mri_glmfit
Thanks, Doug for that quick response! Does mask.mgh varies between different set of subjects and (or) different set of contrasts for a given hemisphere? Since fsavearge doesnt change, the mask that is used for statistical comparisons should change neither unless I change --trgsubject to some other. Am i right? thanks regards VM On Thu, Dec 22, 2016 at 11:32 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > > On 12/22/2016 01:33 PM, neuroimage analyst wrote: > > Hi, > > > > I am just curious whether the mask.mgh file returned in glmdir folder > > created from lh.cortex.label? > In part. It will also include any voxels that have 0 values in any of > the inputs (--y) > > > > If so, how can I create my own surface mask from the label file? > > (mri_label2vol and mri_vol2surf ?) > mri_label2label with the --mask option > > > > > > Second: How can I compare the subcortical volumes between the 2 groups > > using glm tools in freesurfer? Specifically, how do I call > > mris_preproc and mri_glmfit? > Run asegstats2table to create a table, then run mri_glmfit as before but > with --table instead of --y > > > > I appreciate your response. > > > > Thank you > > > > Regards > > > > --VM > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cortical label mask fro mri_glmfit
Hi, I am just curious whether the mask.mgh file returned in glmdir folder created from lh.cortex.label? If so, how can I create my own surface mask from the label file? (mri_label2vol and mri_vol2surf ?) Second: How can I compare the subcortical volumes between the 2 groups using glm tools in freesurfer? Specifically, how do I call mris_preproc and mri_glmfit? I appreciate your response. Thank you Regards --VM ___ 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] Fwd: Registering ASL-CBF maps to fsaverage
Thank you! Regards --VM On Wed, Dec 21, 2016 at 10:41 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > > On 12/21/2016 01:02 PM, neuroimage analyst wrote: > > Hi, Doug. > > > > Thank you for your response. > > > > _Step 1: _I think what I want to really do is perform group analysis > > on my CBF maps that are mapped to cortex after smoothing 10mm . In > > such a scenario, I have to map the CBF to fsavearge to bring all the > > subjects in the same space and then smooth them and perform statistics. > > I think to do this I will do: > > > > *a) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg > > mean_asl_to_fs_T1 --bold --init-fsl * > > *b) mri_vol2vol --mov perfusion_calib.nii.gz --targ > > T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz > > --reg register.dat --no-save-reg* > > *c) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --trgsubject > > fsaverage --regheader T1_data/ --hemi lh --projfrac 0.5 --interp > > trilinear --o perfusion_CBF_to_T1_surf_lh.mgh --reg register.dat > > --noreshape --cortex * > > *d) mris_fwhm --s fsaverage --hemi lh --fwhm 10 --smooth-only --i > > perfusion_CBF_to_T1_surf_lh --o > > perfusion_CBF_to_T1_surf_lh_smooth_10mm --cortex * > > > I would not include the vol2vol. It will needlessly introduce another > interpolation. You can just used vol2surf and go straight from the CBF > space. > > > > _Step 2: _Once and if I want any cluster that are different then I > > want to use the same cluster and extract the CBF maps in the native > > space of each subject. Here, I have to use mri_surfcluster and > > mri_segstats. But, I am not sure what to pass here. *.ocn* file has > > the values in the cluster but my guess is they are in the fsaverage > > space. How do I get these values in the native space? > If you want to make stats based on the cluster, I would not go back to > native space. There will be a dat file that comes out of the clustering > with the values for each subject (rows) and cluster (cols). > > > > I will again appreciate your response as to whether my steps are right? > > > > Thanks > > > > Regards > > > > --VM > > > > On Wed, Dec 21, 2016 at 7:49 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Sorry for the delay > > > > > > On 12/21/16 12:15 AM, neuroimage analyst wrote: > >> Hi, > >> > >> I am attaching this message again and I wI'll appreciate if > >> somebody could kindly comment on the approach. > >> > >> Thanks > >> > >> Regards > >> > >> -VM > >> > >> -- Forwarded message -- > >> From: "neuroimage analyst" <neuroimage.anal...@gmail.com > >> <mailto:neuroimage.anal...@gmail.com>> > >> Date: Dec 18, 2016 2:22 PM > >> Subject: Registering ASL-CBF maps to fsaverage > >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu>> > >> Cc: > >> > >> Hi, all. > >> > >> I want to register CBF maps derived using pCASL to > >> freesurfer's surface and derive CBF values in the same > >> regions where I report my cortical thickness, and volumes. > >> Hence, I did the following: > >> 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz > >> --reg mean_asl_to_fs_T1 --bold --init-fsl > >> > >> asldata_mc_even_brain is the mean of the control images > >> > >> 2) mri_vol2vol --mov perfusion_calib.nii.gz --targ > >> T1_data/mri/T1.mgz --interp nearest --o > >> perfusion_CBF_to_T1.nii.gz --reg register.dat --no-save-reg > >> > >> where perfusion_calib is the CBF map in the same space > >> asldata_mc_even_brain. > >> > >> 3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref > >> orig.mgz --regheader T1_data/ --hemi lh --projfrac 0.5 > >> --interp trilinear --o perfusion_CBF_to_T1_surf_gray.mgh > >> --reg register.dat --noreshape --cortex --surfreg sphere.reg > >> > >> Step (3) takes the CBF map to cortical ribbon and hopefully > >> now I can run mri_segstats and extract CBF values and > >> thickne
Re: [Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage
Hi, Doug. Thank you for your response. *Step 1: *I think what I want to really do is perform group analysis on my CBF maps that are mapped to cortex after smoothing 10mm . In such a scenario, I have to map the CBF to fsavearge to bring all the subjects in the same space and then smooth them and perform statistics. I think to do this I will do: *a) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold --init-fsl * *b) mri_vol2vol --mov perfusion_calib.nii.gz --targ T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz --reg register.dat --no-save-reg* *c) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --trgsubject fsaverage --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o perfusion_CBF_to_T1_surf_lh.mgh --reg register.dat --noreshape --cortex * *d) mris_fwhm --s fsaverage --hemi lh --fwhm 10 --smooth-only --i perfusion_CBF_to_T1_surf_lh --o perfusion_CBF_to_T1_surf_lh_smooth_10mm --cortex * *Step 2: *Once and if I want any cluster that are different then I want to use the same cluster and extract the CBF maps in the native space of each subject. Here, I have to use mri_surfcluster and mri_segstats. But, I am not sure what to pass here. *.ocn* file has the values in the cluster but my guess is they are in the fsaverage space. How do I get these values in the native space? I will again appreciate your response as to whether my steps are right? Thanks Regards --VM On Wed, Dec 21, 2016 at 7:49 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Sorry for the delay > > On 12/21/16 12:15 AM, neuroimage analyst wrote: > > Hi, > > I am attaching this message again and I wI'll appreciate if somebody could > kindly comment on the approach. > > Thanks > > Regards > > -VM > > -- Forwarded message -- > From: "neuroimage analyst" <neuroimage.anal...@gmail.com> > Date: Dec 18, 2016 2:22 PM > Subject: Registering ASL-CBF maps to fsaverage > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: > > Hi, all. > > I want to register CBF maps derived using pCASL to freesurfer's surface > and derive CBF values in the same regions where I report my cortical > thickness, and volumes. Hence, I did the following: > 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg > mean_asl_to_fs_T1 --bold --init-fsl > > asldata_mc_even_brain is the mean of the control images > > 2) mri_vol2vol --mov perfusion_calib.nii.gz --targ T1_data/mri/T1.mgz > --interp nearest --o perfusion_CBF_to_T1.nii.gz --reg register.dat > --no-save-reg > > where perfusion_calib is the CBF map in the same space > asldata_mc_even_brain. > > 3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref orig.mgz > --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o > perfusion_CBF_to_T1_surf_gray.mgh --reg register.dat --noreshape --cortex > --surfreg sphere.reg > > Step (3) takes the CBF map to cortical ribbon and hopefully now I can run > mri_segstats and extract CBF values and thickness + do a group comparison > using mri_glmfit. In order to do the latter, I have to map the perfusion > maps to fsaverage. Can I then simply set --ref to fsaverage in step 3 or > what is the correct call to take CBF maps to fsaverage in (3) ? > > No, but you can set --trgsubject fsaverage and it will do what you need. > If you want to run mri_segstats to get segmentation statistics, you should > run mri_vol2vol to map the CBF to the native anatomical space, then run > mri_segstats --seg aparc+aesg.mgz --i cbf-in-anat.nii.gz ... This will give > you segstats that are specific to the segmentation of a particular > subject; if you use mri_segstats in fsaverage space, then you lose that > specificity (not sure if it really matters). You can use asegstats2table to > merge the segstats from different subjects together into one file, then use > mri_glmfit --table to get the stats. > > > Second, Do i have to pass --surf argument pial or white in step 3? What is > the correct way to do this? > > No, it will use white by default (which is what you want). You don't need > to set --surfreg either (will use sphere.reg by default) > > > Third, The statistical comparisons on thickness were done using 10 mm > smoothing using -qcache argumentin recon-all.I want to generate several > smoothing of CBF maps (5-25 in steps of 5 mm) In the call to mri_vol2surf > I can set --surf-fwhm 5 and my understanding is it will smooth the output > surface 5 mm. Is that right? or should I call mri_fwhm on the output > returned from step 3. > > You can do it like that. It is a little more computationally efficient to > do them in separate steps, but probably not a big deal unless you have a > lot of data. &g
[Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage
Hi, I am attaching this message again and I wI'll appreciate if somebody could kindly comment on the approach. Thanks Regards -VM -- Forwarded message -- From: "neuroimage analyst" <neuroimage.anal...@gmail.com> Date: Dec 18, 2016 2:22 PM Subject: Registering ASL-CBF maps to fsaverage To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Cc: Hi, all. I want to register CBF maps derived using pCASL to freesurfer's surface and derive CBF values in the same regions where I report my cortical thickness, and volumes. Hence, I did the following: 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold --init-fsl asldata_mc_even_brain is the mean of the control images 2) mri_vol2vol --mov perfusion_calib.nii.gz --targ T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz --reg register.dat --no-save-reg where perfusion_calib is the CBF map in the same space asldata_mc_even_brain. 3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref orig.mgz --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o perfusion_CBF_to_T1_surf_gray.mgh --reg register.dat --noreshape --cortex --surfreg sphere.reg Step (3) takes the CBF map to cortical ribbon and hopefully now I can run mri_segstats and extract CBF values and thickness + do a group comparison using mri_glmfit. In order to do the latter, I have to map the perfusion maps to fsaverage. Can I then simply set --ref to fsaverage in step 3 or what is the correct call to take CBF maps to fsaverage in (3) ? Second, Do i have to pass --surf argument pial or white in step 3? What is the correct way to do this? Third, The statistical comparisons on thickness were done using 10 mm smoothing using -qcache argumentin recon-all.I want to generate several smoothing of CBF maps (5-25 in steps of 5 mm) In the call to mri_vol2surf I can set --surf-fwhm 5 and my understanding is it will smooth the output surface 5 mm. Is that right? or should I call mri_fwhm on the output returned from step 3. Thank you for your suggestions. I will really appreciate your thoughts. Regards -VM ___ 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] Registering ASL-CBF maps to fsaverage
Hi, all. I want to register CBF maps derived using pCASL to freesurfer's surface and derive CBF values in the same regions where I report my cortical thickness, and volumes. Hence, I did the following: 1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold --init-fsl asldata_mc_even_brain is the mean of the control images 2) mri_vol2vol --mov perfusion_calib.nii.gz --targ T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz --reg register.dat --no-save-reg where perfusion_calib is the CBF map in the same space asldata_mc_even_brain. 3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref orig.mgz --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o perfusion_CBF_to_T1_surf_gray.mgh --reg register.dat --noreshape --cortex --surfreg sphere.reg Step (3) takes the CBF map to cortical ribbon and hopefully now I can run mri_segstats and extract CBF values and thickness + do a group comparison using mri_glmfit. In order to do the latter, I have to map the perfusion maps to fsaverage. Can I then simply set --ref to fsaverage in step 3 or what is the correct call to take CBF maps to fsaverage in (3) ? Second, Do i have to pass --surf argument pial or white in step 3? What is the correct way to do this? Third, The statistical comparisons on thickness were done using 10 mm smoothing using -qcache argumentin recon-all.I want to generate several smoothing of CBF maps (5-25 in steps of 5 mm) In the call to mri_vol2surf I can set --surf-fwhm 5 and my understanding is it will smooth the output surface 5 mm. Is that right? or should I call mri_fwhm on the output returned from step 3. Thank you for your suggestions. I will really appreciate your thoughts. Regards -VM ___ 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] Question about mri_glmfit-sim
Thank you, Doug. Regards MV On Fri, Oct 28, 2016 at 8:46 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Using perm will certainly avoid a lot of questions. You should still use > the --2spaces. You changed the threshold from 2.3 to 1.3. This threshold is > arbitrary, you don't necessarily need/want a lower threshold for perm. I've > been doing some experiments lately, and a threshold of 2.3 with >5mm of > smoothing gives about 5-10% false positive rates (when expecting 5%) on > thickness. So it is not nearly as bad as the fMRI results from Eklund. Note > that if your cluster p-value is much less than .05, then you're probably in > good shape. > > On 10/24/16 9:49 PM, neuroimage analyst wrote: > > Hi FreeSurfer experts, > > I am currently performing some cortical thickness comparisons in my group > of subjects and using > mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces > found some clusters that have significantly different cortical thickness > values, > > Given Eklund et al PNAS paper, do you suggest I should rather use > mri_glmfit-sim --glmdir my_dir --sim perm 5000 1.3 perm.pos.13 --sim-sign > pos > > in order to convince that the results are not due to false positive? > > Thanks > > Regards > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Question about mri_glmfit-sim
Hi FreeSurfer experts, I am currently performing some cortical thickness comparisons in my group of subjects and using mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces found some clusters that have significantly different cortical thickness values, Given Eklund et al PNAS paper, do you suggest I should rather use mri_glmfit-sim --glmdir my_dir --sim perm 5000 1.3 perm.pos.13 --sim-sign pos in order to convince that the results are not due to false positive? Thanks Regards ___ 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] Fdr correction using command line
Thank you for that clarification,Doug. VM On Oct 12, 2016 12:09 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > The sign depends on how you set up the contrast. If you are using an > FSGD file and have two classes A and B and a contrast [+1 -1], then > positive indicates A>B. The F.mgh is the map of F values which are > unsigned. The gamma.mgh file will have the contrast values themselves > including sign. The sig.mgh will be the -log10(p) signed by the sign of > gamma.mgh at that vertex > > > On 10/12/2016 02:23 PM, neuroimage analyst wrote: > > Thanks, Doug for the binary. > > > > A quick follow-up: what does the sign in either > > mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are > > only positive and p-values obtained from them has sign of +/-. My > > understanding is + indicates where mean_A>mean_B and vice versa. > > > > If for example, I am interested in mean_A>mean_B then should I pass > > --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected > > cluster defining threshold of p<0.005) in the contrast that was > > designed for that test? > > > > Regards > > > > MV > > > > On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > try this binary > > > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr> > > > > > > > > On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > > > > > Hi, > > > > > > I was wondering if there is a way to perform fdr correction using > > > command line in freesurfer without using matlab as > > mri_glmfit-sim only > > > does bonferroni ? > > > > > > Thanks > > > Regards > > > MV > > > > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <http://www.partners.org/complianceline> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.ed
Re: [Freesurfer] Fdr correction using command line
Thanks, Doug for the binary. A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr indicate? When I open F.mgh, the values are only positive and p-values obtained from them has sign of +/-. My understanding is + indicates where mean_A>mean_B and vice versa. If for example, I am interested in mean_A>mean_B then should I pass --pos (mri_fdr) or --cache 2.30101 pos (mri_glmfit-sim for uncorrected cluster defining threshold of p<0.005) in the contrast that was designed for that test? Regards MV On Wed, Oct 12, 2016 at 10:27 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > try this binary > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr > > > > On 10/07/2016 04:11 PM, neuroimage analyst wrote: > > > > Hi, > > > > I was wondering if there is a way to perform fdr correction using > > command line in freesurfer without using matlab as mri_glmfit-sim only > > does bonferroni ? > > > > Thanks > > Regards > > MV > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Fdr correction using command line
Hi again. I think I can obtain fdr maps by: mri_surfcluster --in sig.mgh --subject fsaverage --hemi lh --annot aparc --sign pos --o fdr_005_lh_pos.mgh --fdr 0.05 --cortex --mask mask.mgh Can anyone comment if the above command is right to generate a clusterwise fdr corrected p<0.05? Thanks Regards MV On Fri, Oct 7, 2016 at 1:11 PM, neuroimage analyst < neuroimage.anal...@gmail.com> wrote: > Hi, > > I was wondering if there is a way to perform fdr correction using command > line in freesurfer without using matlab as mri_glmfit-sim only does > bonferroni ? > > Thanks > Regards > MV > ___ 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] Fdr correction using command line
Hi, I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ? Thanks Regards MV ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical thickness to AAL template
Hello, freesurfer users. Reposting the previous question again here. I would appreciate any response. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the cortical thickness of various ROIs on an atlas (Either the default freesurfer atlas or AAL atlas). 1) How can I map the cortical thickness map to freesurfer template volume so that I can average the cortical thickness in the ROI to build the connectivity matrix? 2) Instead of mapping to freesurfer template, if I have to use AAL atlas can I simply map the cortical thickness map to MNI template and use AAL atlas in MNI template to carry out step (1). If yes, how should I go about doing that? I would appreciate any response. Thanks Regards! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical thickness to volume
Hi, Freesurfer Users. I tried searching for this question on the mailing list but couldn't get an answer. Hence, I am posting this here again. I ran the freesurfer analysis and got cortical thickness map for my group. I want to build an adjacency matrix by finding the correlation between the cortical thickness of various ROIs on an atlas (Either the default freesurfer atlas or AAL atlas). 1) How can I map the cortical thickness map to freesurfer template volume so that I can average the cortical thickness in the ROI to build the connectivity matrix? 2) Instead of mapping to freesurfer template, if I have to use AAL atlas can I simply map the cortical thickness map to MNI template and use AAL atlas in MNI template to carry out step (1). If yes, how should I go about doing that? I would appreciate any response. Thanks Regards! ___ 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.
