[Freesurfer] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
Dear Freesurfer Community, I'm running into the issue of how to deal with testing the interaction effects of a model with multiple categorical variables. I have tried bypassing this issue by running multiple separate FSGD analyses, however, I wonder if this is the best mention to do this To put it into statistical terms, I am interested in creating a model that looks at group differences (2: HC vs Dx), and its interaction with test score (2: High vs Low) while still controlling for nuisance variables (sex, age). in other words: Cortical Thickness ~ Group + Group*Score + Score + Sex + Age Group*Score = interaction term I am mostly confused with how to appropriately create a contrast file that can show the interaction between Group and Score (two categorical variables) and STILL regress out the effects of sex. Is this even possible using fsgd? Thank you in advance! Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
Hello Doug, Thank you for your reply. I misused the word contrast, when I should have said design matrix. It looks at though I should be able to look at an interaction effect between two variables but ignore another. In the case of the example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V you could be able to look at the interaction between Group and Age while ignoring (or controlling) for the effects of weight. But maybe this is not possible to do with a categorical variable? I have also considered using a four group design as shown in https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, where you concatenate two categorical variables however, I dont think you can look at interaction effects between those variables anymore. So I'm still wondering if it is possible to look at the interaction between two categorical variables using fsgd? GroupDescriptorFile 1 #Title SZ vs HC Class HC Class SZ Variables Score Sex Age Input 130 HC high m 50 Input 277 HC low f 53 Input 190 HC low m 25 Input 201 SZ high f 29 Input 250 SZ high f 52 ... Group difference.mtx 1 -1 0 0 0 0 0 0 Group by Score interaction .mtx 0 0 1 -1 0 0 0 0 But this doesn't and should work. How should I proceed? Thanks again, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] Contrast files for a complex ANCOVA (involving multiple categorical covariates) model
Thank you for you help! Yes the contrast 7 in the group 4 example makes complete sense. However, I am still left with not being able to control for the effects of another categorical variable. For example I can look at the interaction of Group X Score, but for this I need to remove the categorical variable sex (M/F): GroupDescriptorFile 1 > #Title SZ vs HC > Class HChigh > Class HClow > Class SZhigh > Class SZlow > Variables Score Age > Input 130 HChigh 50 > Input 277 HClow 53 > Input 190 HClow 25 > Input 201 SZhigh 29 > Input 250 SZhigh 52 > ... > > Group difference.mtx > 0.5 -0.5 -0.5 0.5 0 0 0 0 However, I understand how important it is to control for the effects of sex. Am I better to try 8 groups? GroupDescriptorFile 1 #Title SZ vs HC Class HCmhigh Class HCfhigh Class HCmlow Class HCflow Class SZmhigh Class SZfhigh Class SZmlow Class SZflow Variables Age Input 130 HCmhigh 50 Input 277 HCflow 53 Input 190 HCmlow 25 Input 201 SZfhigh 29 Input 250 SZfhigh 52 ... Group difference.mtx 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 Heres where I am confused: Group by Score interaction.mtx could either be: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 or perhaps? 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 Once again, thank you in advance!! Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] create mask from cluster number?
Hello Freesurfer Developers, The main point of my post is to determine whether its possible to create a mask from a cluster ID run using a subset of the sample, and then use that mask to extract cortical thickness values from a model run with the full sample. I am running a pretty basic cortical thickness- behavioural correlation analysis with two groups using fsgd. Because I have a relatively small sample size (just over 40 participants in each group) I wanted to restrict my analysis to only regions that showed a relationship within the HC group. I ran the model using mri_glmfit: mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx --surf fsaverage rh --cortex --glmdir MCCB.HC.43.rh Behav.fsgd setup: GroupDescriptorFile 1 Title MaineffectofGroup Class HC Variables BehavMC Input 128 HC -5 Input 132 HC 8 Input 192 HC -10 Input 193 HC -6 ... v1.slope.mtx: 0 1 *quick side question - in the past I was curious to see if this could test positive and negative relationships. I tried two different contrasts: 0 1 and 0 -1 to test the positive and negative relationships, respectively, however the results were the direct inverse of each other... it didn't show negative slope relationships. I am curious if its possible to test for negative relationships in freesurfer? How would you set up that contrast? next, I used mri_surfcluster to generate image and table files: mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage --hemi rh --surf pial --annot aparc --thmin 2 --ocn HC.43.rh/v1.slope/results.ocn.mgh --sum HC.43.rh/v1.slope/results.sum.txt my results.sum.txt file shows a number of clusters ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs Annot 13.719 163035270.33 57.7 -34.6 -21.5 234 inferiortemporal 23.499 22608217.35 33.2 -48.2 -15.1 230 fusiform 33.1702804 93.01 42.1 22.1 23.9 132 rostralmiddlefrontal Would it be possible to create a mask defined by say "ClusterNo 1"? Once the mask is created, I want to use it to extract the cortical thickness values for all participants (including those that weren't used to create the mask).. Is this possible? Can that be done using mri_segstats? Let me know if you require any other details. Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you in advance, Lindsay ___ 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 error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com g4v1.73.fsgd Description: Binary data SZ-HC.intercept.73.mtx Description: Binary data ___ 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] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Hello, Has anyone had a chance to look at this? I still haven't been able to solve the problem. Thanks! Lindsay On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford wrote: > Hello Freesurfer Experts! > > I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned > or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve > this problem from other inquiries, however, I still have had no luck. I am > trying to run a 4 group 1 variable analysis: with diagnosis being my > variable of interest and trying to regress out the effects of sex and age. > > 1. Command line: > mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C > SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh > 2. The FSGD file (if using one) (see attached) > 3. And the design matrix: >0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) > > To the best of my knowledge, all my files are the right format and I > believe I have adequate number of participants per group? > I also tried mean centering my age variable. I had success when I ran just > a two group analysis (diagnosis) not controlling for sex or age, however, > as soon as I try to run four groups, I encounter this error. I have no idea > how to proceed. > > I am looking forward to your response! > Thanks, > > > Lindsay > > -- > Lindsay Hanford, BSc, PhD Candidate > McMaster Integrative Neuroscience Discovery & Study | *Department of > Psychology, Neuroscience & Behaviour * > McMaster University *|* 1280 Main Street West, PC329 Psychology Building > *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com > ___ 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] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford wrote: > > Hello, > > Has anyone had a chance to look at this? I still haven't been able to > solve the problem. > Thanks! > > Lindsay > > On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford > wrote: > >> Hello Freesurfer Experts! >> >> I am encountering the dreaded mri_glmfit error: matrix is >> ill-conditioned or badly scaled, condno = 1e+08. I have tried to >> troubleshoot how to solve this problem from other inquiries, however, I >> still have had no luck. I am trying to run a 4 group 1 variable analysis: >> with diagnosis being my variable of interest and trying to regress out the >> effects of sex and age. >> >> 1. Command line: >> mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C >> SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh >> 2. The FSGD file (if using one) (see attached) >> 3. And the design matrix: >>0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) >> >> To the best of my knowledge, all my files are the right format and I >> believe I have adequate number of participants per group? >> I also tried mean centering my age variable. I had success when I ran >> just a two group analysis (diagnosis) not controlling for sex or age, >> however, as soon as I try to run four groups, I encounter this error. I >> have no idea how to proceed. >> >> I am looking forward to your response! >> Thanks, >> >> >> Lindsay >> >> -- >> Lindsay Hanford, BSc, PhD Candidate >> McMaster Integrative Neuroscience Discovery & Study | *Department of >> Psychology, Neuroscience & Behaviour * >> McMaster University *|* 1280 Main Street West, PC329 Psychology Building >> *|* Hamilton, ON, L8S 4L8 >> 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com >> > > -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
Thank you Doug! I replaced all my spaces with new spaces and it worked! Much appreciated! Lindsay On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford wrote: > > Hi Doug! > > Thank you very much for your reply. I made the fsgd file in a plain-text > file using the textedit program on a Mac and when that didn't work I tried > modifying in the terminal window using: nano -w g4v1.73.fsgd. > This also didn't solve the problem. I am not sure what to try next. > > Lindsay > > On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford < > lindsay.hanf...@gmail.com> wrote: >> >> Hello, >> >> Has anyone had a chance to look at this? I still haven't been able to >> solve the problem. >> Thanks! >> >> Lindsay >> >> On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford < >> lindsay.hanf...@gmail.com> wrote: >> >>> Hello Freesurfer Experts! >>> >>> I am encountering the dreaded mri_glmfit error: matrix is >>> ill-conditioned or badly scaled, condno = 1e+08. I have tried to >>> troubleshoot how to solve this problem from other inquiries, however, I >>> still have had no luck. I am trying to run a 4 group 1 variable analysis: >>> with diagnosis being my variable of interest and trying to regress out the >>> effects of sex and age. >>> >>> 1. Command line: >>> mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C >>> SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh >>> 2. The FSGD file (if using one) (see attached) >>> 3. And the design matrix: >>>0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) >>> >>> To the best of my knowledge, all my files are the right format and I >>> believe I have adequate number of participants per group? >>> I also tried mean centering my age variable. I had success when I ran >>> just a two group analysis (diagnosis) not controlling for sex or age, >>> however, as soon as I try to run four groups, I encounter this error. I >>> have no idea how to proceed. >>> >>> I am looking forward to your response! >>> Thanks, >>> >>> >>> Lindsay >>> >>> -- >>> Lindsay Hanford, BSc, PhD Candidate >>> McMaster Integrative Neuroscience Discovery & Study | *Department of >>> Psychology, Neuroscience & Behaviour * >>> McMaster University *|* 1280 Main Street West, PC329 Psychology >>> Building *|* Hamilton, ON, L8S 4L8 >>> 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com >>> >> >> > > -- > Lindsay Hanford, BSc, PhD Candidate > McMaster Integrative Neuroscience Discovery & Study | *Department of > Psychology, Neuroscience & Behaviour * > McMaster University *|* 1280 Main Street West, PC329 Psychology Building > *|* Hamilton, ON, L8S 4L8 > 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com > -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com ___ 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] Extract individual vertex thickness values from cortical parcellations
External Email - Use Caution Hello Freesurfer Community, I am looking for a way to extract thickness values at the level of each vertex from Freesurfer atlas-based parcellated regions (aparc.annot), or more generally lobes. Is this possible? Using mri_segstats I know it is possible to get more general metrics such as min, max and average thickness values, and # of voxels. Is it possible to use an annot file to read out the raw thickness values? This post was the closest I could find to answering my question, however, this was at the group level and not specified for parcellated regions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html Thank you in advance, Lindsay -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] using tkregister2 to check registration to custom atlas
External Email - Use Caution Hello Freesurfer Community, I am interested in seeing how well my subject scan registered to a custom atlas after being run through recon-all. From Freesurfer Wiki, although it is possible to see this in freeview, tkregister2 seems to be the best method as manual edits can be made if the registration went badly. I am however running into issues trying to load the subject image, atlas image, and surfaces in the same space. If I understand correctly, when I ran my recon-all specifying a custom atlas (-custom-tal-atlas RLB700_atlas_as_orig) the transform files (talairach.xfm) are to the custom atlas rather than the talairach atlas. If I load: tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs the subject scan, talairach atlas and surfaces load just fine. It is clear the talairach atlas was not used. I have tried running multiple variations of the following, and in all cases, the atlas is in a different space. tkregister2 --mov RLB700.nii.gz --s 180523_HTP02168_ANAT5_init2base --regheader --reg 180523_HTP02168_ANAT5_init2base/mri/transforms/talairach.xfm --surfs Resources used: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview https://surfer.nmr.mgh.harvard.edu/fswiki/MulitModalIntegration Any suggestions? Thanks, Lindsay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
External Email - Use Caution Hello Freesurfer Community, I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask. Using mri_surf2surf to register scans to the same space and then mri_surface_stats to create the std maps I have been comparing the variability of cortical thickness across the cortex for multiple scans across the same subject. From this I can determine a SD threshold point (0.5 say) or create a mask that includes all regions above that threshold. I would like to use this to threshold the regions showing the highest variability out of my calculations for mean hemispheric thickness and also regional thickness. Is there a way to use an SD threshold within mri_segstats or aparcstats2table? Otherwise apply a mask image to exclude specific vertices? Thank you in advance, Lindsay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
External Email - Use Caution Hi Bruce, Sorry for the late reply. I have been searching the forum and the freesurfer wiki. Are there instructions somewhere on how to do this in matlab? Thanks, Lindsay On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford wrote: > Hello Freesurfer Community, > > I am wondering if it is possible to recalculate cortical thickness metrics > (perhaps using mri_segstats or aparcstats2table) while including either a > SD threshold or an exclusion mask. > > Using mri_surf2surf to register scans to the same space and then > mri_surface_stats to create the std maps I have been comparing the > variability of cortical thickness across the cortex for multiple scans > across the same subject. From this I can determine a SD threshold point > (0.5 say) or create a mask that includes all regions above that threshold. > > I would like to use this to threshold the regions showing the highest > variability out of my calculations for mean hemispheric thickness and also > regional thickness. > Is there a way to use an SD threshold within mri_segstats or > aparcstats2table? Otherwise apply a mask image to exclude specific > vertices? > > Thank you in advance, > > Lindsay > > > > -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138 412-218-4368 *|* lindsay.hanf...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask
External Email - Use Caution
Hi Bruce,
Thank you, I didn't realize it would be so simple in matlab!
To help others who might be looking for a solution:
I was able to use MRIread for both my data.mgh file (created using
mri_surf2surf, resampled to template space for the thickness values) and
mask file (which i inverted using mri_binarize --binval 0 --binvalnot 1).
Then I was able to use a simple multiplication across the two vectors (as
they have the same number of vertices) to conserve the thickness values
from vertices of interest and remove values from vertices I wanted to
exclude.
matlab code:
datafile_lh=MRIread('data_lh.mgh')
maskfile_lh=MRIread('mask_lh.mgh')
newmatrix=datafile.vol.*mask.vol).
Thanks again!
Lindsay
On Fri, Jan 4, 2019 at 10:05 AM lindsay hanford
wrote:
> Hi Bruce,
> Sorry for the late reply. I have been searching the forum and the
> freesurfer wiki. Are there instructions somewhere on how to do this in
> matlab?
> Thanks,
> Lindsay
>
> On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford
> wrote:
>
>> Hello Freesurfer Community,
>>
>> I am wondering if it is possible to recalculate cortical thickness
>> metrics (perhaps using mri_segstats or aparcstats2table) while including
>> either a SD threshold or an exclusion mask.
>>
>> Using mri_surf2surf to register scans to the same space and then
>> mri_surface_stats to create the std maps I have been comparing the
>> variability of cortical thickness across the cortex for multiple scans
>> across the same subject. From this I can determine a SD threshold point
>> (0.5 say) or create a mask that includes all regions above that threshold.
>>
>> I would like to use this to threshold the regions showing the highest
>> variability out of my calculations for mean hemispheric thickness and also
>> regional thickness.
>> Is there a way to use an SD threshold within mri_segstats or
>> aparcstats2table? Otherwise apply a mask image to exclude specific
>> vertices?
>>
>> Thank you in advance,
>>
>> Lindsay
>>
>>
>>
>>
>
> --
> *Lindsay Hanford, PhD*
> *The Buckner Laboratory* *|* *Harvard University*
> 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138
> 412-218-4368 *|* lindsay.hanf...@gmail.com
>
--
*Lindsay Hanford, PhD*
*The Buckner Laboratory* *|* *Harvard University*
280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138
412-218-4368 *|* lindsay.hanf...@gmail.com
___
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Re: [Freesurfer] using tkregister2 to check registration to custom atlas
External Email - Use Caution Hi, I just wanted to follow up on this post. Is there a way to load the command below, but with a different atlas? tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs Again, I have tried other options but am unable to the get the surfs in the same space. Thanks, Lindsay On Wed, Dec 19, 2018 at 10:36 AM lindsay hanford wrote: > Hello Freesurfer Community, > > I am interested in seeing how well my subject scan registered to a custom > atlas after being run through recon-all. From Freesurfer Wiki, although it > is possible to see this in freeview, tkregister2 seems to be the best > method as manual edits can be made if the registration went badly. I am > however running into issues trying to load the subject image, atlas image, > and surfaces in the same space. > > If I understand correctly, when I ran my recon-all specifying a custom > atlas (-custom-tal-atlas RLB700_atlas_as_orig) the transform files > (talairach.xfm) are to the custom atlas rather than the talairach atlas. > > If I load: tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs > the subject scan, talairach atlas and surfaces load just fine. It is > clear the talairach atlas was not used. > > I have tried running multiple variations of the following, and in all > cases, the atlas is in a different space. > tkregister2 --mov RLB700.nii.gz --s 180523_HTP02168_ANAT5_init2base > --regheader --reg > 180523_HTP02168_ANAT5_init2base/mri/transforms/talairach.xfm --surfs > > Resources used: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview > https://surfer.nmr.mgh.harvard.edu/fswiki/MulitModalIntegration > > Any suggestions? > Thanks, > Lindsay > > -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138 412-218-4368 *|* lindsay.hanf...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using tkregister2 to check registration to custom atlas
External Email - Use Caution Just had a chance to try the command. Thanks, it worked! I was struggling to also have the surface projections in the same space, but found a way to do that. For anyone else who might need this: tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --targ $SUBJECTS_DIR/subject/mri/orig.mgz --ixfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm --reg deleteme.reg --s subject --surfs Best, Lindsay On Wed, Jan 16, 2019 at 10:04 AM lindsay hanford wrote: > Hi, > I just wanted to follow up on this post. > Is there a way to load the command below, but with a different atlas? > tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs > > Again, I have tried other options but am unable to the get the surfs in > the same space. > > Thanks, > Lindsay > > On Wed, Dec 19, 2018 at 10:36 AM lindsay hanford < > lindsay.hanf...@gmail.com> wrote: > >> Hello Freesurfer Community, >> >> I am interested in seeing how well my subject scan registered to a custom >> atlas after being run through recon-all. From Freesurfer Wiki, although it >> is possible to see this in freeview, tkregister2 seems to be the best >> method as manual edits can be made if the registration went badly. I am >> however running into issues trying to load the subject image, atlas image, >> and surfaces in the same space. >> >> If I understand correctly, when I ran my recon-all specifying a custom >> atlas (-custom-tal-atlas RLB700_atlas_as_orig) the transform files >> (talairach.xfm) are to the custom atlas rather than the talairach atlas. >> >> If I load: tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs >> the subject scan, talairach atlas and surfaces load just fine. It is >> clear the talairach atlas was not used. >> >> I have tried running multiple variations of the following, and in all >> cases, the atlas is in a different space. >> tkregister2 --mov RLB700.nii.gz --s 180523_HTP02168_ANAT5_init2base >> --regheader --reg >> 180523_HTP02168_ANAT5_init2base/mri/transforms/talairach.xfm --surfs >> >> Resources used: >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview >> https://surfer.nmr.mgh.harvard.edu/fswiki/MulitModalIntegration >> >> Any suggestions? >> Thanks, >> Lindsay >> >> > > -- > *Lindsay Hanford, PhD* > *The Buckner Laboratory* *|* *Harvard University* > 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138 > 412-218-4368 *|* lindsay.hanf...@gmail.com > -- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138 412-218-4368 *|* lindsay.hanf...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
