[Freesurfer] Extracting Group Means for Cortical Thickness

. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building

Re: [Freesurfer] Extracting Group Means for Cortical Thickness

is the function of the flag --id 1? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http

Re: [Freesurfer] Extracting Group Means for Cortical Thickness

Hi Doug, Thanks again for your prompt response. That is all very clear! Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399

[Freesurfer] GLM contrast vector for continuous variable interaction

me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.5 0.50.50.5 000000000.50.50.50.5 0 0 0 0 -- Kind regards, Bronwyn Overs

Re: [Freesurfer] GLM contrast vector for continuous variable interaction

Thanks Douglas. That is exactly what I wanted. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

[Freesurfer] Trouble specifying contrast vectors

0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Kind regards, Bronwyn Overs Research Assistant Neuroscience Research

[Freesurfer] Unknown problem with fsgd file

haplotypeXgender.mtx --C groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building

[Freesurfer] Different significant regions with different cluster wise thresholds

is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399

[Freesurfer] mri_glmfit error

-MelbVsPer.mtx --C --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir Unfortunely, I keep getting the following error: ERROR: Option lh unknown Do you know why this would be? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience

Re: [Freesurfer] mri_glmfit error

Thanks Douglas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Doug, The problem is with the int_genderXgroup contrast (between .05 .01 cluster forming thresholds). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031

Re: [Freesurfer] Different significant regions with different cluster wise thresholds

Hi Doug, Thanks, that makes it very clear. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

confirmed that I am using the exact same model for each, so it is only the analysis method that differs. Do you know why these two methods would produce such disparate results? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

and then view the mapped label for an individual subject in freeview, it appears to be a continuous label for all of the parcellated regions combined. Is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

Hi Doug, That makes perfect sense. Just one more thing then, how do you conduct an FDR via the command line for an ROI mri_glmfit analysis? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

and received the following error: ERROR: could not determine file for DesikanROIAnal_case-control.thick.lh.glmdir/mask Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

-0.067 -4.074 lh_transversetemporal_thickness-0.009 -1.618 lh_insula_thickness 0.553 -6.063 Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

Thanks. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au

[Freesurfer] Freesurfer Calculation of Vertex-Wise Area

Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? -- Kind regards, Bronwyn Overs Research

Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area

On 01/16/2015 12:00 AM, Bronwyn Overs wrote: I meant that as well as the mapping of the area to the average space. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

to Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow

[Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

of reduced cortical thickness in schizophrenia subjects. I was surprised not to find the same pattern of effects using the GLM analysis. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street

[Freesurfer] mri_glmfit skipping .mtx files

you know how I can fix this? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

Hi Doug, Sorry which file should the mri_segstats command be in? Also, I am still unclear on how the individual values in cache.th13.abs.y.ocn.dat are calculated. Could you possibly explain this? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

Hi all, I am still a little confused as to how the individual values are calculated for the significant clusters in the GLM model. Is the cluster mapped backed on the individual brain and the mean thickness for that region is printed out for each individual? Kind regards, Bronwyn Overs

Re: [Freesurfer] Excluded high intensity gray matter

Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au

Re: [Freesurfer] Excluded high intensity gray matter

HI Bruce, It isn't messing stuff up elsewhere, but I am just worried about including this participant in GLM analysis if this problem cannot be fixed. What would you recommend? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

Dear Freesurfer Mailing List, I sent the below email last week and have not yet recieved a reply. Does anyone have any ideas about the problem I am experiencing? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete

Re: [Freesurfer] mri_glmfit skipping .mtx files

Hi Doug, Yes the appear on the 2nd run (including only the missing contrasts). Thanks for that suggestion. Still unsure why they didn't appear with the 1st run though. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete

[Freesurfer] Extreme mean values for significant clusters (using GLM)

mean values (in cache.th13.abs.y.ocn.dat) generated? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2

[Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

;surf" directory and starting matlab, could I use the following command and file to extract the data I want?: [thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh') Also, how do I then determine the annotation associated with each vertex for each subject? -- Kind regards, Bro

Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

my aparc file has 116407. Or should I be reading in the lh.aparc.annot from fsaverage? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769

[Freesurfer] Problem with fsgd file

-groupCtl -nan -nan 3 genderM-groupAR -nan -nan 4 genderF-groupAR -nan -nan INFO: gd2mtx_method is dods ERROR: Option dods unknown Can you tell me what is wrong? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

thickness --label case-control.fsaverage.cortex.label --cortex mri_glmfit-sim --glmdir long_case-control--cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Build

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au>

[Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Hi Douglas, Sorry I don't know what you mean by the different mri_glmfit levels? Also how do you use two fsgd files simultaneously (I assume one file for time 1 and the other for time 2)? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

itter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 25/09/2015 10:55 am, Bronwyn Overs wrote: Hi Martin, I wanted to ask about getting the st

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

Hi Martin, Thanks for clarifying. As a follow-up, is it ok to use age or mean centered at each scan as the timing variable with the two-stage model? Regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

--do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Do I need to run another command to produced a stacked spc file for use with glm_fit? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia

[Freesurfer] Get summary stats for ROI

in another unrelated MRI sample. What is the simplest means of mapping these clusters to my other sample so that I can extract the stats? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randw

[Freesurfer] Create surface overlay from p-values

to create a .mgh overlay from our array of p-values using fsaverage as the subject? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T

[Freesurfer] Yeo 2011 Functional Cortical Parcellations

.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Resear

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

with version 5.1? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraus

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

Thanks very much Thomas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu

[Freesurfer] Longitudinal analysis with single timepoint scans

(2 timepoints) with cross images (1 timepoint) in the same analysis, or can they not be used together because the cross sectional images have not undergone the same processing steps? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research

[Freesurfer] MNI coords in GLM cluster

to know if this is included in any of the significant clusters from an alternate GLM in freesurfer. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M

Re: [Freesurfer] Longitudinal analysis with single timepoint scans

Thanks very much Martin. That's perfect. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <h

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

ich if any of these should I designate as the source in step 3a? Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Ba

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

Hi Thomas, Thanks, I have taken your advise and used the LooseMask for the 7 network parcellation in steps 3a and b. How do I now mask it again with FreeSurfer's segmentation of striatal regions as you have suggested? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research

[Freesurfer] Stats for Yeo and Choi Parcellations

stats for the 7Network parcellation? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <h

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

-annot unknown [b.overs~]$ I could not see any --save annot option in the help file. I am running this correctly? Should I be suing the .mgz file as the input or is the annotation file ok as this is what I want to resample? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research

[Freesurfer] Percentage of cortex showing significant differences

of the significant clusters for each coefficient, but I don’t know what value to use in the denominator (the total size of the cortex). Would it be the total area of the fsaverage inflated surface that I used in my analysis? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete

Re: [Freesurfer] mri_label2label problem

Hi Doug, Yes i was visualising it on fsaverage. I switched to sub003 and the ROI looks perfect. What a simple mistake, thanks for your help. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031

[Freesurfer] LME mass univariate model

) with a model excluding the random effect for age? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu

Re: [Freesurfer] LME mass univariate model

the square bracketed numbers refer to the random effects as well? So would this be run for random effects at B0 and B2: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 3],Y,ni,lhcortex,3); Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker

[Freesurfer] Comparing LME models

for both models? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neur

Re: [Freesurfer] Comparing LME models

do I use? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neur

Re: [Freesurfer] Comparing LME models

Great thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://tw

Re: [Freesurfer] LME mass univariate model

all groups and genders, or just years for male controls: CM.C = [0 1 0 0 0 0 0 0 0] Also, what contrast should I use to examine the effect of years in my patient group irrespective of gender? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth

[Freesurfer] Recon-all error

you have any alternate suggestions for fixing this problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http

Re: [Freesurfer] Recon-all error

://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C> Should I try running the recon-all -all for each subject? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydn

Re: [Freesurfer] Error with recon-all long

-r-- 1 b.overs GroupID 501887 Aug 9 13:35 lh.sulc … Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu

[Freesurfer] Error with recon-all long

iki/BugReporting> I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Ra

Re: [Freesurfer] Medial Surface Problem

a. 100% |***| 2017 MiB 51.01 KiB/s00:00 ETA 226 Transfer complete. 2116019235 bytes sent in 11:15:08 (51.01 KiB/s) Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308

Re: [Freesurfer] Medial Surface Problem

Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neur

Re: [Freesurfer] Medial Surface Problem

Hi Bruce, Just wanted to check in on the status of reviewing our medial surface problem. Any luck so far? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883

Re: [Freesurfer] Medial Surface Problem

Hi Mailing List, Still trying to solve the below medial surface problem. Does anyone have any ideas? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F

Re: [Freesurfer] Medial Surface Problem

re any additional information. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <http

Re: [Freesurfer] Medial Surface Problem

Hi Bruce, Just wanted to check in and see if you had examined the files I uploaded yet? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

Re: [Freesurfer] Medial Surface Problem

Hi Bruce, Sure, files have been dropped again. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu

Re: [Freesurfer] Medial Surface Problem

Hi Bruce, That's fine, thanks very much. Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 [ http://neura.edu.au/ | neura.edu.au  ] [ https

Re: [Freesurfer] Recon-all error

Hi Douglas, Do you have any thoughts about the new missing directory error I am getting detailed below? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883

Re: [Freesurfer] Error with recon-all long

1 or two timepoints per subject. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/>

Re: [Freesurfer] Recon-all error

Hi Emma, Thanks for your reply. I just tried running the recon-all process from the beginning using the -all flag and it seems to have fixed whatever the error was and the processing completed successfully. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia

[Freesurfer] DF for Longitudinal LME

at baseline (group has two levels, 0 or 1) 4) Interaction between years and group Any assistance you can provide would be great. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

External Email - Use Caution Hi Kersten, Thanks you so much for your reply and sorry I missed your earlier message. I'll implement the suggestions you've suggested. Thanks again. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia

[Freesurfer] Max threshold marked as '-inf' in cluster summary file

which encompasses most of the brain surface is reported as infinity ('-inf'). Please find an example file attached. As I was hoping to use these values to generate effect size estimates, can you please tell me what alternate value I could substitute here for 'Max'? Kind regards, Bronwyn

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

of the following contrast vector: 0 1 0 0 0 0 0 1 Do you know how I could estimate the effect size for this contrast given that it corresponds to two beta values (1 and 7)? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

External Email - Use Caution Thank you very much Kersten! Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

External Email - Use Caution Hi Kersten, That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

External Email - Use Caution Hi Kersten, Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')? Kind regards, Bronwyn Overs Research

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

' in my cluster summary files. Do you have any idea how to get around this problem so that I can use my max threshold values to calculate cluster-wise effect sizes? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

, do you have any suggestions? Finally, do you know why the max vertex is listed as '-inf' for my largets cluster and is this a problem at all? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

for generating effect sizes for these clusters? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au

Re: [Freesurfer] Viewing labels in freeview

External Email - Use Caution Hi Ruopeng, Thank you for looking into this for me, changing the threshold as you suggested has solved my problem. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker

Re: [Freesurfer] Viewing labels in freeview

was 6.6MB in size so was too large to send by email). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au

[Freesurfer] MNI to RAS conversion

. The coordinates I need to convert are x = − 31, y = 25, z = − 7 and x = 41, y = 25, z = − 9 . Any assistance you can provide would be much appreciated. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney