[Freesurfer] ERROR in long_mris_slope

Dear Freesurfer experts, I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack ?do-label ?time time --qcache fsaverage command for my longitudinal processing. However I keep getting the error message: mris_cal

[Freesurfer] error --qdec long

Dear Freesurfer experts, I am trying to prepare my data for linear mixed modeling using the matlab add ons, with this command mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh However I keep getting this error message ERROR: flag

[Freesurfer] error in lme_mass_fit using matlab tools

Dear Freesurfer experts, I have a question about fitting linear mixed models to mass-univariate data using the lme tools in matlab. I am currently trying to compute the initial vertex-wise temporal covariance estimates by [lhTh0lhRe] = lme_mass_fit_EMinit(X,[2],ni,lhcortex,3] However, I ke

[Freesurfer] error in lme_mass_fit using matlab tools

Hi, Thank you for your response. I am actually using two random effects (time and intercepts), and have fixed my design matrix to incorporate this. We are actually running R2011b Matlab, however I just realised that we do not have the Statistics toolbox. Could this be what is causing the e

[Freesurfer] lme issues + failure to converge

Dear Jorge/freesurfer group, I am using the scripts you sent me that do not require the newer version of matlab, and now using a computer that has the Statistics toolbox. I can get the scripts (with the suffix 1) to run with; lhstats = lme_mass_fit_vw(X[1 2],ni,lhcortex);) however it "fails

[Freesurfer] Error for mri_glmfit contrast

Dear Freesurfer experts, I am currently trying to do a cortical thickness group analysis with one factor, three levels . I have run mri_preproc and mri_surf2surf, and am now trying to run mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C contrast1.mtx --surf fsaverage lh --cort

[Freesurfer] Re asegstats2table

Dear Freesurfer experts, I am currently trying to obtain mean thickness values for certain sub-regions of the cortex. I have previously used this command asegstats2table --subjects X_* --meas thickness --tablefile aseg_stats.txt however now (Ive updated to v 5.3) I receive this error asegsta

[Freesurfer] freeview

Hi, I am trying to use freeview to look at wm/brainmask etc however the command wont work. The command Im suing is freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 wm1_edits_before/mri/brainmask.mgz \ -f wm1_edits_before/surf/lh.white:edgecolor=blue wm1_edits_before/surf/lh.pial:e

[Freesurfer] bad reconstructions; why?

Hello, I have a question re reconstructing brains (ie after doing the edits and running them again to ensure the edits went through). Before the reconstruction, the whole brain was there, however afterwards, large chunks of the brain is missing. Im worried whether this is something to do with the

Re: [Freesurfer] bad reconstructions; why?

, Catherine Bois wrote: > Hello, > > I have a question re reconstructing brains (ie after doing the edits and > running them again to ensure the edits went through). Before the > reconstruction, the whole brain was there, however afterwards, large chunks > of the brain is missing.

[Freesurfer] re reconstructions

Hi, I am currently in the process of reconstructing my brains after performing edits. I am submitting them to a system named condor, which allows them to be processed in parallel, reducing time. However, I am unsure of how to best use the script that takes into account all the changes made. Is it

Re: [Freesurfer] re reconstructions

Ps. To make it clearer; would this command recon-all -autorecon1 -autorecon2 -autorecon3, incorporate all the edits amde, or would it merely overwrite them and just regenerate the brain surface from scratch? Thanks On 26 November 2012 13:13, Catherine Bois wrote: > Hi, > > I am cur

[Freesurfer] bad reconstructions

Hi, sorry I have an additional question; when reconstructed 9with edits), if the scan seemingly is worse off than before the edits were made; is there a "recon clean" command; that one can use that takes away all the edits and "starts from scratch? Thank you, Cathy _

[Freesurfer] missing brain

Hi, I am currently in the process of reconstructing my brains after edits. However, the brains keep being reconstructed with large portions of brain missing/cerebellum missing; ie they are much worse than before I edited them. However, I am sure that I have only put control points in white matter

[Freesurfer] files not in individual's folder

I have noticed that when I reconstruct the brains (with edits) three files appear; fsaverage, lh/EC_average and rh.EC_average...I only recently noticed these and have before then been under the impression that all the useful data for analysis is in each individual's subject folder. Therefore I have

[Freesurfer] which step comes first

Hi, when reconstructing the brains including manual edits, does the step that incorporates control points "come before" the white matter edits? Ie so if I do both control points and white matter edits, will the white matter edits be take into account even if I just use -autorecon -cp , and not -wm

[Freesurfer] freesurfer question

Hi, I am currently editing some scans (ie adding control points etc), however I keep finding that after the editing often the brains look "worse" than they did before; especially the medial temporal lobe area. I have taken care not to put too many control points in/made sure not to place t

[Freesurfer] longitudinal processing

Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a chari

[Freesurfer] longitudinal processing

? Thanks, - Forwarded message from c.b...@sms.ed.ac.uk - Date: Wed, 09 Jan 2013 13:35:12 + From: Catherine Bois Subject: longitudinal processing To: freesurfer@nmr.mgh.harvard.edu Hi, just to clarify, When beginning longitudinal analysis, the first step is the same

[Freesurfer] commands to extract thickness values

Hi, I am trying to extract stats files from my subjects using this command aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thickness --parc --aparc --tablefile lh.thick.table however I keep getting this error message Parsing the .stats files Skipping /sdata/images/projects/EHRS/2/

[Freesurfer] qdec

Hi, I am considering using qdec, however due to our large dataset (and different individuals having been in charge at different times) I just realized that the folders fsaverage etc are "missing". As these are necessary for the qdec use, is there anything else I can do? Eg a command line t

[Freesurfer] error when using stats import in qdec

Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the

[Freesurfer] Fwd: error when using stats import in qdec

Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set th

Re: [Freesurfer] Fwd: error when using stats import in qdec

Sorry, just to clarify; it lists age as a discreet variable rather than continuous for some reason, not the other way round as I accidentally wrote=) Regards Quoting Catherine Bois on Tue, 12 Feb 2013 14:58:45 +: > > Dear all, > > I have a question; > > I am trying

[Freesurfer] re error when making average subject

Hi all, I was trying to create an average subject however received this error message. I temporarily removed that subject however I was wondering what a possible cause for this error is? Applying LTAtransformInterp (resample_type 1) writing to /sdata/images/projects/EHRS/2/Freesurfer_EHRS/R