Re: [Freesurfer] Problem with quantifyHAsubregions.sh

External Email - Use Caution Dear Eugenio, Thank you for your kindly reply. Actually, I tried both options and neither worked. When I renamed one subject and ran the following command, an error occurred. Please see below: Georginas-MacBook-Pro:ALBION georginaangelopoulou$ qua

[Freesurfer] Problem with quantifyHAsubregions.sh

External Email - Use Caution Hello Freesurfer experts, I have accomplished hippocampal subfields segmentation using Freesurfer 7.3.2. However, I have trouble when I try to gather all volumes of all subjects in one single txt file. I type quantifyHAsubregions.sh hippoSf T1 testh

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, Apologies for double posting. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me to resolve the pro

Re: [Freesurfer] nuisance factors

External Email - Use Caution Apologies for sending again, I would like to verify that you have received the email. Thank you in advance for you help, Georgina I am sorry, please let me rephrase. I want to compare patients vs controls in Surface area and grey matter volume. I

[Freesurfer] nuisance factors

External Email - Use Caution I am sorry, please let me rephrase. I want to compare patients vs controls in Surface area and grey matter volume. I have already checked age slope and it is not significant for either GMV or SA. However eTIV slope is significant in both cases (we do ch

[Freesurfer] nuisance factors

External Email - Use Caution Thank you very much Douglas, It worked! I have one last question: in case of Volume, age slope is not significant, yet eTIV slope appears significant. Is it possible to include both age and eTIV as nuisance variables, in order to control my analysis for

Re: [Freesurfer] nuisance factors

External Email - Use CautionDear Douglas,  age_sim.mtx Description: Binary data CMTX_b.fsgd Description: Binary data Thank you once again for your reply and your help.Attached please find the fsgd file (CMTX_b.fsgd) including age row scores and the contrast file. The command line

[Freesurfer] nuisance factors

External Email - Use Caution Thank you very much! That makes a lot of sense. However, when I tried to run the analysis using that contrast (0.5 0.5 -0.5 -0.5 0), the following error appears: dimension mismatch between X and contrast Contrasts/age_sim.mtx X has 4 cols, C h

[Freesurfer] nuisance factors

External Email - Use Caution Dear FreeSurfer Developers, I am trying to design a matrix in order to run a group comparison analysis and I would like to verify if I am following the right steps. I have read a lot of things in the forum, but I got confused regarding how to treat

[Freesurfer] Problem with calculating significant clusters' values

External Email - Use Caution Hello FreeSurfer Developers, I have compared two groups in area, volume and thickness (using mri_glmfit and mri_glmfit-sim) and I want to extract the total value from each significant cluster so that I can run analysis with behavioural variables in S