[Freesurfer] XL Defect Correction

Dear Freesurfer experts, During my recon-all I encountered a problem for one of my subjects, where the process got stalled at "CORRECTING DEFECT 12 (vertices=21293, convex hull=1791) XL defect detected...". I've checked the output and it seems that skull-stripping hasn't been performed prope

[Freesurfer] Skullstrip commands not working

Dear experts, I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following

Re: [Freesurfer] Skullstrip commands not working {Disarmed}

Hi Bruce, I performed the -autorecon-pial as a means of regenerating the surfaces as instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does not have the skull but it has some dura left over. The issue I had before was that the skull would re-appear after the subject fin

[Freesurfer] Skull-strip issues: commands not working

Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the fol

Re: [Freesurfer] Erroneous output after recon-all: Bad segmentation and surfaces

Hi Bruce and Emma, I am running the latest version of Freesurfer, version 6.0. I will try manually erasing the voxels then and try re-processing the subject. Thank you so much for your help. Best, Arsenije ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Editing brainmask and white matter volumes when erasing dura

Dear experts, After I erasing dura from my brain mask volume, I noticed that the white matter volume still had dura when I clicked on it. Is it usually fine to only edit the brain mask when we’re trying to erase the dura and regenerate the surfaces? The dura on the white matter volume has both

[Freesurfer] Qdec Table Loading Error

Dear experts, I'm currently trying to import some of my data into Qdec in order to perform a group analysis on cortical thickness. All of my data was originally in an excel sheet and it had the following variables (fsid, gender, age, and thickness). I tried converting it into a file that would

[Freesurfer] Control Points Not Working

Dear experts, I’m currently performing quality control for my data, and most of my issues so far have been that in many cases adding control points has not been able to extend the white surface. I’ve also noticed that most of the regions where I have needed to add CPs are in the parietal region

[Freesurfer] Potential ways to overlay perfusion ROIs onto cortical thickness maps

Dear experts, I am trying to figure out the best way to overlay areas of low CVR reactivity and correlate that with cortical thickness measurements in those given regions. I was able to overlay our CVR map onto an inflated cortical surface in 3D and modify the configuration to see areas of low

[Freesurfer] Hippocampal subfields

Hi all I would like to use subfield specific hippocampus maps that were produced Dr Iglesias's Lab: https://sites.google.com/site/jeiglesias/hippocampal-subfields These maps are available via FreeSurfer, however our lab is trying to segment hippocampus subregions from already manually extracted

[Freesurfer] Quality of fMRI registration

Dear experts, When it comes to assessing the quality of fMRI integration in Freesurfer, is a value of > 0.5 considered a good registration? I was led to believe that from the multimodal tutorial website, and after checking the quality of my output I was satisfied with the result for each of my

[Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

Dear experts, I would like to create an average surface template of fMRI activation for two groups, and then determine areas of low cerebrovascular reactivity in my disease group, create a ROI, and extract the cortical thickness in this region and see how it compares to a control group by tran

Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

Hi Doug, I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI Analysis, but it does not indicate how a comparison should be made between the two groups that I have. It only gives information on how to perform a one sample group mean test (osgm). In addition, when you menti

[Freesurfer] QDEC vs. Command Line Stream

External Email - Use Caution Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to be the consensus when it comes to using QDEC as opposed to using the command line stream? I've seen QDEC used plentifully in the l

[Freesurfer] Longitudinal processing: cannot find input volume error

External Email - Use Caution Dear Freesurfer experts, I’m having problems with one of my participants when I am trying to create the base template for my longitudinal analysis. I get an error saying that the input volume (norm.mgz) for my followup time-point cannot be opened, ev

[Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

External Email - Use Caution Dear experts, For our study, we are planning on combining two different datasets to examine cortical thickness. There is a slight difference in the inversion time (400 vs 650) and flip angle ( 8 vs 11) between the two datasets. I know that free surf

[Freesurfer] Calculating global thickness

+ rh.thickness x rh.area)/(lh.area +rh.area)? Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subot...@ucalgary.ca

[Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

the line long.thickness-spc. Is there a way to bypass this problem somehow? Thank you, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subot...@ucalgary.ca

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

order to see if I should go with a DOSS approach, but using those contrasts still gives me the same error. Thanks for your help! Best, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi Doug, Thank you for your reply. My command was: mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir My FSGD file

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

at the interactions between group and age after controlling for sex etc. in order to see if I should go with a DOSS approach, but using those contrasts still gives me the same error. Thanks, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

thickness after controlling for effects of age and sex) I’ve also attached the FSGD file that I’ve been using. Please let me know if there is something wrong with the file (although I have used a similar file without the covariates and did not have any issues). Thanks! Arsenije --- Arsenije

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi Doug, I realized this error a couple of days ago and now it works. Thank you, Arsenije ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

[Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

External Email - Use Caution Hello, I am planning on running a correction for multiple comparisons, and I was hoping to use a vertex wise cluster forming threshold of 1.3, however after reading more when I ran the mri_glmfit-sim —help command it recommends using the permutation

[Freesurfer] One Group GLM Command Line Stream: correlating thickness with cognitive scores

mples? Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subot...@ucalgary.ca ___ Freesurfer mailing list Frees

[Freesurfer] Longitudinal Two Stage Model Question

gests? I was just confused because the code is different. I have a longitudinal table so I assumed that would be enough, but do I still need to make a FSGD file that is basically the same as the longitudinal file? Thank you for your help, Arsenije --- Arsenije Subotic | MSc Student Depar

Re: [Freesurfer] Longitudinal Two Stage Model Question

was planning on simply using contrasts i had designed before for my cross-sectional analysis, controlling for age at baseline and gender. Thanks and my apologies for all the questions! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute

Re: [Freesurfer] Longitudinal Two Stage Model Question

with those from the other and one group has more participants than the other. I will however use the the link you gave me to compute the difference within one of my groups. Best, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Inst

[Freesurfer] Changing colour of clusters generated after MonteCarlo Correction

colours that may confuse readers at first glance. Thank you, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subot...@ucalgary.ca