Freesurfer

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19 participants
30088 discussions

combine orthogonal stacks
by Dianne Patterson 02 Mar '19

02 Mar '19

External Email - Use Caution Dear Experts, I don't know if this is even possible, but I'm hoping you can help. I have 3 clinical T1 scans in NIFTI format: one has good resolution in the axial plane one has good resolution in the coronal plane one has good resolution in the sagittal plane My dream is to combine the 3 orthogonal planes into a single high-resolution 3d image. Is such a thing possible? Does anyone have suggestions? Thanks so much, Dianne -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============

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Edit wm in the cingulate
by Abazid, Leen 01 Mar '19

01 Mar '19

External Email - Use Caution Dear FS supporter, Freesurfer is not accurately drawing the cingulate gyrus on our T1 images. See attached image 1, FS segments the cingulate cortex as white matter continuous with the corpus callosum. To correct this, we tried editing the white matter segmentation. Question: please look at image 2, below and tell us whether the cingulate cortex is now correctly assigned to gray matter? Or is it still assigned to white matter, and if so, please advise how to edit our command. Command that we used: freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=blue \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=blue \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 Image 1 [cid:3FAE3B51-56FA-4655-973E-53490426EA09] Image 2 [cid:04C87447-3E0C-4CA8-9076-962C4D395733] Any suggestions or help would greatly appreciated. Thanks, Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 01 Mar '19

01 Mar '19

External Email - Use Caution Hi Doug, This is the bulk of the text I wrote initially in my first email: Dear experts, I have recently tried to use the command line to examine thickness differences between two groups after controlling for the effects of age and sex. I get the following error : ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: 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 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=611.699463 (col 4) The scale is much different between columns 5 and 4, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same I did not get this error when I was only looking at the difference in thickness between the two groups, so I am guessing there is not an issue with the file format? Looking at the log, does this mean that I also need to demean the age variable? I was planning on running some contrasts looking 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 Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 01 Mar '19

01 Mar '19

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 is attached. It contains 2 classes and two covariates (Age and Sex). My design matrix is: 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects of age and sex) Please let me know what the issue is. Best, Arsenije

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dt_recon and mri_vol2vol issue
by Daniel Callow 01 Mar '19

01 Mar '19

External Email - Use Caution Hello freesurfer experts, I am running dt_recon with the following script dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}. and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space with the script below mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv --interp nearest --o $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg However, one of my subjects shows a major issue with the mri_vol2vol registration (for most of the subject scans it seems to work no problem). When looking at the wmparc2diff.mgz I created (screenshot attached), it is apparent that the registration of the wmparc to wmparc2diff space actually causes wmparc2diff.mgz to be further from the lowb than wmparc is. This same registration issue occurs for aseg.mgz. I assume this means there is an issue with the register.dat file for this subject? If so is there any way to troubleshoot the issue and get a correct register.dat file? For reference, the following commands and registration steps have worked for other subjects, as well as this same subject's scans under another condition. Any advice with troubleshooting would be greatly appreciated. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Second order (square) link function for GLM
by Abhinav Yadav 01 Mar '19

01 Mar '19

External Email - Use Caution Hello, I am trying to do GLM analysis for cortical thickness with a behavioral score. I wanted to explore square fit in the GLM. Basically wanted to see weather the behaviour is related in a quadratic function instead of linear one. Couldn't find any option for this is GLM fit. I was thinking of feeding a squareroot values of the behavioural parameter in the GLM as an alternative. But not sure weather that will work. Please any one can help me with this. Thanks, Abhinav

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dt_recon field map for eddy correct
by Daniel Callow 01 Mar '19

01 Mar '19

External Email - Use Caution Hi Doug, I was looking at the dt_recon code and was wondering if it would be possible to incorporate a field map into the eddy_correct portion? I tried to test it on one subject and tried to add --field=$pathtofieldmap to the eddy_correct command however I got the following error. cd /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./ectmp eddy_correct /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec.nii 0 --field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp0000 Unrecognised interpolation method: --field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp0001 Unrecognised interpolation method: --field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed I probably did this in a silly way. I wonder if and how I could add a field map I created to the eddy_correct command in dt_recon. Below is what I tried to change.... set fec = $OutDir/dwi-ec.nii if($DoEddyCorrect) then echo "#@#-------------------------------" | tee -a $LF echo "Eddy/Motion Correct" | tee -a $LF date | tee -a $LF set ectmp = $OutDir/ectmp mkdir -p $ectmp pushd $ectmp > /dev/null set cmd = (eddy_correct $f $fec $ECRefTP *--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed*) #set cmd = ($cmd; mri_convert ${fec:r} $fec) #set cmd = ($cmd; rm -f ${fec:r}) #set cmd = (cp $f $fec) echo "cd `pwd`" | tee -a $LF echo $cmd | tee -a $LF $cmd |& tee -a $LF if($status) exit 1; if(! -e $fec) then echo "ERROR: when running eddy_correct" | tee -a $LF exit 1; endif popd > /dev/null rm -r $ectmp echo "" | tee -a $LF echo "" | tee -a $LF else echo "#@#-------------------------------" | tee -a $LF echo "Skipping Eddy/Motion Correct" | tee -a $LF set fec = $f endif Thanks for any help you can provide, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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hippocampal-subfields segmentation failure
by Xiaofu 28 Feb '19

28 Feb '19

External Email - Use Caution Hello, I am running segmentation of hippocampal subfields in FreeSurfer 6.0 but one subject failed running the segmentation with the following error message. Wrote image to file asmr2.mgz This file does not contain MRI parameters This file does not contain MRI parameters In an assignment A(:) = B, the number of elements in A and B must be the same. Error in segmentSubjectT1_autoEstimateAlveusML (line 1848) Any suggestions on this? Thank you very much! Best, Xiaofu

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dt_recon --> tbss
by Daniel Callow 28 Feb '19

28 Feb '19

External Email - Use Caution Hello, I am working through dt_recon troubleshooting (One subjects registration to anatomical is skewed leading to incorrect masking of that subjects FA image). I would like to use the dt_recon's FA outputs and input them into FSL's tbss pipeline. My question is are there any steps I should take converting or modifying the FA images so they are compatible with the tbss pipeline. My intention was to take the dt_recon fa or fa-masked into the tbss_1_preproc command? Are there any considerations I should take into account? Best *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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White Matter Edit
by Abazid, Leen 28 Feb '19

28 Feb '19

External Email - Use Caution Dear FreeSurfer supporter, We are working on a PTSD project and we used FreeSurfer to obtain the subcortical and cortical volumes for our MRI images in our patients. We ran our images through the recon-all pipeline. We then extracted the volumes from the lh/rh.aparc.stats files. We plotted the volume data for all the subjects for all the structures using SPSS to compare the volumes between the right and left hemispheres to identify outliers. After further inspection of our plots for the cingulate structure, we believe the volumes are not accurate. The cingulate is very important in the pathogenesis of PTSD and we want to make sure the volumes we are getting are correct. We loaded the data into Freeview to check the gray and white matter segmentations and it appears that the white matter segmentation is including gray matter. We used the following command to edit the wm.mgz: freeview -v mri/brainmask.mgz \ mri/wm.mgz:colormap=heat:opacity=0.4 \ -f surf/lh.white:edgecolor=blue \ surf/lh.pial:edgecolor=red \ surf/rh.white:edgecolor=blue \ surf/rh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 After editing/cleaning we saved the new wm.mgz image and ran the following command: recon-all -autorecon2-wm -autorecon3 -subjid# Following completion we checked the new lh/rh.aparc.stats files? and the total white matter volume is increasing in some patients and decreasing in others while the gray matter is increasing in some of the subjects (which is what we expect). Do you have any suggestions for why the WM volumes would be increasing if we are removing what we think is not WM? Are we running the correct commands to edit the WM segmentation? Any suggestions or help would greatly appreciated. Thanks, Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532

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