Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Omitting aseg regions from segmentation
by zalewk 04 Mar '19

04 Mar '19

External Email - Use Caution Hello Freesurfer team, I am currently working processing the volumetrics of exvivo brains, many of which do not have a brainstem/cerebellum. It seems this often results in a subcortical alignment that isn't optimal, and fails to create the pial/wm surface where freesurfer attempts to label more ventral non-zero voxels as brainstem/cerebellum. Currently, I have to manually edit the aseg.auto_noCCseg.label_intensities.mgz and aseg.presurf.mgz to fix this. Is there a way to omit aseg labels (like the brainstem/cerebellum) from the processing stream that I've overlooked? If not, would there be a potential alternate solution such as creating a second atlas from the original sans these ROIs and have the cross-sectional stream still run normally? Best, Kody Zalewski

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Interpolate one volume into raster coordinate system of a second volume
by Stockmann, Jason 02 Mar '19

02 Mar '19

Hello, I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or DICOMs) into the raster coordinates of a second volume. I simply want a naive interpolation into the second volume’s coordinate system without performing registration. For my application I do not want to actually register the two volumes, just interpolate/resample. I tried using mrivol2vol.m in Matlab but it crashes because it can’t find the field ‘mov.vox2ras0’ in my NIFTI headers (I use either mri_convert or dicm2nii to convert Siemens DICOMs to NIFTI). I then tried manually calculating the raster coordinates for the two volumes by creating integer voxel coordinates for (i,j,k) and then multiplying them by the NIFTI vox2ras matrix to get (x,y,z). I then use ‘scatteredInterpolant’ in Matlab to interpolate one volume into the second volume’s coordinate system, but this has only worked for me some of the time. I have been able to interpolate 2D axial MRI slices into an oblique 2D coordinate system, but I’m having trouble with 3D acquisitions like MPRAGE, etc. Does anyone know of a “foolproof” and simple standalone tool for this task (ideally for Matlab)? --- Jason -- Jason Stockmann Instructor in Radiology Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann(a)mgh.harvard.edu<mailto:jstockmann@mgh.harvard.edu> +1 315 450 3309

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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

2 1

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

2 7

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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