Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Extracting anatomical locations for a set of RAS coordinates
by Sparsh Jain 20 Mar '19

20 Mar '19

External Email - Use Caution Good afternoon Is there is way to automatically extract the anatomical locations corresponding to a set of RAS coordinates using Freesurfer's atlas? I have a set of 200 points and I am trying to get their anatomical labels automatically. Thank you Sparsh

3 9

QDEC Longitudinal Analysis: Missing spc option from dropdown menu
by Arsenije Subotic 18 Mar '19

18 Mar '19

External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it is not there. The spc files are all present in my participants files and the Qdecrc file is in the qdec subdirectory containing 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.subotic1(a)ucalgary.ca

3 2

Cortical thickness values extraction issue
by Giuliana Klencklen 18 Mar '19

18 Mar '19

External Email - Use Caution Hi FS experts, I did group-level, surface-based, vertex-wise analysis for baseline and longitudinal data. I used Qdec and do the same work with the fsgd version (mri_glmfit-sim command) to double-check the data. I created label files with tksurfer for each of the clusters showing a significant between-group difference. Then, I used the following command stream to extract the cortical thickness values for each subject and cluster: mri_label2label, mris_anatomical_stats, and aparcstats2table. E.g., mri_label2label --srcsubject fsaverage --srclabel /home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label --trgsubject ${s}_tp1 --trglabel ${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh --regmethod surface mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats ${s}_tp1 lh aparcstats2table --subjects ${s}_tp1 --hemi lh --parc ac-baseline-rostralmiddlefrontal --meas thickness --tablefile ${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt Subsequently, when I conducted between-group comparisons for each cluster, a couple of clusters (7 out of 16) do not show a significant difference - which does not make sense. This problem seems to appear randomly. Help to the FS archives, I tried to use mri_segstats command but was not able to find a correct combination of arguments. If this is the right track to solve this problem, what combination of arguments should I use? And if this is not, do you have any idea how I can solve this problem? Many thanks in advance. Regards, Giuliana -- Giuliana Klencklen, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 118 Barker Hall Berkeley, CA 94720-3190 510-395-0040 giuliana.klencklen(a)berkeley.edu

2 8

projfrac question
by Nasiriavanaki, Zahra 08 Mar '19

08 Mar '19

Dear Freesurfers Hi I was trying to look at the activation in different cortical layers in a single subject. I ran my preproc-sess command three times, once without using -projfrac flag, once -projfrac 0.5 and lastly -projfrac 0.2 The activation patterns are exactly the same. My voxel sizes are 1.1*1.1*1.1 . My question is: 1-Is it normal that the activations do not change at all the more I get closer to white matter? 2-when I use -projfrac 0.2 , does it mean that I am averaging the activation between white matter layer to 0.2 of gray matter layer? Or is it averaging the activation between pial surface to 0.2 gray matter? I hope my questions are clear. Thanks Mona

2 11

Gray matter segmentation
by Maxime Perron 07 Mar '19

07 Mar '19

3 5

How to extract cortical features of a ROI
by 310913949 06 Mar '19

06 Mar '19

External Email - Use Caution Dear Freesurfer Experts, I want to extract cortical features of a ROI that I drawn manually on the rawavg.mgz in Freesurfer, but i don't know how to do that. I think maybe first the lesion mask should be registered to the standard templates fsaverage, but I don't know what the command line is , could you tell me? And secondly, I should use mri_label2label to map the label to individual subject and extract the cortical features of the ROI, am I right? I am looking forward to your reply!Thanks. Best wishes! Kan Deng

3 4

Choroid plexus analysis
by Benjamin Luerweg 06 Mar '19

06 Mar '19

External Email - Use Caution Dear community, anyone out there who can give me some information regarding how valid a volume detection of the choroid plexus is? I used fs 6.0. Kind regards, Ben

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

2 3

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

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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Freesurfer February 2019