Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

Re: [Freesurfer] hippocampal subfield as CONN seeds
by Nelson, Eric A 12 Jun '19

12 Jun '19

External Email - Use Caution Im not sure I understand the question because I have not successfully registered the hippoSfLabels file to mni space. I can load the hippoSfLabels.mgz file into CONN at the subject level, but I have two problems. 1st it is not in MNI space. 2nd it is the whole hippocampus and I want to be able to use masks of the individual subfields. To try and convert the hippoSfLabels file to MNI space though I used the following. mri_vol2vol --mov lh.hippoSfLabels-T1-T2.v10.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm \ --o test.mgz Eric

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Problem with lme_mass_fit_vw
by Hua, Jessica 12 Jun '19

12 Jun '19

External Email - Use Caution Dear Kersten, Thank you so much for your help! I made a duplicate copy of the matlab directory, and the scripts worked perfectly. I had one quick question regarding the CM.C. Based on the Linear Mixed Effects model page, I modified the CM.C to fit my research question. I am interested in looking at change over time with BAC. If this is my model: Yij = ß1 + ß2*tij +ß3*adjBACi + ß4*adjBACi*tij + ß5*sexi + ß6*ICVi + b1i + b2i*tij + eij Would this be my CM.C?: [0 0 0 1 0 0] Just wanted to make sure that I was understanding the CM.C correctly. Best, Jessica Hua

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mri_gtmpvc with amended aparc+aseg
by Albrecht, Daniel S. 11 Jun '19

11 Jun '19

Hello, I’ve been using PETSurfer for partial volume correction of PET images using the RBV option. I’m amending the parcellations/segmentations to add in extracortical areas of high PET signal (to prevent spill-in into the brain), and after adjusting the *ctab file this runs successfully. However, I noticed the output resolution of the rbv.nii.gz image is the same as the input segmentation mask, not the expected 0.5mm iso. I’ve run a test incorporating the --rbv-res 0.5mm flag into the command line. The output rbv.nii.gz image is similar to the previous one (without the –rbv-res flag), again not as smooth as the typical output image. Is it satisfactory to run the command with my amended seg image and the --rbv-res 0.5mm flag, and are there any additional recommendations for running PVC with an amended seg image? Thanks very much, Dan

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hippocampal subfield as CONN seeds
by Nelson, Eric A 11 Jun '19

11 Jun '19

External Email - Use Caution Hi all, I have successfully ran hippocampal subfields for a sample but would like to be able to use some of those subfields as seed regions in CONN. Is there a method I can use to convert the individual subfields to MNI space so I can import some of subject level subfields to an existing CONN project? I thought using mri_vol2vol on the hippoSfLabels-T1.v10.mgz might be the best solution but get the following error regio_read_mincxfm: No such file or directory ERROR: could not read transforms/talairach.xfm Best, Eric

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label a ROI
by Francesca Pentimalli 11 Jun '19

11 Jun '19

External Email - Use Caution Dear Freesurfer experts, I am trying to create a mask and run the analysis into it considering just the following anatomical regions: (1) inferior frontal gyrus pars opercularis (IFGOp) (2) inferior frontal gyrus pars orbitalis (IFGOr) (3) inferior frontal gyrus pars triangularis (IFGTr) (4) Heschl3s gyrus (HG) (5) the superior temporal gyrus (STG) (6) planum polare (PP) (7) planum temporale (PT) (8) supramarginal gyrus (SMAR) (9) angular gyrus (AG) (10) fusiform gyrus (FFG) (11) inferior occipital gyrus (IOG) (12) insula Which technique do you suggest? Is there a good tutorial for it? Thank you very very much!! Best regards, Francesca *Francesca Pentimalli Biscaretti di Ruffia * Via S. Eufemia 3, 35121 Padova (Italy) Mobile: +39 3483862788 francesca.pentimallibiscarettidiruffia(a)studenti.unipd.it fpentimallibdr(a)gmail.com fpenti(a)mit.edu fpbdr(a)bu.edu

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Correlate Dose Distribution with Cortical Thickness Change
by Janneke Janssens 11 Jun '19

11 Jun '19

External Email - Use Caution *We already send this email from a Medaustron email address but for some reason the response was blocked and cannot be seen anymore* Dear FreeSurfer Developers, We are doing research on cortical changes after radiation therapy to the brain. We are trying to compare the thickness of the cortex at the beginning of the radiation (T0) and after one year of treatment (T1). Subsequently, we would like to correlate the thickness change to the dose given to the specific brain areas. We ran the ‘recon-all’ commands for longitudinal data. All the commands executed without errors according to the log file. *“recon-all -all -i IM1.DCM -s Subj001_MR1”* *“recon-all -all -i IM1.DCM -s Subj001_MR2”* *“recon-all -base Subj001 -tp Subj001_MR1 -tp Subj001_MR2 –all”* *“recon-all -long Subj001_MR1 Subj001 –all”* *“recon-all -long Subj001_MR2 Subj001 –all”* We could find cortical changes and load them into qdec. However, the problem now is that we want to correlate the dose distribution to these thickness changes. We encounter the next issues: - How to insert the dose files (DICOM-format) into FreeSurfer/qdec to make it part of the analysis? - We have searched for instructions, both in the archives and in the tutorials, how to import the dose files into FreeSurfer but we cannot find any documentation. Does anybody have experience with loading dose-files into FreeSurfer software? - How to execute statistical analysis within a subject? In this case, correlate thickness changes and dose distribution from one patient? - In the tutorials and the archives we couldn’t find any within-subject analysis. Nevertheless, in the paper ‘Dose-Dependent Cortical Thinning After Partial Brain Irradiation in High-Grade Glioma’ of Karunamuni et al. (2016) ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747044/) this type of analysis is done, so we know it is possible. We already contacted the authors of this paper but they do not respond. The version of Freesurfer we are using is: Freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on a macOS Mojave operating system. Thank you very much in advance, it would be of great help if you could advise us regarding this experiment. We are looking forward to your response. Kind regards, Janneke Janssens and Piotr Andrzejewski E: janneke.janssens(a)medaustron.at T: +43 2622 26 100 660

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Cerebellum and brainstem mask
by Miguel Ángel Rivas Fernández 11 Jun '19

11 Jun '19

External Email - Use Caution Dear Freesurfer devs, I would like to exclude from the T1 image those voxels that correspond to the cerebellum and brainstem. I tried to do this using the following commands although I am not completely sure if they are the right ones: 1. Extract cerebellum and brain stem labels from the aseg.mgz file mri_extract_labels aseg.mgz 45 46 47 6 7 8 16 cerebellum_brainstem.mgz 2. Binarize the mask mri_binarize --i cerebellum_brainstem.mgz --o cerebellum_brainstem_mask.mgz --min 0 --max 0 3. Convert the mask to native space mri_convert -rl orig/001.mgz -rt nearest cerebellum_brainstem_mask.mgz cerebellum_brainstem_mask.nii Any help would be appreciated. Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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Surface Mesh Mapped to Voxels
by Raunak Swarnkar 10 Jun '19

10 Jun '19

External Email - Use Caution Hi I am using freesurfer to extract just the cortical surface mesh. Next, I want to map each vertex on the surface mesh to its corresponding voxel in the volumetric atlas. Any help how to go forward with it? Regards Raunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar

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mri_compute_volume_fractions input volume
by Pfannmoeller, Joerg Peter 10 Jun '19

10 Jun '19

Hello, I always used mri_compute_volume_fractions to compute the volume fractions in my GE-EPI images (percentage of gm,wm, and csf in each voxel). That does not seem to be possible anymore. I can still define a registration matrix and an outstem but no input execpt of the standard FreeSurfer anatomical input. Can you help me with that? Best Joerg

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Using mean thickness / total area as covariates
by Pedro Rosa 10 Jun '19

10 Jun '19

External Email - Use Caution Dear all, I read previous threads on the list concerning the use of 'total measures' (e.g., mean thickness, total brain volune, total area) as covariates in FreeSurfer's group analysis Given that FreeSurfer analyses brain hemispheres separately, would it make more sense to use hemispheric values (i.e., lh total area in the lh area analysis and rh total area in rh area analysis) than the mean cortical value (e.g., mean between lh and rh total area in both lh and rh analyses)? Best, Pedro.

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Freesurfer June 2019