Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

2 2

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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Re: [Freesurfer] How to get the difference between orig.mgz and original image
by chen 09 Jun '19

09 Jun '19

External Email - Use Caution Hi Bruce, Thanks for your reply. I appreciate your help a lot! Just a simple question. How to check the ratio of amygdala in intensity in the orig.mgz with other gray matter? I am looking forward to your suggests. Cheers, Jiachen

3 2

transformation from volume to surface
by Yamada, Takashi 08 Jun '19

08 Jun '19

External Email - Use Caution Hi there, I try to transform from volume-based ROI mask (nifty file) to suface-based file. I input the following. mri_vol2surf --mov (volume.nii) --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --0 (output.mgh) Then, mri_info tells me 134583 dimesions. However, I cannot overlay this mgh file on the lh.inflated. freeview -f lh.inflated:overlay=.../output.mgh How should I do? Best regards, Takashi Yamada --------------------------------------------------------------------------------------------------------------------- Takashi Yamada, MD & PhD Postdoctorial Research Associate Department of Cognitive, Linguistic and Psychological Sciences (CLPS) Brown University Box 1821 190 Thayer Street Providence, RI 02912 TEL : +1 401 863 9488 FAX : +1 401 863 2255 Email: takashi_yamada(a)brown.edu --------------------------------------------------------------------------------------------------------------------------------

2 1

Uncorrected cluster information
by Pedro Rosa 08 Jun '19

08 Jun '19

External Email - Use Caution Dear all, I would like to obtain information regarding clusters yielded by GLM group analysis before correction for multiple comparisons (hence uncorrected). I used tksurfer to look at the clusters (sig.mgh) and was able to apply statistical thresholds, but could not obtain further information from them (as available in the .summary file after correction for multiple comparisons, such as mean cluster value, cluster size). Can you help me? Many thanks in advance, Pedro.

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