Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

A Question Regarding the Command "mris_divide_pacellation"
by Maedeh Khalilian 06 Jun '19

06 Jun '19

External Email - Use Caution Dear experts, I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the command "mris_divide_parcellation" in order to have a parcellation with more regions. Now I have a question: for example if in my splitfile I write 4 in front of the region "precuneus", how does it divide this region into 4 subregions? Is it based on a specific pattern or it is random? I mean if I repeat this command line 100 times with the same splitfile, will the results be the same? I would be grateful if you could help me. Best regards, Maedeh,

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correlate dose distribution with cortical thickness change
by Janneke Janssens 06 Jun '19

06 Jun '19

External Email - Use Caution 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 Disclaimer: Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/

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How to get a circle mask on surface
by Zhi Li 05 Jun '19

05 Jun '19

External Email - Use Caution Dear Freesurfer experts, Now I would like to find the peak vertex showed significant group effect in a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred this peak point. May I know whether it is applicable and how should I do it with command line? Any suggestions would be much appreciated. Best regards, Lizhi

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Segmentation of hippocampal subfields and nuclei of the amygdala
by Boris Rauchmann 05 Jun '19

05 Jun '19

External Email - Use Caution Dear all, depends the Segmentation of hippocampal subfields and nuclei of the amygdala pipeline on the fs-recon all pipeline? I made some changes mainly by defining control points to fix intensity normalization in my dataset and rerun recon all. I´m not sure if I also have to rerun the subfields pipeline now? Thanks, Boris

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CSF mask
by Marina Fernández 05 Jun '19

05 Jun '19

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina.

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How to transfer previous FS edits to the new runs?
by Reetta-Liina Armio 05 Jun '19

05 Jun '19

External Email - Use Caution Dear Freesurfer experts, I have run subcortical segmentation with FS development version 6.0. I did manual edits to these runs. Now I’m running the same data with FS stable version 6.0. I tried to run the data with stable version from the same location so that the earlier brainmask file with the previous edits would be used. This did not happen and the previous edits were not transfered to the new runs. How can I preseve the previous edits in these new runs? Thank you for the help! Best, Reetta-Liina Armio Lähetetty iPhonesta

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error in matlab with segmentHA_T1.sh
by stdp82＠virgilio.it 05 Jun '19

05 Jun '19

External Email - Use Caution I have installed matlab 2018b and removed 2014b. When I run segmentHA_T1.sh the error reported below occurs: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:3955 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args Darwin iMac-di-Stefano.local 17.7.0 Darwin Kernel Version 17.7.0: Wed Apr 24 21:17:24 PDT 2019; root:xnu-4570.71.45~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Tue Jun4 00:55:25 CEST 2019 For more details, see the log file /Applications/freesurfer/subjects/subj/scripts/hippocampal-subfields-T1.log

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how to obtain a mean .mgh file
by Barletta, Valeria 04 Jun '19

04 Jun '19

Dear Freesurfers, Is there a way to turn N .mgh files in to a single output .mgh file in which each vertex is the mean of the corresponding vertices in my input files? For example, input lh.Ctrl029.fsaverage.mgh , lh.Ctrl030.fsaverage.mgh , lh.Ctrl031.fsaverage.mgh , lh.Ctrl032.fsaverage.mgh >>> output lh.mean.fsaverage.mgh Thanks, Vale

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Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
by David S Lee 04 Jun '19

04 Jun '19

External Email - Use Caution Hello FreeSurfer Experts, I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version. - 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but in the volumetric output, there are values for the regions. - 2 subjects' medical nuclei masks are located in the Putamen region (more superior/detached from the rest of the amygdala). I found the exact same inquiry RE: AAA region posted on April 30, 2019, but I did not see any response. What would be your recommended course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions? Thank you for your time, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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T2/Flair benefits in freesurfer 6.0
by Aaron Tanenbaum 04 Jun '19

04 Jun '19

External Email - Use Caution I am not too sure if I have asked you this question before. I know the use of a flair or T2 helps with dealing with the dura. I was wondering if there are other benefits?

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