Freesurfer June 2019

freesurfer@nmr.mgh.harvard.edu

82 participants
138 discussions

FW: Query regarding way to quote covariates in fsgd file
by Basavaraju, Rakshathi 06 Jun '19

06 Jun '19

External Email - Use Caution Hi all FS users, I have the basic doubt of including age and gender as co-variates for a cortical thickness comparison between 2 groups. I read extensively many mails answering these questions but still could not get a satisfactory answer for the question. As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 levels and one continuous variable of age my contrast matrix should be like this: [0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2] I understood that if I have to test the effect of only the groups my contrast matrix should be: [0.5 0.5 -0.5 -0.5 0 0 0 0] What should be my contrast matrix if I have to include age and gender as covariates respectively? I know gender cannot be included as columns of 1s and 0s by my reading of previous mails. In one of the mail I read that if we want to test for interaction of group and gender (disregarding effect of age) the contrast matrix file should be: [0.5 -0.5 -0.5 0.5 0 0 0 0] But is testing for gender as a covariate same as testing group*gender interaction? I do not feel so. Hence requesting you all to throw some clarity on this. If this is not the way to study gender as a covariate how else should the contrast matrix be written? And regarding age should it be four 0.5s for the last 4 columns of the matrix if we want to study age as a covariate? Kindly let know. Finally I want a contrast matrix that studies the group differences in cortical thickness covarying for the effect of age and gender. Kindly help me. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute Columbia University Irving Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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CSF MASK
by Marina Fernández 06 Jun '19

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

06 Jun '19

External Email - Use Caution Dear Bruce, Thank u very much for replying. sorry I'm still a little bit doubtful, just as a confirmation: by repeatable you mean I can repeat it and every time get a a new result? or every time the result will be the same? Best, Maedeh, Hi Maedeh I think it divides along the maximum variance eigen-axis, so should be repeatable. cheers Bruce On Thu, 6 Jun 2019, Maedeh Khalilian wrote: > > ????????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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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

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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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Freesurfer June 2019