Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Discrepancy between thresholded surface and cluster labels
by Bronwyn Overs 31 Oct '19

31 Oct '19

External Email - Use Caution Dear Freesurfer mailing list, I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Error in running make_average_subject
by Himanshu Aggarwal 10 Oct '19

10 Oct '19

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the same problem which direct the users to the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/) But this patch does not have a readme file which can instruct the users about the steps that need to be followed to get rid of this bug. However, I have replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) with the files given in this patch directory. But the problem still persists. Kindly provide the steps that need to be followed to make use of this patch properly. Regards Himanshu

2 1

negative values of hippocampal subfields volumes
by Krzysztof Gbyl 08 Oct '19

08 Oct '19

External Email - Use Caution Hi all, I am currently running a longitudinal hippocampal subfields analysis using version 6.0. Based on the visual inspection of images, I see that Freesurfer is doing a great job. The problem is that I get negative values of the subfields volumes e.g. Hippocamap_tail -420.400366 subiculum -368.134590 The values seems to be reasonable, but why they are negative, i.e. why they have a '-' sign. Could the minus sign be a hyphen? Has anybody encounther this problem? I hope you can help BW, Chris

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Corpus Callosum area
by Fernanda Hansen P. de Moraes 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, how can I extract the corpus callosum cross sectional area for each hemisphere? Thank you very much in advance, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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mri_surf2vol -lost cluster
by Albrecht, Daniel S. 07 Oct '19

07 Oct '19

Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsaverage surface with the following command: mri_vol2surf --mov MNIvol.nii --projfrac-max 0 1 0.1 --hemi rh --o rh.out.mgz --mni152reg This works well, but I'm losing a small temporal gyrus cluster that sits close to pial surface. I was assuming this was due to the proximity to the pial surface and resampling, but are there any other options or flags I could use to get this to project successfully? Thanks very much, Dan

2 1

What's the difference between FSFAST and SPM in the 1-st level GLM?
by Zhi Li 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, May I ask what's the difference between FSFAST and SPM in the 1st level GLM? Now I use fsfast to pre-process my task-based imaging data, then model the data with FSFAST and SPM respectively. I expected to get very similar results from FSFAST and SPM in the whole brain volume-based analysis. Although there is some overlap between FSFAST and SPM on the whole brain activation, however, there is a lot of difference. Activation in some regions based on SPM was not found in that based on FSFAST. Please see below for my mkanalysis information: mkanalysis-sess \ -fsd Num -mni305 2 -fwhm 8 \ -event-related -paradigm Num.par -nconditions 18 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 0 -polyfit 0 \ -hpf 128 -mcextreg \ -analysis Num.sm08.mni305 -per-run -force Any suggestions? In addition, I am not clear if I convert the volume data from FSFAST to SPM in a right way. I replace the mask of subcortical mask with the whole brain mask. Then I convert the pre-processed data from mni305 to mni152 and model it with SPM. However, there is a lot of loss in the prefrontal and subcortical regions. Seems like the whole brain data shrinkage in SPM (please see attached figure). Looking forward to your kind reply. Thanks and best, Li Zhi

2 1

Freesurfer three groups: group A vs C power.
by cody samth 02 Oct '19

02 Oct '19

External Email - Use Caution Hi I have a question regarding how freesurfer calculates the degrees of freedom when you have three groups in the FSGD/contrast files but are running analyses on group A vs C. For example I have an analysis with 3 groups and 2 covariates. My primary question is: is there a difference between any groups. Which I have the contrast: 1 -1 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 When I write a contrast for A vs C: (1 0 -1 0 0 0 0 0 0) Does freesurfer consider this model as 9 regressors? Or 6 regressors; which would be present in a typical group 1 vs group 2 analysis that could be modeled by (1 -1 0 0 0 0) if group B didn't exist?

2 1

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"
by Caspar M. Schwiedrzik 02 Oct '19

02 Oct '19

External Email - Use Caution Hi! I am following up on this thread trying to understand how to make the color wheel visible in rtview, or, if necessary, in freeview. Thank you! Caspar

3 10

Re: [Freesurfer] CUDA 9.1 with freesurfer
by fsbuild 30 Sep '19

30 Sep '19

External Email - Use Caution Hello Vasudev, With the 6.0 source, you can use options to the configure command to point to a coda distribution and try to build freesurfer..  See the post by user buildqa at this link, https://github.com/freesurfer/freesurfer/issues/107#issuecomment… followed by the posts from user melrobin.  User melrobin reported he was able to get it to work with coda 9.1. - R. On Sep 30, 2019, at 09:57, Dev vasu <vasudevamurthy.devulapally(a)gmail.com> wrote:        External Email - Use Caution        Dear HCP team ,Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCPIt is taking a long time by using openmp to run recon-all.please let me know if you have any suggestions for parallelization.ThanksVasudev_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

CUDA 9.1 with freesurfer
by Dev vasu 30 Sep '19

30 Sep '19

External Email - Use Caution Dear HCP team , Could you please let me know how i can configure CUDA 9.1 with freesurfer 6.0 or Freesurfer 5.3.0 -HCP It is taking a long time by using openmp to run recon-all. please let me know if you have any suggestions for parallelization. Thanks Vasudev

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Freesurfer September 2019