Re: [Freesurfer] LME univariate data

Hello, this is a little bit hard to tell from the outside. So for the moment I have only some general ideas: Did the algorithm converge in both cases? If not, I would have less confidence in the results. One thing to consider besides the effect size and direction is the variability of the

[Freesurfer] Postdoctoral position at the NIH/NIMH

We are seeking enthusiastic applicants for a Post-Doctoral Fellowship position to help with the collection and analysis of large brain-imaging datasets. The successful candidate will use state-of-the-art artificial intelligence methods, with the aim of better understanding psychiatric disorders in

[Freesurfer] Cohen's D from gamma and rstd: size mismatch

Hello FreeSurfer Experts, I am trying to calculate Cohen's d effect sizes for a contrast I created in QDEC. I have found multiple sources suggesting this code: cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh But when I use it (replacing the glmdir and contrast with my own),

[Freesurfer] unable to open freeview

Dear experts, I encountered a problem when trying to open freeview. I am using FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the terminal, as described in this link: http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart but the

Re: [Freesurfer] Cohen's D from gamma and rstd: size mismatch

if they are different sizes, then something is wrong. Try deleting the folder and re-running qdec. On 4/17/18 9:04 AM, Kelly Vaughn wrote: Hello FreeSurfer Experts, I am trying to calculate Cohen's d effect sizes for a contrast I created in QDEC. I have found multiple sources suggesting

[Freesurfer] Brainhack San Francisco 2018 - May 3-5

Dear Freesurfer mailing list, Join us for Brainhack San Francisco 2018: 2.5 days of fun hacking around brain data! When: May 3-5 2018 Where: UCSF Mission Bay Campus More info: sfbrainhack.github.io The event is open to anyone with a passion for the brain and/or data: neuroscientists, hackers,

Re: [Freesurfer] unable to open freeview

Hi Darko, how are you sourcing freesurfer? And what is the output of running “which freeview” and “which freeview.bin”? best, Andrew From: on behalf of Darko Komnenić Reply-To: FS Help Date:

[Freesurfer] mri_deface keeps seg faulting

Hi, I'm trying to deface an MEMPRAGE dataset using the following command: [jazz:test_deface] (nmr-stable53-env) mri_deface outSubDir/mri/orig/001.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz and am getting the output: logging results to

Re: [Freesurfer] mri_deface keeps seg faulting

That worked, thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Dicamillo, Robert Sent: Tuesday, April 17, 2018 11:47:02 AM To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] how to use annotation file in FSFAST for seed based analysis

Map the annotation into the indididual subject space with mris_apply_reg. Then create a segmentation from the annotation using mri_aparc2aseg. Look inside any recon-all.log file for an example command line. You will need to change the annot and the output. Then run fcseed-config specifying the

Re: [Freesurfer] unable to open freeview

Do you have tcsh properly installed? You can check by running the command “tcsh --version”. If it is installed, I’m not quite sure why you’re experiencing this problem, but I would suggest modifying the freeview script at /home/lisak/Desktop/freesurfer/bin/freeview to debug. Try adding the

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can

Re: [Freesurfer] problem with mri_label2vol for aseg

something strange is going on because that mri_vol2vol command has worked for years. Can you upload your subject's dir to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2 On 4/16/18 5:40 PM, Michelle VanTieghem wrote: Hi Bruce, If I *just run the mri_convert command that you

Re: [Freesurfer] unable to open freeview

also, not sure if this info will be useful, but libvtkverdict.so.5.6 exists on my computer in /home/lisak/Desktop/freesurfer/lib/vtk/lib/vtk-5.6 subfolder, but from the error message above it seems as if Freesurfer expects the file to be located in lib/vtk/*bin *subfolder. On Tue, Apr 17, 2018 at

Re: [Freesurfer] unable to open freeview

Hi Andrew, FreeSurfer is being sourced automatically each time I open the terminal, and I see the usual lines: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/lisak/Desktop/freesurfer FSFAST_HOME /home/lisak/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz

Re: [Freesurfer] Group Analysis Contrast (Follow-up)

You need to put in age, weight, AND age*weight. If you have two classes and use DODS, then the contrast would be 0 0 0 0 0 0 0.5 0.5 On 4/13/18 8:02 PM, David S Lee wrote: Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1

Re: [Freesurfer] FSFAST, Beta values and Percent Signal Change questions

On 4/16/18 11:56 AM, Sarah Cole wrote: Hi Doug, I need your recommendations on two topics. I really appreciate your help. 1.) I have two runs of the same experiment, each for about 12 minutes. These 2 runs are different only in the presentation order of the stimuli. I also have one

Re: [Freesurfer] FSGD design for multi-centre study

sorry for the delay ... You will definitely need to change the contrast values so that the positives and negatives both add to the same number (with opposite sign). It is a bit of a judgement call in terms of removing them entirely. With an unbalanced design, you cannot remove the fixed effect

Re: [Freesurfer] How FDR was used to correct for multiple comparisons

You should read the FDR paper for more detail. But the FDR is the number of false positives relative to the total number of positives. The way it is interpreted is that when you look at an image, 5% of the voxels above threshold are false. You don't know which 5%. If the 5% came out of a big

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

There is not an easy way to do this. If you have access to the original hammersmith data, you can run each subject through FS, copy/convert the manual labels into the conformed space for each subject, then build your own volume-based atlas. If that is something you are up for, let me know and

Re: [Freesurfer] unable to open freeview

Hi Darko, the freeview wrapper script sets up libraries used by freeview.bin, so the error you get when only calling freeview.bin is expected. There is something odd going on with your PATH after sourcing the TCL package. Can you send me your tcl_setup file in $FREESURFER_HOME/bin? It would

Re: [Freesurfer] Non-rigid registration approaches

Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for

Re: [Freesurfer] fmriprep to fsfast interface

sorry for the delay, see below On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote: Hello, I just wanted to follow up to see if anyone could help with any of my questions, particularly # 1. Thank you! Matt Boggess

Re: [Freesurfer] mri_anatomical_stats with lobeStrict annot for multiple subjects

Run it for each subject using -f subject/stats/lh.lobesStrict.stats, then use aparcstats2table with -p lobesStrict to get a summary across all subjects On 4/16/18 7:18 AM, Fernanda Hansen P. de Moraes wrote: Douglas, I'm already extracting the data with mris_anatomical_stats -a

Re: [Freesurfer] unable to open freeview

Hi Andrew, thanks for getting back so quickly. Here are the outputs: “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14 (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec" I added echo $PATH right before the “freeview.bin $argv” line in the freeview script, and the output

Re: [Freesurfer] mri_deface keeps seg faulting

Can you ls /usr/local/freesurfer/stable6/bin If so, you could put that at the start of your path to get the release 6 binaries. -rob On Apr 17, 2018, at 11:39 AM, Warner, Graham Cary > wrote: Hi, I'm trying to deface an MEMPRAGE dataset

Re: [Freesurfer] Map the vertices that show a relationship between the FC (obtained by FS-FAST)

Yes, that looks correct. If you are interested in the offset, you should probably demean the thickness. You can do this by running mri_glmfit --y rh.thickness.10B.mgh --osgm --surface fsaverage rh --o glm.thickness --save-eres This will produce a file called eres.mgh in the output. This is

Re: [Freesurfer] unable to open freeview

Hi Darko, there’s a big difference between using single vs double quotes in shell scripting – single quotes prevent variable expansion. Your modification to tcl_setup actually renders your PATH completely unusable. The quote syntax in the setup scripts shouldn’t cause any problems, and your

Re: [Freesurfer] unable to open freeview

Hi Andrew, thanks a lot for your feedback! I renamed the original fine, so it is now called just tcl_setup, and here is the output I got after typing "freeview" /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi n:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/

Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

Hi Doug, I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI Analysis, but it does not indicate how a comparison should be made between the two groups that I have. It only gives information on how to perform a one sample group mean test (osgm). In addition, when you

Re: [Freesurfer] unable to open freeview

Hi Andrew, OK, so here is what happened: After adding the echo $PATH under the first line, my output is now this: "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/b in:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/ Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/

Re: [Freesurfer] unable to open freeview

Are you using a bash shell? If you are, there should be a file located at ~/.bashrc (it’s a hidden file in your home folder) Andrew From: Darko Komnenić Date: Tuesday, April 17, 2018 at 2:24 PM To: "Hoopes, Andrew" Cc: FS Help

Re: [Freesurfer] Recon-all w/ Hammersmith atlas

Hi Doug, Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference. Best, Ryan -- Ryan Flores Clinical Research Coordinator From: