[Freesurfer] Postdoc position at MGH/Harvard

External Email - Use Caution Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts,

Re: [Freesurfer] c_ras for HCP compatibility

External Email - Use Caution Were the images acquired with the animal in a funny position relative to humans? That might be the issue. I would convert DICOMs to NIFTI prior to FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels match the brain (e.g. i

[Freesurfer] Longitudinal stream finalsurfs misalignment?

External Email - Use Caution Hey all, I have a group of subjects with 2 time points that I've run thru the longitudinal processing stream. All goes OK until I run the recon-all -long and the resulting .long. subject dirs have the finalsurfs misaligned (i.e. one subject has the

[Freesurfer] Questions about labels and tkmedit

Hi all, ? I know tkmedit has been deprecated, but we're thinking about using it just for quality check purposes since we found that it is less resource intensive. We're trying to load multiple labels, is there a way to do that so that each label is assigned a different color (we know that's po

[Freesurfer] mkcontrast-sess question

Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single subject functional data with 18 different contrasts, and I am willing to weight the different contrasts as (for example) ascending linear. Something like: mkcontrast-

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

This is a bug. I've fixed it in our development version. You can download an update from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote: External Email - Use Caution Dear FS's experts, I am trying to downsample some surfac

Re: [Freesurfer] timewindow parameter in mkanalysis-sess {Disarmed}

External Email - Use Caution Yes I did. Caspar On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Did you put -timewindow before -gammafit ? > > > On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > Hi

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

Did you put -timewindow before -gammafit ? On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi Doug, apart from the question whether or not to set the timewindow parameter to 80 for MION responses, I noticed that there is a discrepancy between analysis.info

Re: [Freesurfer] multiple comparisons correction for brain-behaviour correlations

I think you could get the p-valueus for the clusters and do FDR on those (or maybe the most significant of more than one cluster in a given comparison) On 9/11/19 9:26 AM, Annelies Vant Westeinde wrote: External Email - Use Caution Dear members, I have run several analyses in which we

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

oh I see. I thought you meant the file format was not binary. Hmmm, not sure. Maybe Doug will have some insight, as I didn't think surf2surf would binarize by default Bruce On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote: External Email - Use Caution Hi Bruce, The input file h

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

External Email - Use Caution Hi Bruce, The input file has not only binary values (0 or 1) it is made of float values, whereas the output mri_surf2surf contains only binary values. Best, Matthieu On 13/09/2019 15:52, Bruce Fischl wrote: Hi Matthieu sorry, I don't understand.

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

Hi Matthieu sorry, I don't understand. All the files are binary, no? Are you getting an error? cheers Bruce On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote: External Email - Use Caution Dear FS's experts, I am trying to downsample some surface data from fsaverage to fsaverage6 with th

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

glad it worked out Bruce On Fri, 13 Sep 2019, 3 6 wrote: External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong 在 2019年9月13日，上午12:00，f

[Freesurfer] c_ras for HCP compatibility

External Email - Use Caution Hi Y’all, I was wondering if Y’all could tell me how c_ras is calculated in the x_form matrix for orig.mgz? I’ve been using some animal brains, and the pipeline works very well at creating surfaces and aligning them to their coresponding image for f

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong > 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道： > > Re: Hippocampal-subfie