Re: [Freesurfer] selxavg3-sess /tmp dir out of space

External Email - Use Caution /usr/local/freesurfer/stable5_3_0/bin/freesurfer On Wed, Jun 6, 2018 at 12:23 AM, Douglas Greve wrote: > what version of fs are you running? > > On 6/5/18 10:02 PM, Jiahe Zhang wrote: > > External Email - Use Caution >

Re: [Freesurfer] selxavg3-sess /tmp dir out of space

t; set the TMPDIR env variable to point anywhere you want > > > > On 06/04/2018 02:57 PM, Jiahe Zhang wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > While running selxavg3-sess on a large functional s

[Freesurfer] selxavg3-sess /tmp dir out of space

like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern

[Freesurfer] subcortical analysis in native space

mkanalysis-sess -surface $subjectname and the output is as expected. Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] preproc-sess

; On 08/31/2017 11:47 AM, Jiahe Zhang wrote: > > Dear Freesurfer experts, > > > > I have two questions regarding preproc-sess: > > > > 1) What is the default algorithm that does the functional-anatomical > > registration? And is there any way to change the

[Freesurfer] preproc-sess

to keep the image in native space, should I be using -noreg or -noinorm? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] mri_glmfit-sim --grf question

Hi Doug, it turned out to be just a viewer glitch. I can see the map now with the expected clusters. Thanks so much for your help! On Mon, Jul 24, 2017 at 4:15 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 7/24/17 4:12 PM, Jiahe Zhang wrote: > > That ma

Re: [Freesurfer] mri_glmfit-sim --grf question

too > small for GRF. Probably you need something like 3 (p<.001). If you want to > use 1.3, then use permutation. > > On 7/19/17 2:56 PM, Jiahe Zhang wrote: > > Dear Freesurfer experts, > > I'm trying to run multiple comparisons correction using mri_glmfit-sim. > Si

[Freesurfer] mri_glmfit-sim --grf question

? Is there anything I should change in my command? Here is the command: mri_glmfit-sim --glmdir r_PCC_glm --grf 1.3 pos --cwp 0.05 --2spaces Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789

[Freesurfer] selxavg3-sess outputs

if the t.nii.gz and z.nii.gz maps contain standard t and standard z scores. Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] FsFast Functional Connectivity Analysis

.fsaverage.lh.nii.gz -t fmcpr.up.sm6.fsaverage.lh.nii.gz This will bring up an overlay as well as a time course On 08/11/2014 05:05 PM, Jiahe Zhang wrote: Both looked fine. First value in .mincost is .45 On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] FsFast Functional Connectivity Analysis

-config specify -seg yourseg.mgz 1 where yourseg.mgz is the output of mri_label2vol and 1 refers to the fact that the output volume is a binary mask where your ROI is 1 and everything else is 0 doug On 09/12/2014 09:05 AM, Jiahe Zhang wrote: Hi Doug, I was able to get the surface

Re: [Freesurfer] FsFast Functional Connectivity Analysis

. Does this happen in the volume and the surface? Have you checked the registration to assure that it is accurate? On 08/06/2014 06:33 PM, Jiahe Zhang wrote: Hi Doug, I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http

Re: [Freesurfer] FsFast Functional Connectivity Analysis

is for a good registration, but typical values are about .5 or so. If it is .8 or more, it is probably a problem (and probably the initialization is not good) On 08/11/2014 04:35 PM, Jiahe Zhang wrote: I'm not sure how to check the registration. I see a register.dof6.dat being produced for each run

[Freesurfer] FsFast Functional Connectivity Analysis

-surface fsaverage lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 5 -per-run -lpf .1 5. ANALYSIS selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 Thanks, Jiahe -- Jiahe Zhang Ph.D. Student

[Freesurfer] mri_convert fails to properly convert DTI dicoms

Hi, I had a strange problem trying to convert DTI dicoms. When I used the following command to convert a raw dicom to nifti image, I obtained a 64-volume nifti that only contains one horizontal slice of the brain. mri_convert [input Dicom] [output nifti name] Does anyone have ideas for why this