Re: [Freesurfer] Unpacking mosaic dicoms

08/10/2015 08:31 AM, Eiran Vadim Harel wrote: > Hello Freesurfers, > I am using freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0. > I tried unpacking mosaic functional dicoms taken with siemens prisma > scanner using: > > dcmunpack -src > /users/ei

[Freesurfer] Unpacking mosaic dicoms

Hello Freesurfers,I am using freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.I tried unpacking mosaic functional dicoms taken with siemens prisma scanner using: dcmunpack -src /users/eiran/Desktop/BSMT/201_/Study20150415_184518_65000 -targ /Applications/freesurfer/BSMT_PROJECT/bsmt201 -run

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

Doug,It works well now,Many thanks!,Eiran On Friday, March 6, 2015 9:28 PM, Douglas N Greve wrote: sorry, gave you a linux binary. Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit.mac On 03/06/2015 02:25 PM, Eiran Vadim Harel wrote: > Hi D

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

e wrote: > Can you upload the ces.nii.gz and cesvar.nii.gz files to our filedrop?f > > On 03/06/2015 12:23 PM, Eiran Vadim Harel wrote: >> Hi Doug, >> It seems ok, no isolated voxels. >> I attach it. >> Any other ideas? >> Thanks, >> Eiran >>

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

/mask.nii.gz and see if there are a bunch of isolated voxels? On 03/05/2015 11:50 PM, Eiran Vadim Harel wrote: > > > > > Hi Doug, > Thanks for your reply. > This is the terminal output: > > [Eran-Harels-MacBook-Pro:doors_group_51014/doors11.lh/r-vs-nr] eiran% > m

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

ull terminal output from the first call  to mri_glmfit-sim? doug On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote: > Hello Freesurfers, > > I use freesurfer v5.3.0 > > When I do group analysis correction for multiple comparisons for lh as > follows: > > mri_glmfit --y ces.nii.gz

[Freesurfer] mri_glmfit-sim Error

Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows:  mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I

Re: [Freesurfer] confirm 5db71d8d19a634948b059d302f95d798f665a638

Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows:  mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I

Re: [Freesurfer] recon-all problem

x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Fri Sep 14 13:32:22 EDT 2012 > > /cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358 > > > > On 09/14/2012 01:01 PM, Eiran Vadim Harel wro

Re: [Freesurfer] recon-all problem

harder/slower to > unpack data here. > doug > > On 09/14/2012 11:06 AM, Eiran Vadim Harel wrote: >> Hi all, >> Is there a change in the unpacking of the MPRAGE and DICOM files? >> The names of the files have changed. >> what file name should be put in the command

[Freesurfer] recon-all problem

Hi all, Is there a change in the unpacking of the MPRAGE and DICOM files? The names of the files have changed. what file name should be put in the command: recon-all -i./file name -s subjectname Thanks, Eiran ___ Freesurfer mailing list Freesurfer@nmr.mgh

[Freesurfer] Error in preprocessing

Hi, I am using stable5.0-env. I have run the pre[processing command: preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I got this ERROR message: /autofs/space/shimshon_002/users/eiran/contproc/1411_MC RunList: 005 006 007 --- ** --- --

[Freesurfer] funcroi-config -frame question

Hello, I did an FIR analysis and want to get the activation measure for specific ROI at consequent time frames. mkanalysis-sess -analysis context_FIR.rh -surface fsaverage rh -fwhm 5 -paradigm sca_wca.par -event-related -fir 4.4 17.6 -refeventdur 2.2 -mcextreg -TR 2.2 -nconditions 2 -force