[Freesurfer] FDR in FS-FAST

Hi list,I have two concerns, please:1) It is possible to apply FDR correction on rs-fMRI seed based analysis by FS-FAST? If yes, I can I do it?2) I have apply the FS guidelines and I have used Montecarlo correction with threshold at 1.3 but in the within group analysis the clusters are very larg

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

Hi Fengji we are looking into it and will hopefully have an answer in the next day or so cheers Bruce On Mon, 7 Dec 2015, Fengji Geng wrote: Hi Bruce,  Thank you for your response on my question.  I am also wondering how long it would take to fix the bug. As we are looking forwarding to us

Re: [Freesurfer] Left and right white matter intensity ratio

Hi again, Just following up with my last email. Also, is it more accurate to compare the gray-white contrast on both hemispheres in the same ROI than to compare white matter intensity only? Thanks, Sabrina On Fri, Dec 4, 2015 at 10:53 AM -0800, "Sabrina Yu" mailto:sabrina@ucalgary.ca>>

Re: [Freesurfer] FDR in FS-FAST

On 12/07/2015 08:35 AM, std...@virgilio.it wrote: > Hi list, > I have two concerns, please: > 1) It is possible to apply FDR correction on rs-fMRI seed based > analysis by FS-FAST? If yes, I can I do it? try this binary ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr > 2) I

Re: [Freesurfer] ASCII Error

can you send me /Users/marc/Desktop/brainscan/DICOM/PA00/ST00/SE01/IM00 ? Also, what version of FS are you using? On 12/05/2015 01:39 PM, Marc Callison wrote: > Yes I don't think that is it because it processes some of the files. > Not sure though. > > I did try the mri_convert

Re: [Freesurfer] Left and right white matter intensity ratio

On 12/04/2015 01:53 PM, Sabrina Yu wrote: > Thanks Doug, those are calculated by pctsurfcon correct? yes > > Is there also a way to separately measure white matter intensity, not > a gray-white contrast? You can re-run pctsurfcon specifying the tmp dir. When you do this it will not delete the t

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Can you send me one of the e0070_CC12_new.aseg.stats files? On 12/06/2015 08:12 AM, UQAM wrote: > Hi Bruce, > > We used these: > > mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d > 12 e0070 > ... (for all the subjects from e0042 to a0040) > > mri_segstats --seg $SUBJECTS_DI

Re: [Freesurfer] Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)

For those who do not know, Apple's latest release of OSX 10.11 (El Capitan) implements SIP (https://support.apple.com/en-us/HT204899), a sort of security protection technology, that unfortunately breaks the way freesurfer passes library paths. We are currently making changes to the code so that f

Re: [Freesurfer] Freesurfer 6 - exited with errors

Not sure. Can you run this command cd /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/label mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white and send the terminal output. Does it not fail for th

Re: [Freesurfer] Freesurfer 6 - exited with errors

Hi Scott, hmmm, I know it says "exited with ERRORS", but I don't actually see any errors. Did it appear to finish properly? Are the results visually ok? ZBruce On Tue, 8 Dec 2015, Scott Quadrelli wrote: Hi All,  I am trying to track down the source of an error on one of my first runs usi

Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

Hi Doug, See attached an example of an aseg.stats file for subject e0070 ( e0070_CC12_new.aseg.stats) Regards, Genevieve On Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve wrote: > Can you send me one of the e0070_CC12_new.aseg.stats files? > > On 12/06/2015 08:12 AM, UQAM wrote: > > Hi Bruce,