Re: [Freesurfer] tksurfer vertex location

Dear Bruce, Thank you for the reply but as you mentioned that tksurfer is deprecated, is it possible to do the same from QDEC ? i.e Can I get all the values from the plot (or save the plot) which we get in QDEC for significant cluster ? Thank you. Regards, Nabin On Fri, Jan 20, 2017 at 4:06 PM,

[Freesurfer] qdec on LGI data

Dear FS experts I want to perform a 2-sample test on my LGI data using qdec (whole brain analysis with potential covariates). I already ran the recon-all -s my_subject_id -qcache -measure pail_lgi command for each of the subjects and included pial_lgi as measure in the QDEC Design tab. However

[Freesurfer] Edits to aseg [repost]

Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid I assume the -subjid is the name of the edited time point and is the name of the recreated volumes? Thank you, Tamar

Re: [Freesurfer] tksurfer vertex location

btw, in tksurfer you can type the vertex no you want into the vertex field. If you want to extract it programatically, then you can run something like mri_segstats --vox vertexno 0 0 --id 1 --i yoursurfacemap.mgh --avgwf out.dat On 01/23/2017 05:29 AM, Nabin Koirala wrote: > Dear Bruce, > > T

Re: [Freesurfer] QDEC - Controlling for gender

Have you tried normalizing BDI and age? By normalizing, I mean subtracting the mean and dividing by the stddev On 01/20/2017 05:46 PM, Jennifer Szeto wrote: > > Sorry, hope this is the right one! > > > Thanks, > > Jen > > > > --

Re: [Freesurfer] Extracting significant clusters after qdec analyses

Try mri_surfcluster. Run it with --help to get usage. You can set the threshold with --fdr. Make sure to use the --mask option passing it the mask.mgh from the qdec output On 01/22/2017 07:56 PM, Katherine Damme wrote: > Hello Everyone, > > Is there a way to extract the significant clusters as

Re: [Freesurfer] Extracting significant clusters after qdec analyses

Hi, I am not sure that someone responded you yet. Once you get results on the qdec using the shift mouse you can draw an ROI out of your cluster. Once done there is a bottom in the guy called “add the selection to the ROI you will see the entire ROI highlighted. Under the “file” command you will

Re: [Freesurfer] Cortical volume from masked region

Can you upload the subject, the 500_lobes_1-in-fs.mgz file and lh.mask.mgz to https://gate.nmr.mgh.harvard.edu/filedrop2 and I'll take a look On 01/20/2017 12:08 PM, Eli Johnson wrote: > > *Hi Doug,* > > * > * > > *Thanks a lot for your help!* > > * > * > > *I have run these commands and they

Re: [Freesurfer] mri_vol2surf

Yes. Easiest way it probably in matlab. Read in a surface overlay to use as a template overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh'); overlay.vol = yourdata; MRIwrite('lh.yourdata.mgh') On 01/20/2017 11:13 PM, Zhivago wrote: > Hi, > > If I know the activation values at each ve

Re: [Freesurfer] qdec on LGI data

no, you just include demographics/diagnosis/etc in the qdec file. You should be able to select the dependent measure from the qdec control panel On 01/23/2017 05:58 AM, André Schmidt wrote: > Dear FS experts > > I want to perform a 2-sample test on my LGI data using qdec (whole > brain analysis

[Freesurfer] ?h.pial_lgi does not look right

Hello FreeSurfers, I successfully ran the command recon-all -s -localGI for one of my subjects. However, the resulted ?h.pial_lgi files don't look right to me. I am attaching a pic for the right hemi (I made sure the overlay is rh.pial_lgi). Can someone help me figure out what went wrong? Thank

[Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Dear experts, I am currently starting longitudinal analysis of data I previously corrected in cross-sectional stream (FreeSurfer v5.3). The analysis comprises quite large number of subjects - approx 150 subjects, each scanned twice. All subjects are already inspected and errors corrected in cros

[Freesurfer] Stable version of freesurfer 6.0

Hello. I noticed that the stable version of FS 6.0 was released today however, the release was dated  January 23th, 2016. Shouldn't it be January 23th, 2017? Best,Paul Sent from my BlackBerry 10 smartphone. ___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] FreeSurfer Version 6

Dear Freesurfers, At long last, the new version of Freesurfer v6.0 is available for download! For a list of what it contains, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes To download it, see this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall We are w

Re: [Freesurfer] longitudinal stream v 5.3 - transfer edits of the wm.mgz from cross to base?

Hi Antonin, in most cases it should be sufficient to only edit wm.mgz in the base, instead of editing all time points. This is a big time saving especially if you have many time points. I don’t think merging edits from cross will work well, as there could be atrophy and lots of non-linear def

Re: [Freesurfer] Extracting significant clusters after qdec analyses

Thank you so much! This got me to the stage of having separate labels for each significant cluster, but I would like to extract the values from each subject to look at the raw data. Do I have to use mri_label2label to move the label into each individual's space? Can I use aparcstats2table to get

Re: [Freesurfer] Extracting significant clusters after qdec analyses

It is probably better to work with the y.mgh file that qdec produces. It is in fsaverage space. If you create an ocn file with mri_surfcluster, you can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the output with --avgwf to get a matrix of nsubjects by nclusters (make su

Re: [Freesurfer] FreeSurfer Version 6

Congratulations! I just updated the FreeSurfer BIDS App to version 6.0.0: https://github.com/BIDS-Apps/freesurfer It's already on Docker Hub. All you need to do to grab it is to run: docker run -ti --rm bids/freesurfer:v6.0.0-1 Best, Chris On Mon, Jan 23, 20

Re: [Freesurfer] mri_vol2surf

That makes life so easy! Thanks Douglas. Cheers, Zhivago... On Tue, Jan 24, 2017 at 1:03 AM, Douglas N Greve wrote: > Yes. Easiest way it probably in matlab. > > Read in a surface overlay to use as a template > > overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh'); > > overlay.vol =