[Freesurfer] Multiple Comparison Question for surface-based analyses

Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on them

Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

That recon-all command will not work as the FLAIR input should be a simple FLAIR image. The FLAIR will only correct the pial surface and will have nothing to do with lesion segmentation. Emily Lindermer has a tool that can take a T1 and FLAIR and produce a lesion map; but given that you already

Re: [Freesurfer] brain mask and T1 are not the same size

So you're saying that the dimension changed after you ran freeview and  saved the volume? Can you replicate it? ie, if you make a copy of the  brainmask.mgz, then edit the copy, does it do the same thing every time  you make a copy and edit it? Yes it does. I tried multiple time your suggest

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

I think there is an example on the wiki in the ROI analysis section. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs

Re: [Freesurfer] Where are time series from adjusted (post selxavg3) ROIs

Run selxavg3-sess with -svres. This will create a new folder called "eres" in the output analysis directory where the residuals will be stored. Assuming that you have mapped your data to fsaverage space, you can then create a post cing label (mri_annotation2label) and then use mri_segstats wit

Re: [Freesurfer] Running Retinotopy in FSFAST, Design Matrix has Empty Regressors

Unfortunately, the way I have the retinotopy analysis set up, both polar and eccen must be there. However, you can just copy the polar into a new folder and call it eccen and it should complete. Then you can ignore the eccen part. On 7/29/16 3:04 PM, Taylor, Johnmark wrote: Hello, I am tryi

Re: [Freesurfer] Fwd: question about volume of mask

Hi Dorsa, please remember to include previous correspondence. I'm not sure what you are referring to, but when you reslice a volume, the size of the voxels usually changes so it is impossible to have exactly the same volume. Probably the original file is closest On 7/29/16 12:08 PM, Dorsa Haj

Re: [Freesurfer] ALE map to surface

You need to run recon-all on the MNI152 T1 brain, then run mri_vol2surf passing your activation map to --mov and with --regheader, then run freeview to visualize On 8/1/16 6:38 PM, Carla Ammons wrote: Hi! I am new to freesurfer so this may be a basic question. I have an activation map (.ni

Re: [Freesurfer] Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)

The contrasts are correct. I think you have done the right thing (or as good as you can) in controlling for the scanners. On 8/1/16 10:46 AM, Oana Georgiana Rus wrote: Dear FreeSurfer Experts, I want to compare structural measures(eg. thickness) between patients and controls controling fo

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

ps. you can always just load the xyz in the label into matlab and compute the centroid On 8/1/16 10:23 AM, Sabin Khadka wrote: Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka mailto:mr.sabinkha...@gmail.com>> wrote: Hi Doug, I tried to pick up from the threa

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

Try setting thmin to something small but non-zero (eg, 10e-6) On 8/1/16 10:23 AM, Sabin Khadka wrote: Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka mailto:mr.sabinkha...@gmail.com>> wrote: Hi Doug, I tried to pick up from the thread below to get MNI coo

Re: [Freesurfer] Long seg for hippo subfields

Hi Adam, yes, a newer version is hiding. Best, Martin P.S. it is still unclear if this will make it into 6.0. But if we get lucky with a long delay of the release, the chances will significantly increase ;-) On 08/01/2016 06:50 PM, Thomas, Adam (NIH/NIMH) [E] wrote: > This look very cool: > ht

[Freesurfer] Long seg for hippo subfields

This look very cool: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields But the flag is not being recognized by recon-all using the most recent build: [adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec [adamt@f

[Freesurfer] ALE map to surface

Hi! I am new to freesurfer so this may be a basic question. I have an activation map (.nii) created via ALE meta-analysis in MNI space that I want to visualize on the surface. Do I use bbregister for this? Thanks! Carla ___ Freesurfer mailing list Frees

[Freesurfer] Poor automatic segmentation of the cerebellum

Dear list, I'm interested in measuring cerebellar volumes using freesurfer. However, the automatic segmentation (aseg) seems to be doing a poor job of capturing the whole structure for many subjects. Specifically, it is chopping off the bottom of the cerebellum. Here is an example: https://drive.

Re: [Freesurfer] mris_label2annot

Hi Caroline the colortables are in $FREESURFER_HOME. Usually we use $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Mon, 1 Aug 2016, Caroline Beelen wrote: Dear FS,   Sorry to bother again, but I’m currently in need for some quick help. Today, I also ran into another problem. I

Re: [Freesurfer] freesurfer 6.0 release date

Hi Fengji we have frozen the code and are going through various tests now so are hoping sometime in the next few weeks, but of course it's impossible to say as it depends on how well the tests turn out. cheers Bruce On Mon, 1 Aug 2016, Fengji Geng wrote: Hi fs developers,  I am wonderin

Re: [Freesurfer] Freesurfer dev version

Hi Daniel, The issue is fixed, but I don’t know if the updated version is already in dev. Zeke, can you shed some light on this? Cheers, /Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 1 Aug 2016, at 1

Re: [Freesurfer] Freesurfer dev version

It was the invalid MEX file problem mentioned in this exchange https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html I was told it would be fixed sometime this week in the dev version (and in 2 weeks when the next beta version was released). Thanks, Daniel _

[Freesurfer] freesurfer 6.0 release date

Hi fs developers, I am wondering if you have any estimation when fs 6.0 will come out. The reason that I ask this is because we are running some analysis using fs 5.1 and planning to switch to a more recent version of fs. If fs 6.0 will come out soon, we will probably hold and wait for it. If not

[Freesurfer] Cannot launch freeview

Hi Freesurfer Developers, I tried to run freeview but got this following error message. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux version:

Re: [Freesurfer] Freesurfer dev version

which error? The mri_normalize problem? If so, then yes I believe that is now fixed On Mon, 1 Aug 2016, Liu, Daniel wrote: > Hi, > > > I wanted to follow up on the error that came up in the freesurfer dev version > this past week. Has it been fixed yet? If so, has the link to the download > p

[Freesurfer] Freesurfer dev version

Hi, I wanted to follow up on the error that came up in the freesurfer dev version this past week. Has it been fixed yet? If so, has the link to the download page been changed? The one I booked marked does not lead me to the page anymore and I would appreciate it if you could direct me to th

[Freesurfer] mris_label2annot

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-at

[Freesurfer] Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)

Dear FreeSurfer Experts, I want to compare structural measures(eg. thickness) between patients and controls controling for the effects of age, gender and scanner (parts of sample were scanned in scanner 1 parts in scanner 2). I want to answer the question: *do patients and controls differ si

Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage

Anyone? Cheers, Sabin Khadka On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka wrote: > Hi Doug, I tried to pick up from the thread below to get MNI coordinates > of each destrieux parcellation region. > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html > > I create

Re: [Freesurfer] mri_label2label error

Hi > Domenico I think the problem is that you have a forward slash in your subject name, as well as your SUBJECTS_DIR and FREESURFER_HOME. Did you perhaps but them inside double quotes or something? Usually the forward slash \ let's you extend command over multiple lines, but in this case it a

[Freesurfer] Fw: Running recon-all with T1 and FLAIR

Dear FreeSurfer team, I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when run

Re: [Freesurfer] How does Optseq2 arrange order of conditions?

Dear Douglas, Thanks for your explanation. These information are helpful to me. >I'm not sure what you mean. How can it be a delay if it is after the trial is >over? I’m sorry for I didn’t describe my second question well. I think I can take another situation to describe my question. If I h

[Freesurfer] significance overlay Freeview

Dear FS, Yes, I'm running FS 5.3. :) How can I visualize the significance overlay (correctly)? Which command should I use to view a significance overlay in freeview in FS 5.3? See also my email below. Thank you very much in advance! Best, Caroline Hi Caroline, Are you running FS 5.3? The com