[Freesurfer] Recon-all (Data for test )

Hi Where can i find data to test freesurfer I want to test recon-all command and then get volume of hippocamp!! Thanks alot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Th

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

awesome! thanks a bunch Don. -zack On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N. wrote: > Hi Zack, > > > > It looks like mris_info send that matrix out on the error output rather > than the standard output. > > I just tried it and you can get it by redirecting both to your file like > th

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

hmmm, not sure why. If this is a problem we can certainly change it, just let us know On Thu, 5 Mar 2015, Krieger, Donald N. wrote: Hi Zack,   It looks like mris_info send that matrix out on the error output rather than the standard output. I just tried it and you can get it by redirecting

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Hi Zack, It looks like mris_info send that matrix out on the error output rather than the standard output. I just tried it and you can get it by redirecting both to your file like this: Try mris_info lh.pial >& lh_info.txt Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurolog

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Thanks bruce. It will work out fine if I can just pull out that c_(ras) array in a pipelined way to apply it to the ascii data. I'm struggling a bit to achieve that though. I think because mris_info outputs the tables of *_(ras) info in a strange way. For example, if I try to cat the output of mri

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Hi Zack the ascii format I don't think supports the c_ras info, which is why you see a shift cheers Bruce On Wed, 4 Mar 2015, Zachary Greenberg wrote: Ok I figured out that this shift corresponds to the c_(RAS) value in the header of lh.pial, which you can get with 'mris_info lh.pial' Altern

Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Ok I figured out that this shift corresponds to the c_(RAS) value in the header of lh.pial, which you can get with 'mris_info lh.pial' Alternatively you can get the first coordinate and subtract it from the first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0' Is there a way I'm not thin

Re: [Freesurfer] tksurfer overlay threshold

Phew! > On Mar 4, 2015, at 5:05 PM, Hirsch, Gabriella > wrote: > > It works. I will play with this a bit. Thank you! > > > Gabriella > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fisch

Re: [Freesurfer] tksurfer overlay threshold

It works. I will play with this a bit. Thank you! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, March 04, 2015 4:42 PM To: Freesurfer support list Subject: Re: [Frees

Re: [Freesurfer] TRACHEAL error

* I’m trying to use trac-all > On Mar 4, 2015, at 4:42 PM, Emad Ahmadi wrote: > > Hello Freesurfers! > > I’m trying to use tracheal -prep, and I’m getting an error. Would you please > help me with figuring out where the problem is? The log file is attached. > > Thank you very much, > Emad >

Re: [Freesurfer] tksurfer overlay threshold

you need it to be: % sclv_set_current_threshold_from_percentile .7 .8 .9 or something like taht On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > OK, I tried that, and it does load however I get this message in the terminal: > > tksurfer: run tcl script: threshold.tcl > Wrong # args: sclv_set_curr

[Freesurfer] TRACHEAL error

Hello Freesurfers!I’m trying to use tracheal -prep, and I’m getting an error. Would you please help me with figuring out where the problem is? The log file is attached.Thank you very much,EmadEmad Ahmadi, MD---Research FellowDepartment of RadiologyMassach

Re: [Freesurfer] tksurfer overlay threshold

OK, I tried that, and it does load however I get this message in the terminal: tksurfer: run tcl script: threshold.tcl Wrong # args: sclv_set_current_threshold_from_percentile thresh mid slope% Also, the threshold continues to be the same as the default Thanks! Gabriella

Re: [Freesurfer] tksurfer overlay threshold

try: sclv_set_current_threshold_from_percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Hi Bruce, > > I have been in touch with Zeke, who was kind enough to help me update my > version of Tksurfer. Unfortunately, this has not solved my problem (see > below). > > I am atta

[Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Hi all, I discovered that converting the mesh data from freesurfer lh.pial format to ascii (.asc) causes a shift in the coordinates of the mesh. You can see this by overlaying the two surfaces in freeview, and looking at the difference between the [0 0 0] surface RAS coordinate in lh.pial vs lh.pi

Re: [Freesurfer] lGI ?h.pial-outer-smoothed

Hi Giedre, Can you send me just the pial surface of this subject, and the recon-all.log (in the scripts folder) and I'll have a look. Please also let me know which version of freesurfer you are running, and which matlab version. Best, Marie On Mar 4, 2015, at 3:08 AM, "Stripeikyte, G." mail

Re: [Freesurfer] tksurfer overlay threshold

Hi Bruce, I have been in touch with Zeke, who was kind enough to help me update my version of Tksurfer. Unfortunately, this has not solved my problem (see below). I am attaching here my command prompts in case I have missed anything; tksurfer subject rh inflated -overlay /media/seagate_extern

[Freesurfer] Fwd: OHBM Glass Brain Award Reminder: Nomination Deadline March 13th

fyi Forwarded Message Subject:OHBM Glass Brain Award Reminder: Nomination Deadline March 13th Date: Wed, 04 Mar 2015 11:20:59 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] tksurfer overlay threshold

Hi Zeke and Bruce. Thanks for catching the type. Though, I'm still getting the "invalid command name" error Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, March

Re: [Freesurfer] tksurfer overlay threshold

oh, thanks Zeke for catching that Bruce On Wed, 4 Mar 2015, Z K wrote: > Hi Gabriela, > > You might have a typo. Its "set_current_threshold_from_percentile" not > "set_threshold_from_percentile" as you have in your email. > > -Zeke > > On 03/04/2015 11:07 AM, Bruce Fischl wrote: >> you would nee

Re: [Freesurfer] tksurfer overlay threshold

Hi Gabriela, You might have a typo. Its "set_current_threshold_from_percentile" not "set_threshold_from_percentile" as you have in your email. -Zeke On 03/04/2015 11:07 AM, Bruce Fischl wrote: > you would need to include parameters, but that doesn't explain your error. > What version of tksurfe

Re: [Freesurfer] tksurfer overlay threshold

I'm using freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I'm not sure how to check the version of tksurfer specifically? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fisch

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

mris_preproc might work. You could also use mri_concat (mris_preproc is a front end for mri_concat) On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote: > > Am 03.03.2015 um 14:42 schrieb Douglas N Greve : > >> Some of this Martin will have to comment on, but my comments below >> >> On 03/03/201

Re: [Freesurfer] fsFast by Octave - minor problems

Thanks Antonin, I've incorporated the rho1 change into fast_selxavg3.m. Was there a change that would fix the parfile problem? On 03/04/2015 08:00 AM, Antonin Skoch wrote: > Dear Freesurfer experts, > > I run fsFast by Octave and I came across minor problems, which are > specific to Octave, to

Re: [Freesurfer] tksurfer overlay threshold

you would need to include parameters, but that doesn't explain your error. What version of tksurfer are you using? It is probably too old On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Hi Bruce, > > I tried using the command set_threshold_from_percentile as a tcl script but I > got the followin

Re: [Freesurfer] order of fMRI prepro

My conclusion at the time that I put the stream together (15 or so years ago!) was that there was not a clear case to be made for doing it in either order when using an interleaved acquisition. When using a sequential acq, then it is clear that you do mc first then stc. Given that a strong cas

Re: [Freesurfer] tksurfer overlay threshold

Hi Bruce, I tried using the command set_threshold_from_percentile as a tcl script but I got the following error: tksurfer: run tcl script: threshold.tcl invalid command name "set_threshold_from_percentile"% Do I have to add values to the tcl command as well?

Re: [Freesurfer] tksurfer overlay threshold

Hi Gabriela did you try my suggestion to call set_threshold_from_percentile from the tcl command line? You can also try it from the tksurfer command line with -pthresh where all the args should be in [0,1] cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > I'm just trying to fig

Re: [Freesurfer] tksurfer overlay threshold

Hi Gabriela they set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Thanks Bruce! > > I tried using the command: > > sclv_set_current_threshold_from_percentile > > The tri

Re: [Freesurfer] tksurfer overlay threshold

Thanks Bruce! I tried using the command: sclv_set_current_threshold_from_percentile The tried using the values .92, .925, .99 as noted on the wiki but I'm still not quite sure what these percentages do in terms of setting the threshold? Thanks! Gabriella -Original Message- From: fr

Re: [Freesurfer] tksurfer overlay threshold

I'm just trying to figure out what the min. and max. threshold should be in function of the distribution in order to obtain the most accurate representation of the overlay data in the visualizer. Any thoughts? Thanks! Gabriella -Original Message- From: freesurfer-boun...@nmr.mgh.harva

[Freesurfer] order of fMRI prepro

Dear Doug,   I have a small question. What is the reason that FsFast does motion correction first and then slice time correction? Does it really make a lot of difference if you change the order of the preprocessing or is this just some ideological stuff?     P.S.   Excuse me for writing y

Re: [Freesurfer] Problems with quantitative T1 images and Freeview

If I set window min to 0 and window max to 3000 the images are displayed as expected. Christina Rossmanith -- Dept. of Neurology University Hospital Mannheim University of Heidelberg On 06.02.2015 12:17, Pernille Iversen wrote: ​ g466_qMRI_R1.nii.gz

Re: [Freesurfer] label

Hi Fabrizio the strange error message is a bug in our reporting (which I just fixed), but it isn't the source of your problem. Does the cortex.label file exist? Note that you are specifying the right hemi label file for the left hemi stats, which is almost certainly wrong. I also don't think y

Re: [Freesurfer] Fwd: Recon-all Error

Hi Hassan you need to add some directives to recon-all to tell it what to do. For example, if you add "-all" to your command line it will do everything it knows how to (pretty much) cheers Bruce On Wed, 4 Mar 2015, Hassan bakhshi wrote: HI, Im using freesurfer newly, i have a folder of a

[Freesurfer] fsFast by Octave - minor problems

Dear Freesurfer experts, I run fsFast by Octave and I came across minor problems, which are specific to Octave, to get it to work: I needed to update Octave from my default version 3.2.4 to version 3.8.1. (version 3.2.4. did not have required textread function). Paradigm file cannot have trail

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Dear Douglas, thank you for the file and response. This new cluster-sess file works OK. Antonin _ From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] To: Antonin Skoch [mailto:a...@medicon.cz], Freesurfer@nmr.mgh.harvard.edu [mailto:Freesurfer@nmr.mgh.harvard.edu] Sent: Tue, 03 Mar

[Freesurfer] label

Dear FreeSurfers, I need to extract mean thickness from a manually defined label which is now in subjid/label (named mpfc.label) I tried with mris_anatomical_stats using the -l flag but here is what I got iMac-di-Mac:label fabriziopiras$ mris_anatomical_stats -l subjid/label/rh.cortex.label -b