Re: [Freesurfer] Cortical thickness

Hi Doug, I did not specify anything in the mris_preproc, so it would be using the unsmoothed data. I only specify smoothing during the mri_surf2surf, which is 15 and then run glmfit. So what could be the reasons why i'm getting a residual fwhm of 47? Regards, Joshua On Thu, Jun 6, 2013 at

Re: [Freesurfer] max thickness value

I just found mris_thickness. which has a setting to override the default 5mm. you just run it. whoops. I'm very tired. apologies. I just assumed it would be hard. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] averaging tracts?

Hi all, Thanks for tracula , which I think is a terrific tool. Is there any way to average tracts across subjects for viewing purposes? I have in mind somehting along the line of a group average merged_avg33_mni_bbi.mgz. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S.

[Freesurfer] Group analysis

Under fsaverage/surf there is both an lh.white and an lh.white_avg file, while under average/surf there's only lh.white_avg. I repeated the mri_surf2surf command above with --s fsaverage instead of --s average (since I understand in this case it's the same thing), and then it ran to

Re: [Freesurfer] maximum thickness value?

Hi Colin you can use mris_thickness -max 100 ... to change the saturation point of the thickness measures. cheers Bruce On Thu, 6 Jun 2013, Colin Reveley wrote: I'm using data that's 0.35mm isotropic (and lower, but I've just noticed this). to do that I alter the header so that the voxels

Re: [Freesurfer] Saving subjects

Hi Gari I took a quick look at the images and the surfaces look reasonable. What are the problems you are having? There's a lot of dropoff at the vertex in the data, probably because of your coil geometry. Is this the problem you are referring to, that superior wm/gm is not captured by the

Re: [Freesurfer] Saving subjects

Thanks Bruce, yes, the problem was that the box wasn't set up properly and we lost several subjects because of that (head cut at the top). I'll just try with the control points then, thanks! Gari On Thu, Jun 6, 2013 at 3:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Gari I took a

Re: [Freesurfer] SPM ROI to Cortical Thickness

I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land. tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img I am wondering because when I look at the segmentation for

[Freesurfer] (no subject)

Hello, I am currently attempting to download the freesurfer software onto my mac device from the website, but I am having trouble. None of the links will open, and when I tried typing the wget (curl-O for me) command into my command line, nothing happened. Any suggestions? Thanks, David

Re: [Freesurfer] SPM ROI to Cortical Thickness

Hi Stephanie, I don't know which recommendation you are referring to. We get a lot of emails, and I can't remember each one. Can you repost with the full thread? doug On 06/06/2013 10:40 AM, McMains, Stephanie wrote: I am wondering why you didn't tell them to go through fsvarege space? I

Re: [Freesurfer] (no subject)

David, Are you using the links from this page? http://surfer.nmr.mgh.harvard.edu/fswiki/Download I just tested the download from two different computers on two different networks and both were successful. There was another post to the freesurfer list a couple weeks ago claiming to have the

Re: [Freesurfer] averaging tracts?

Hi Matt - Thanks for your kind words! The merged_*.mgz file is just a 4D mgz file where each frame corresponds to one of the 18 tracts. The only special thing about this mgz file is that it has some special fields in its header that tell freeview how to display each tract (color, name, and

[Freesurfer] Enquire about running FreeSurfer {Disarmed}

Hello I have a question regarding the installation/running FreeSurfer.I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot.However when I follow the steps for testing (https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer), I

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

what command is not found? On 06/06/2013 11:58 AM, pablo najt wrote: Hello I have a question regarding the installation/running FreeSurfer. I have just completed the installation and got the confirmation that Free surfer was installed. Please see snapshot. However when I follow the steps for

[Freesurfer] autorecon3 error

Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this

Re: [Freesurfer] autorecon3 error

Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name

[Freesurfer] mri_convert

Hi free-surfer folks, I have some subjects with L-R header flipped in nifti's. Is it possible to flip the header using mri_convert so that I can have the right orientation information for subjects. Please let me know. Thanks, -Siddharth ___

[Freesurfer] The feasibility of this procedure

Dear FS, I want to do an analysis with freesurfer but this is relatively complicated. I would like to know whether this is doable by freesurfer. I first want to create a custom template based on my subjects and I have seen the SurfaceRegAndTemplate page and this should be the place where I

Re: [Freesurfer] mri_convert

You will be much better off if you can convert properly from DICOM. If that is not possible, you can use --left-right-reverse with mri_convert to change the header (put not pixel data) or --left-right-reverse-pix to change the pixel data (but not head). doug On 06/06/2013 12:27 PM, Ray,

Re: [Freesurfer] The feasibility of this procedure

Hi Miao yes, it should be. Why do you need to create your own template? That makes it a lot more complex (and computationally intensive) cheers Bruce On Thu, 6 Jun 2013, 淼 wrote: Dear FS, I want to do an analysis with freesurfer but this is relatively complicated. I would like to know

Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 17

was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130606/bd5b6a96/attachment-0001.html -- Message: 2 Date: Thu, 6 Jun 2013 08:03:25 -0700 From: David Dalton d...@rice.edu mailto:d

[Freesurfer] Base Pial Surface Edits

We have recently run a set of longitudinal data (FreeSurfer5.3) and are making edits to the base pial surfaces. It is clear that there are two different ways of doing pial edits including: 1. editing the brainmask.mgz and 2. the brain.finalsurfs.mgz. I recognize that they are specific ways

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

HelloMy previous problem seemed to be fixed by reinstalling xquartz.However, the strange thing that I get it that I can perfectly run the following and display the images.This is what I have done. (commands in yellow) * setenv FREESURFER_HOME /Applications/freesurfer/* *source

[Freesurfer] AR2 Error

Hi everyone-- I emailed the other day about hyperintensity after running motioncor. We've skipped motioncor in our processing now, but we keep getting this error while running AR2. \n mri_ca_register -invert-and-save transforms/talairach.m3z \n mri passed volume size is different from the one

Re: [Freesurfer] AR2 Error

Hi Erin, thanks for reposting. Can you post the recon-all.log file? doug On 06/06/2013 02:37 PM, Erin Browning wrote: Hi everyone-- I emailed the other day about hyperintensity after running motioncor. We've skipped motioncor in our processing now, but we keep getting this error while

Re: [Freesurfer] AR2 Error

The log file for recon-all is too large. How should I send it? On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Erin, thanks for reposting. Can you post the recon-all.log file? doug On 06/06/2013 02:37 PM, Erin Browning wrote: Hi everyone-- I emailed

Re: [Freesurfer] AR2 Error

Yes, it was. I tried copy and pasting it and just attaching the log file. Can I paste urls here? I'll just upload it to pastebin or something like that. On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: That's weird, people upload their recon-all.log files all the

Re: [Freesurfer] AR2 Error

Here is the log file. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9 Thank you! On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning brown...@uwm.edu wrote: Yes, it was. I tried copy and pasting it and just attaching the log file. Can I paste urls here? I'll just upload it to pastebin or

Re: [Freesurfer] AR2 Error

Thanks Doug! I'll run it with AR2+AR3 from now on. On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: OK, this is a known problem when running recon-all with -autorecon1 -autorecon2 but not autorecon3. If you run it with -autorecon3, then it should run all the

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

As suggested, I have modified the .csh file (since the last version does not have a .cshrc file).I have edited according with my current directories, but when I try source $FREESURFER_HOME/SetUpFreeSurfer.csh I get the following: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0

Re: [Freesurfer] Still confused by group analysis..

Thanks Doug, So if I want to use the study-specific average subject surface with mri_surf2surf, rather than the generic fsaverage one, how can this be done given that the required ls.white file only exists in the latter but not in the former? Can I just rename (or duplicate) ls.white into

[Freesurfer] field of value too small, wrap-around

Hello, We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc

[Freesurfer] R: R: Re: R: Re: Tracula

Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in command line. Now I'm running trac-all -prep but I have this error: writing registered surface to

Re: [Freesurfer] field of value too small, wrap-around

Hi Maria if the brain wraps from back to front then it can't be recovered. Nothing to do with the analysis - the imaging data itself is corrupted. sorry Bruce On Thu, 6 Jun 2013, Maria Kharitonova wrote: Hello, We have a relatively small FOV in our study because we mostly scan kids.

Re: [Freesurfer] R: R: Re: R: Re: Tracula

HI, A patch is now available for the mris_resample : Command not found error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample --Lilla On Thu, 6

Re: [Freesurfer] R: R: Re: R: Re: Tracula

This issue has come up on the list a few times recently. Please search for your error in the email archives before posting to the list. Thanks. On Thu, 6 Jun 2013, std...@virgilio.it wrote: Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in

Re: [Freesurfer] field of value too small, wrap-around

Hi Maria, if the warp around is such that the wrapped part of the brain ends up outside the brain but on the other side of the FOV, you can maybe fix it partially (e.g., if the frontal cortex is wrapped to the back but not into the occipital cortex). You would just need to copy the respective rows

[Freesurfer] Yeo_JNeurophysiol11_FreeSurfer.zip

Hello, I'm trying to download ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip (as linked from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011), however, the file doesn't seem to be available, or the server is not responsive. Is there another

[Freesurfer] R: Re: R: R: Re: R: Re: Tracula

The file that I have downloaded is named unKnow and it is of 7.6 MB. I have placed it in $FREESURFER_HOME/bin directory but the error persist. Anastasia, I apologize. Please, have patience with me :-) but .. when I search for mris_resample in mail list I did not found any indication. I found my