Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

Hi Esther I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus is indeed weird. Why don't you use the 2009 version of the atlas that includes major improvements ; this parcellation is fully described in Automatic parcellation of human cortical gyri and sulci using stand

[Freesurfer] poor wm segmentation

Hello all, I have a subject for whom I have been trying to edit the wm segmentation. This last time was the fifth time I have run the subject through autorecon2 and I am still achieving quite poor wm segmentation and pial tracings. To try and solve the problem I keep drawing in more of wher

Re: [Freesurfer] poor wm segmentation

Hi Kareem, Did you check the skullstrip to see if it's correct? Sometimes that can cause problems with the surfaces. If you can send the subject over, I can take a look. -Khoa On Tue, 31 May 2011, k...@rice.edu wrote: > Hello all, > > I have a subject for whom I have been trying to edit the

Re: [Freesurfer] poor wm segmentation

You can upload this subject and we will take a look if you want Cheers Bruce On May 31, 2011, at 6:46 AM, k...@rice.edu wrote: > Hello all, > > I have a subject for whom I have been trying to edit the wm > segmentation. This last time was the fifth time I have run the subject > through aut

[Freesurfer] PhD position in functional neuroimaging

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[Freesurfer] fsaverage error with recon-all

Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage. Thanks Ayaz #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...

Re: [Freesurfer] fsaverage error with recon-all

Hi Ayaz you need to create a symlink to the fsaverage subject we distribute in your SUBJECTS_DIR if you want to get the estimate Brodmann area labels. cheers Bruce On Tue, 31 May 2011, Ayaz, Muhammad wrote: > Dear All, > I ran recon-all using single MPRAGE data set. Processing exited with an

Re: [Freesurfer] fsaverage error with recon-all

Hi Ayaz, > #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 > INFO: fsaverage subject does not exist in SUBJECTS_DIR > INFO: Creating symlink to fsaverage subject... > > ln -s /usr/local/freesurfer/subjects/fsaverage > /usr/local/subjects/fsaverage > > ln: creating symbolic link `/usr/local/subjec

Re: [Freesurfer] fsaverage error with recon-all

Thanks Bruce and Joerg, How can I create symlink to the fsaverage? I recently have installed freesurfer and I was able to run a subject last week without any error not sure why all the subjects I ran now over the weekend ended up with same error. Thanks -Original Message- From: Bruce

Re: [Freesurfer] problem creating contrast matrix for f test

Hi Pablo, unfortunately, you've run into a bug in FSFAST in that some contrast matrices cannot be easily run. It uses some complicated (overly complicated?) logic behind the scenes to create the contrast matrices, and using a custom contrast matrix is not so easy. I'll write a patch to fix this

Re: [Freesurfer] converting .nii.gz label to .label for FS

Don't use the temporal pole mask as the input to the registration. You need something with some anatomical contrast. The TP mask will basically be an empty image with a few 1s. Load a gray-scale image in fslview that matches the TP mask. Then bbregister to that gray scale image (with --12 for 1

Re: [Freesurfer] mgh conversion

Can you drop the image to me (don't email it). The drop site is below at the end of this email. doug Gabriel Go.Es. wrote: > Thank you again Doug, > > I've tryed all the possibilities you said, but still not have a nii > image, It says that it's reshaping to 6, but also when I change to > anoth

Re: [Freesurfer] Tracula bedp error

Hi Shanqing - You could try running FSL's bedpostx directly on /users/cais/STUT/tracula/S01/dmri. Our scripts have only been tested on our clusters running PBS, but the original FSL version is designed to work with SGE. If you find what's going wrong on SGE we'll be happy to incorporate any fi

[Freesurfer] Error: Bad CPU type in executable.

Hi, I recently downloaded and installed FreeSurfer on my Mac and I am having some trouble. I followed the instructions and the installation menu said that everything had been installed correctly. However, when I tried testing if everything worked using the commands provided on the FreesurferWiki

Re: [Freesurfer] Error: Bad CPU type in executable.

Hi Ashley Can you tell us in detail what OS you have? ( The version number ). Also, what commands specifically were you trying to run? Thanks Krish On Tue, May 31, 2011 at 11:45:39AM -0400, an...@pitt.edu wrote: > Hi, > > I recently downloaded and installed FreeSurfer on my Mac and I am having

Re: [Freesurfer] converting .nii.gz label to .label for FS

Okay following that, here is what I did: 1. bbregister the FSL anatomical contrast to the FS space of that subject (using the 12 dof as suggested). Checking registration seemed to be fine. 2. did mri_vol2surf of the FSL-derived mask (because when I extract masks from fslview they are extrac

Re: [Freesurfer] poor wm segmentation

Sure thing -- where and how do you structure your uploading? Thank you, Kareem Quoting Bruce Fischl : > You can upload this subject and we will take a look if you want > Cheers > Bruce > > > > On May 31, 2011, at 6:46 AM, k...@rice.edu wrote: > >> Hello all, >> >> I have a subject for whom I hav

Re: [Freesurfer] converting .nii.gz label to .label for FS

Sorry, I forgot that you were going to the surface, so dont use mri_label2vol. After #1, run tkmedit yoursubject orig.mgz -reg register.dat -overlay TP.nii.gz -fthresh 0.5 -surfs you should see the mask in red. It should also intersect the surface. If not, then something is wrong. doug k...@r

Re: [Freesurfer] converting .nii.gz label to .label for FS

OK, now check whether it overlays on the FSL template correctly in tkmedit: tkmedit -f fslgrayscaleimage.nii.gz -overlay TP.nii.gz -fthresh 0.5 where fslgrayscaleimage.nii.gz is the gray scale image that you used as the mov volume in bbregister and also used as the gray scale image in fslview

Re: [Freesurfer] converting .nii.gz label to .label for FS

This one did not overlay correctly either (see attached). This is the same mov volume/gray scale/extracted mask volume that I used as well. What does this tell us? Best, Kareem Quoting Douglas N Greve : OK, now check whether it overlays on the FSL template correctly in tkmedit: tkmedit -f

Re: [Freesurfer] converting .nii.gz label to .label for FS

Then you need to find a gray scale image/template that it does overlay properly on. We can't help you much until you do. doug k...@rice.edu wrote: > This one did not overlay correctly either (see attached). This is the > same mov volume/gray scale/extracted mask volume that I used as well. > W

Re: [Freesurfer] poor wm segmentation

You can follow instructions on this website. http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 31 May 2011, k...@rice.edu wrote: > Sure thing -- where and how do you structure your uploading? > > Thank you, > Kareem > > Quoting Bruce Fischl : > >> You can upload this subject and w

[Freesurfer] curvature of flattening

Dear FS experts, I'm making some flattenings of one subject on FS and I'm wondering if it is possible to see the ?h.curv or the ?h.sulc on grayscale and not in red-green nor in the binary gray representations of tksurfer. Regards, Gabriel. __

[Freesurfer] Appropriate positive control to for overall quality?

Hi everybody, I have been analyzing a dataset that has produced some unusual results. Does anybody have any suggestions for a general positive control to ensure data and segmentation quality? I am thinking along the lines of comparing the results of measurements with age to Salat, 2004: T

Re: [Freesurfer] curvature of flattening

I don't think so. You can display it in a heat scale by loading it as an overlay. If you save it as an rgb then strip out the color it might give you a decent gray scale. doug Gabriel Go.Es. wrote: > Dear FS experts, > > I'm making some flattenings of one subject on FS and I'm wondering if > it

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Re: [Freesurfer] curvature of flattening

Many thanks Doug, I'll give it a try ;) I guess the mgh file has been delivered to you, right? Bests, Gabriel > Date: Tue, 31 May 2011 15:34:34 -0400 > From: gr...@nmr.mgh.harvard.edu > To: gabriel...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] curvature

[Freesurfer] freeview and wm-segmentation errors

Hi, using FS 5.1 now, I encountered two problems: 1. when I try to start freeview on my personal laptop, this errors appears: [georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory However, lib

[Freesurfer] color scales for retinotopy

I am having trouble getting the script "rtview"  to work so that I can use the color scale to see phase of the polar and eccentric angles. After chmoding the script  I run the following command   ./rtview --reg LOAF_08/bold/002/register.dof6.dat --lh --ploar  --real LOAF_08/bold/rtopy.self.lh/e

Re: [Freesurfer] freeview and wm-segmentation errors

Can you email me one of the wm.mgz volume that fails? On Wed, 1 Jun 2011, von Polier, Georg Ferdinand Anto wrote: > Hi, > > using FS 5.1 now, I encountered two problems: > > 1. when I try to start freeview on my personal laptop, this errors appears: > > [georg@localhost ~]$ freeview > freeview.bi