[Freesurfer] Intensity normalization issues leading to improper segmentation

Dear Freesurfer list, Sorry to bother by posting again, but I am bit stuck by this issue and would be really glad to get some help on that issue. Of course I can upload some data if needed. Thanks a lot! Maybe I am hoping for a miracle with my question, but I am bit desperate after unsuccessf

Re: [Freesurfer] Freeview recon button

Thanks a lot Bruce! I will wait for v6 and check freeview then. for the gyrification question i added a link. Here it is: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again! Best, Walid On Fri, Jul 1, 2016 at 12:08 PM, Bruce Fischl wrote: > Hi Walid >

Re: [Freesurfer] Freeview recon button

Hi Walid Recon editing mode is in the upcoming v6. Our recent hardware woes slowed things down a bit, but we are still hoping to get It out soon What was the gyrification question? Cheers Bruce > On Jun 30, 2016, at 10:39 PM, Walid Yassin wrote: > > Hello freesurfers, > > I downloaded freesur

[Freesurfer] Freeview recon button

Hello freesurfers, I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have the Recon edit button. I saw that someone asked about this questions twice in the archive but was never answered. There was a note in the wiki page that reads "*Note*: Recon edit mode is only available i

Re: [Freesurfer] Any updates on recon-all GPU support?

On 27 June 2016 at 01:27, Derek Pisner wrote: > Was not able to resolve this quite yet. I figured out that I had to backtrack > a bit because I was having trouble getting the complete set of data files > from the Fs ftp server using "git annex ." And now it appears that > freesurfer's entire f

[Freesurfer] Seed based volume output to surface

Good Afternoon Freesurfers, I am running a seed-based connectivity for one individual subject. The seed is in the L_parahippocampus. I have followed the steps outlined in FSFast walkthrough. Below is a list of my commands. Mind you that I was trying to keep my analysis as simple as possible before

Re: [Freesurfer] qdec load error missing BLT

Dear Joshua, we had the same problem with freeSurfer 5.3.0 on Debian GNU/Linux 8.3 (jessie). In our case this was warning, the qdec launched, however the fsgd plot functionality (interactive vertex-wise GLM plot display) did not work. It seems that the error is caused by interference of tk/blt

Re: [Freesurfer] REPOST: Skull Strip and Bad Surfaces

​ 4003_2.zip ​The zipped folder is attached. It was a bit large so please let me know if you have any difficulties opening it. Thanks for your help! Kate Katherine Reiter, M.S. Clinical Psychology Doctoral Student

Re: [Freesurfer] registering to fsaverage

Hi Trisanna what does mri_info show about spam_for_label_id_4_blur_minc1.mnc? You said it has the range of values in [0,100]? Or [0,1]? I'm not sure why mri_vol2surf would modify the values - this might have to wait for Doug to get back Bruce On Thu, 30 Jun 2016, Trisanna Sprung-Much wrote

Re: [Freesurfer] registering to fsaverage

Hi Bruce here is the output of my mri_vol2surf for a volumetric spam created in minc tools. When I then overlay this result in Freeview, it displays a Min of 127 and a Max of 255. trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_m

Re: [Freesurfer] REPOST: Skull Strip and Bad Surfaces

eek, that's pretty awful. If you upload the subject dir we will take a look cheers Bruce On Thu, 30 Jun 2016, Katherine Reiter wrote: Dear FreeSurfer experts, I am working on a data set and am having particular difficulty with one subject. It appeared the skull strip was mistakenly removing occ

Re: [Freesurfer] REPOST: Longitudinal Stream: Recon-all and template

Hi Tamara 1. Run each timepoint through the cross-sectional stream separately. 2. recon-all will figure out what files to use when you tell it to create the base. cheers Bruce On Thu, 30 Jun 2016, Tamara Tavares wrote: Hello All, I am planning to run the longitudinal stream on my data se

[Freesurfer] REPOST: Longitudinal Stream: Recon-all and template

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individua

Re: [Freesurfer] FSFAST- Cerebellum

Hi Sabin, I think fslmeants should work. But you might need to first run mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual ROIs. Also can you tell us which step generated the error "ERROR: must specify a segmentation volume"? Is this the final step? Have you tried overlaying Buck

[Freesurfer] Unsupported slice timing pattern 5 in version 5.3.0

To Whom it may concern, I have tried to run the recon-all pipeline on some T1 data and have encountered the following error: nifti1Read(): unsupported slice timing pattern 5 I have browsed the previous threads about it and it appears that it should have been fixed in version 5.3 but that is