Re: [Freesurfer] Problem in upload file through ftp

Try changing dir into the source directory then do the put with only the file name and no path Cheers Bruce > On Oct 17, 2016, at 10:33 PM, Cong <3110103...@zju.edu.cn> wrote: > > Hi Bruce > full session is listed. Thank you very much. > > Best Wishes > Cong > > BrainwaverdeMacBook-Pro:~

Re: [Freesurfer] Problem in upload file through ftp

Hi Bruce full session is listed. Thank you very much. Best Wishes Cong BrainwaverdeMacBook-Pro:~ Brainwaver$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit

[Freesurfer] Generating aparc statistics that only correspond to a masked region

Hello Freesurfer's, I would like to generate the standard aparc.mgz statistics, but only for ROIs or for segments of an ROI that fall within the bounds of a mask. I've created the mask I want to use, have label files that correspond to the mask, have a masked version of the aparc.mgz, but I can't

Re: [Freesurfer] S. Nigra

not at the moment, sorry Bruce On Mon, 17 Oct 2016, Rockers, Elijah D. wrote: > Is it possible for freesurfer to parcellate the substantia nigra from a T1? > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] S. Nigra

Is it possible for freesurfer to parcellate the substantia nigra from a T1? -- Elijah Rockers Research Data Analyst Houston Methodist Research Institute O: 713-363-7729 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20

[Freesurfer] recon-all -s bert exited with errors

Hello FreeSurfer Developers, I was trying to run recon-all -all, and it failed roughly 30s after it started running, with the error message being: recon-all -s bert exited with errors. Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Platform: Red Hat Enterprise Linux Client

[Freesurfer] tkregister2 + mri_vol2vol do not transform

Dear experts, I am new to freesurfer and I am struggling making transformation of images from one subject to another as well as to a template. I have tried different ways, but I always end up with the original image as if the transformation was never applied. I used tkregister2 from command line

[Freesurfer] Question regarding Checking Longitudinal Runs: Repost

Hello, I have a question regarding the outputs to the longitudinal processing stream. I ran my two participant's scans through the Cross, then created a Base and two longitudinal runs. I am primarily interested in looking at ventricular change over time. Other than the aseg output overlaid on

Re: [Freesurfer] Quantifying volumes

Dear Doug, Thank you for your reply! This label on this specific case is basically the sum of the labels from Heschl's Gyrus, Heschl's Sulcus and Planum temporale. The labels from Heschl's Gyrus, Heschl's Sulcus and Planum temporale are firstly produced inside 'Recon-all'. The aggregation

[Freesurfer] Job offer: research-fellow position in Japan

A research-fellow post is available at the Integrative Brain Imaging Center, National Center of Neurology and Psychiatry. We are looking for a candidate with expertise in MRI, fMRI, PET (optional) image analysis and with a strong publication record. You are expected to take a lead or co-author

[Freesurfer] Volume or surface?

Dear FS experts, I want to know what is the output (volume or surface) of the following scripts. (The input is file.nii.gz which is a volumetric ) 1. spmregister --s subj --mov file.nii.gz --reg reg.dat --o file_t1.mgh #is the output file (file_t1.mgh) is a volume or a surface    2. 

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

Hi Doug, I had some additional questions regarding multiple comparisons in Freesurfer. 1) Do you correct the left and right hemispheres separately or combine both together for muliple comparison correction? 2) Say you are testing multiple contrasts in your model: A > B, A< B etc. Do you