Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

apply a label to an overlay in tksurfer
by Sarah Madsen 27 Aug '13

27 Aug '13

Hello, Is there a way to apply a label to a mgh file? I would like to show a gray brain with values from an mgh shown only in the significant areas (ie only within my label). Is there a way to do this? I have a set of mgh files with beta values from a regression. I also have a set of labels for the significant areas. Both sets of files were created in matlab and are in fsaverage space. I can open the two files together in tksurfer and see the entire beta map, along with the label for the significant regions. Is there a way to zero-out all of values in the mgh overlay which fall outside of my label? A command line option would be preferable, since I have several maps. Thank you very much!

2 1

Freesurfer dependencies
by ye tian 27 Aug '13

27 Aug '13

Dear Freesurfers, Where may I find a list of freesurfer dependent libraries? Thank you very much! Sincerely, Ye

2 2

Otto: update freesurfer to latest version?
by Otto Muzik 27 Aug '13

27 Aug '13

Dear All, I would like to upgrade my freesurfer distribution to the latest version - Is there an automated procedure to do this? My current version is linux-gnu-stable5-20110522 Many thanks! Otto

1 0

tutorial subject not found
by leila nasehy 27 Aug '13

27 Aug '13

Dear Supporter I am new to freesurfer and have started to download tutorial data for tracula.There is an error saying: "hostname: Host name lookup failure" what shall I do? Regards Leyla

1 0

pb reading .annot in matlab/python
by Alexandre Gramfort 27 Aug '13

27 Aug '13

hi, when trying to read the following .annot file: https://dl.dropboxusercontent.com/u/2140486/annot_pb/left_mc-z.negative.sig… using the following matlab code: -- [vertices, label, colortable] = read_annotation('left_mc-z.negative.sig.ocn.annot'); unique(label) unique(colortable.table(:, end)) setdiff(colortable.table(:, end), unique(label)) -- there seem to be a discrepancy between the "label" and the last column of colortable "colortable.table(:, end)" the script outputs: -- Reading from version 2 colortable with 7 entries read (originally none) ans = 0 2244856 3987639 5840816 11298645 13698134 16665710 ans = 2244856 3834223 3987639 5840816 11298645 13698134 16665710 ans = 3834223 -- in other words 0 is in label but not in the colortable. Should I conclude that 0 is 3834223? If so what's the proper way of figuring this out? thanks Alex

2 8

Recon-all error
by pfotiad＠nmr.mgh.harvard.edu 27 Aug '13

27 Aug '13

Hi FS Commuity, I am using the stable version 5.3 of FS to recon-all a subject of mine, but the job is aborted and gives the following message: The command that I ran is: recon-all -all -subjid /cluster/ichresearch/Petechial/MEG/CAA_022_struc Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 Found 2 runs /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax. Exit 1 Also, I tried doing the same recon-all with the stable 5.0 version and it runs fine. Therefore, I was wondering whether you could tell me why is this happening. By the way I have also attached the recon-all.log. Thank you for your time. Best, Panos

2 7

Clarification regarding bvec processing in TRACULA
by Salil Soman 27 Aug '13

27 Aug '13

Hi, After much searching, it appears to be pretty uniform that the product DTI sequence performed on GE requires the y gradient to be flipped. For the datasets with which I am working diffusion toolkit, vistalab and exploredti all require the y gradient to be flipped. However, Tracula makes appropriate outputs when I give it the default gradient table without flipping Y. When I flip Y and run it through Tracula, the forceps major is inverted (noted by checking the overlay of dtifit_fa and dtifit_V1 using fslview and by using TVglyphView using DTI-TK. I suspect that somehow Tracula is flipping the Y sign for the gradient (while the other programs I mentioned do not) - can anyone confirm this? Thanks! -Sal

2 1

bug reading BRIK
by Yuval Harpaz 27 Aug '13

27 Aug '13

Dear Team I tried to convert AFNI BRIK file to mgz using mri_convert. the MRI was shifted strangely. I overcame it by converting the MRI to nii using afni command (3dcopy) and from there to mgz with MRI convert. If you wish to fix the BRIK reader please see the info below. --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-51-generic x86_64 --------------------------------------------------------------------- shifted transformation matrix 0 0 -1 128.5 1 0 0 -127.5 0 -1 0 75.5 correct transformation matrix 0 0 -1 127 1 0 0 -127 0 -1 0 180 The MRI is aligned to a master supplied by brainhull<http://kurage.nimh.nih.gov/meglab/Meg/Brainhull>for MEG position using the procedure described in the link. I can attach a BRIK file if anyone wants to dig into it. thanks Yuval Dr .Harpaz BIU MEG lab <http://faculty.biu.ac.il/~goldsa/index.html>

2 1

Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011
by Michael Kranz 26 Aug '13

26 Aug '13

Hi all, I was wondering how I could go about getting anatomical stats for the different regions from the Choi2012 and Buckner 2011 parcellations. The Yeo 2011 cortical parcellation files were available in the fsaverage folders and I could get stats and labels for those, but I couldn't figure out how to get stats on these other two. Thanks, Mike Kranz

1 0

Re: [Freesurfer] Otto: images again (compressed)
by Douglas N Greve 26 Aug '13

26 Aug '13

This problem has been fixed in version 5.3 doug On 08/23/2013 06:48 PM, Otto Muzik wrote: > Hi Doug, > > Here are the images again - this time compressed. > The uncompressed images were rejected due to excessive > size. > > Hope you get these > > Many greetings > > Otto > > > > On Aug 23, 2013, at 11:37 AM, Douglas N Greve wrote: > >> Can you send a *single* dicom file to me? No need to copy the list >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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