Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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

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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/

1 0

FW: How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

________________________________________ From: Boric, Katica A. Sent: Monday, August 26, 2013 4:02 PM To: Douglas N Greve Subject: RE: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Doug! Thanks for getting back so fast! I did the registration but I only got this email: Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---------------CUT HERE--------------- kboric(a)partners.org 16851 *C9NanJsRCd7o #---------------CUT HERE--------------- and this is where I am stuck.... don't know how to procede! Thanks again, Katica ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Monday, August 26, 2013 3:59 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory? Hi Katica, on that page there is a link to the registration page. Once you register (free), you will be given a .license file doug On 08/26/2013 03:22 PM, Boric, Katica A. wrote: > Hello! > I am new to free surfer and Linux and I am having installing free > surfer. I am using Fedora on a VMware workstation > I successfully (I think) downloaded it and installed it following the > instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) > But now I am stuck trying to copy the three lines of the license info > to the file .license. > Any advice? > Thank you very much, any help is appreciated it! > > Katica > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 6

FDR in different hemispheres
by Emily Boeke 26 Aug '13

26 Aug '13

Hi Freesurfers, I have a contrast that produces comparable activation in both hemispheres. But when I set the threshold using FDR in the Configure Overlay Display window, the threshold is set to 5.1 for left hemisphere and 3.3 for the right hemisphere, leaving significant clusters only in the right hemisphere. Does someone know why the FDR threshold would be so different between the two hemispheres? Thanks! Emily

2 1

How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Boric, Katica A. 26 Aug '13

26 Aug '13

Hello! I am new to free surfer and Linux and I am having installing free surfer. I am using Fedora on a VMware workstation I successfully (I think) downloaded it and installed it following the instructions (https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) But now I am stuck trying to copy the three lines of the license info to the file .license. Any advice? Thank you very much, any help is appreciated it! Katica

2 1

Freesurfer Editing Strategy
by Khadka, Sankalpa 26 Aug '13

26 Aug '13

Dear freesurfer experts, I have a question about making edits in the freesurfer results. During the workshop which I attended this year, I learned about white matter edits and control points edits when white matter is not segmented accurately. I have used these tools quite successfully in our projects. However, in our research in multiple sclerosis, often times we encounter cases with lesions on grey matter. The lesions in grey matter causes intensity of the voxel over that region to become hypo-intense like CSF. Due to this, the pial surface line is pushed inward into the lesion, missing some grey matter around it. Since, cortical thickness is the most important measure in our research, we could like to be able to solve this issue. We would like to make sure that the pial surface line goes around the lesion without missing grey matter for accurate thickness calculation. In order to solve this issue we have tried to first delelte and fill the lesion in the brainmask.mgz with voxels with grey matter intensity in the region using the voxel editing tools (instead of 255(default) used in white matter edit, we use 70-75 for grey matter). After editing, we run recon-all with autorecon-2 and autorecon-3. Quite surprisingly, this strategy has not resolved our problem. My understanding is that the pial and main surface lines (red and yellow) were draw based on the intensity of voxel. Our question is, why would the lesions which are now filled with grey matter not treated as grey matter? We have tried this strategy, and it has not worked. What would you recommend us for solving such issue? I have attached a screen shot of a slice where you can notice that in the top right corner, the lesion on the grey matter causes the pial surface line to miss grey matter around it. Ideally, we would like the pial surface line to go around the normal grey matter surface. Thank you, Sankalpa Khadka Research Assistant Neurolgy, Yale School of Medicine

2 2

regarding adding and deleting voxels in wm.mgz and brainmask.mgz
by Mehul Sampat 26 Aug '13

26 Aug '13

Hi Folks, I see on the tutorial websites that when voxels are added to wm.mgz or brainmask.mgz, the new voxels are given a value of 255; while when voxels are deleted, these locations are set to 1. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Can the deleted voxels can be set to 0 or they have to be set to 1; Or is 0 used to differentiate the background voxels from brain voxels ? Thanks Mehul

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