Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

Regarding: Group analysis of WMHs
by Dr Sampada Sinha 08 Apr '16

08 Apr '16

Dear freeesurfer experts, I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR separately after processing T1 with recon-all. Presently, I don't have any dwi data where I can project the WMHs onto the WM tracts. Will you please tell me how do I project the WMHs of 29 MDD patients on a template (?) showing the WMH abnormalities? Or if you can please recommend a paper or freesurfer page from where I can get a step by step directions of showing WMHs of 29 cumulative MDD patients on subcortical surface. Thanks and regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

2 2

Qdec DOSS
by tom parker 08 Apr '16

08 Apr '16

Hi Freesurfers, I posted this question a few days ago but didn't get any replies. Would you mind answering this for me? I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read on several post that DOSS has some bugs related to the generation of contrasts in qdec and that mri_glmfit should be used to run a DOSS analysis. However, when I ran my analysis with DOSS in qdec I saw that the C.mat file looked like this: 1 -1 0, which seems correct to me. My question is can I use DOSS in qdec in this case? Or are there other bugs related to using it in qdec? Thank you so much!

2 1

Re: [Freesurfer] errors on the WM and Gray inflated surfaces
by pablo najt 08 Apr '16

08 Apr '16

Dear FS expert and users,We are coming across errors on the WM and Gray inflated surfaces.When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) We get only a small part of the cortex displaying. Also when we try file-label-import annotation the following error occurs:colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color table in annotation. There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.Now we are trying to figure what is that could have caused this for all subjects.We have an old instructions for freesurfer saying to to run recon-all as follows.run recon -all -s subjID /autorecon -all As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo

2 5

R-Map
by Morenikeji Adebayo 08 Apr '16

08 Apr '16

Hello Freesurfers, I'm interested in creating a group map where each vertex/voxel represents the correlation (as a correlation coefficient) between a task-related BOLD contrast values (ces.nii.gz) and a single covariate. This is analogous to a cortical thickness GLM with one group and one covariate, but I'd want an r-map instead of a log10p-map. How exactly might I do this? I’m trying to accomplish this using mri_glmfit, but I’m having generating output that is interpretable in terms of a correlation coefficient and in particular, the direction of the effect. Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 keji(a)nmr.mgh.harvard.edu

2 1

Regarding: oblique view
by Dr Sampada Sinha 08 Apr '16

08 Apr '16

Dear freesurfer experts, Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process? Thanks and regards, Sampada -- Sampada Sinha

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Freesurfer install on Debian 7.x
by Robert Welsh 08 Apr '16

08 Apr '16

hi zeke, i’m following your instructions for getting freesurfer 5.3.0 installed on debian, though i’m at 7.x as that is what came from ThinkMate on some recently delivered supermicro machines for our lab. i’m not successful, and have paused at an error. 1) libtool-bin does not exist for debian/wheezy but i decided to just plow ahead 2) in doing the “git annex get .” i get the following error (it worked for some time as grabbing things) thoughts? #———————————————error below this line———————————————————— 2016-03-29 18:12:07 (6.58 MB/s) - `/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s9167701--75de544880a3d0621958725eb3e89d31c78d13fe60276820123ad96541535099' saved [9167701/9167701] ok get vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh (from origin...) --2016-03-29 18:12:07-- http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git/annex… 600222256a7244ccd595cbe67b9ea949/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c0600222256a7244ccd595cbe67b9ea949 Resolving freesurfer.net(freesurfer.net)... 132.183.202.158 Connecting to freesurfer.net(freesurfer.net)|132.183.202.158|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 655672 (640K) [text/plain] Saving to: `/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c0600222256a7244ccd595cbe67b9ea949' 100%[===========================================================================================>] 655,672 1.36M/s in 0.5s 2016-03-29 18:12:08 (1.36 MB/s) - `/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c0600222256a7244ccd595cbe67b9ea949' saved [655672/655672] ok (Recording state in git...) git-annex: get: 5 failed ---------------------------------------- Robert C. Welsh, Ph.D. Associate Professor Department of Radiology Department of Psychiatry University of Michigan rcwelsh(a)umich.edu Associate Director, VA-fMRI Research, VA Ann Arbor ------------------------------ typos due to iPhone 4S

1 0

Issue with license
by Marita Partanen 07 Apr '16

07 Apr '16

Hi there, I'm trying to install Freesurfer onto our Mac OS X 10.10.5. I was able to download the program and install it onto the two users on this computer. I am also able to open bert using freeview, open qdec, and start the recon-all for bert. However when I try to load bert using <tkmedit bert orig.mgz> or <tksurfer bert rh pial>, I get this error ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. I do have a valid license and made a file called "license.txt" in the /Applications/freesurfer/ folder with the information sent to me in an email. I couldn't edit the "LICENSE" file that the program came with and I'm not sure if that is the issue. Any thoughts? thank you Marita

2 2

Altered cortical thickness values within two days for the same subject
by Meng Li 07 Apr '16

07 Apr '16

Hi everyone, I am trying to extract regional cortical thickness but confused with the altered values for the same subject within two days. In our experiment, participants were scanned with the identical protocol in three times continuously: including baseline, 2 hours, 24 hours later. All T1s were processed by FS 5.3 and further normalized into fsaverage space, as well as a customized ROI. Interestingly, both of the regional CT and average CT of whole brain showed impressive variance among three timepoints for the same subjects. Moreover, if the T1 in the second and the third scan was coregister to the baseline scan and rerun the pipeline, the values is not very convincing. I wonder this variance was caused by the different head position in the scanner. Is there any suggestion to get rid of that? Which cortical thickness value could be trust most in my case? Any comments is appreciated. Thank you in advance. Here is one example from my test. Subject regional CT average CT of whole brain bu45_t1 2.49833562 2.18242687 bu45_t2 2.540465325 2.233703478 bu45_t3 2.63002383 2.202483542 bu45_t2_to_t1 2.636101336 2.237099006 bu45_t3_to_t1 2.499173829 2.216584361 All the best Meng

2 1

mris_fix_topology with ROI surface
by Ajay Kurani 06 Apr '16

06 Apr '16

Hi Freesurfer experts, I wanted to create a Freesurfer surface on some of the aseg ROIs. I was able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some of the subcortical volumes for creating a surface. The mri_sphere had a big chunk that was deleted and so I wanted to run mris_fix_topology to fix this issue. In trying to run this command it appears that mris_fix_topology tries to correct based off of a brain sphere (which this ROI is clearly not) and therefore it fails. I plan to then run subsequent steps such as mris_euler number and mris_remove_intersections 1) Is there any way to fix the topology of this ROI using freesurfer tools or a way to work around this issue? Do you feel the sphere is needed for a small subcortical surface (ie globus pallidus) or is this really more for complex structures such as cortical surfaces? 2) Is there a recommended set of steps to accomplish creating a surface from the ROI that is different from what I stated? Thanks, Ajay

2 5

bbregister --init-spm with Freesurfer 6.0
by Ajay Kurani 06 Apr '16

06 Apr '16

Hi Freesurfer Experts, I was running bbregister and came across an issue. I have used previous versions of bbregister (FS 5.3.0 with spm8) with the --init-spm at it worked perfectly for a specific subject. I recently installed FS dev 6.0 with SPM12b and ran bbregister --init-spm option with the same resting state scan, and it did not move at all. When looking at the terminal I saw that when matlab started up within bbregister, the command fs_spmreg was not found. I also installed spm8 and reran the subject with the same issue. When I changed the option to --init-fsl everything worked. I checked the matlab installation and everything looks fine, so I think the issue may be the fs_spmreg function not being found. I am not sure if there is an easy fix for this, but any help would be appreciated. Thanks, Ajay

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Freesurfer April 2016