Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Tracula Error -preproc Segmentation fault (core dumped)
by Kristina Jelinkova 01 Sep '16

01 Sep '16

Hello everyone, I've been using Tracula for a while now with much success (and help from the archive) but I've run into an error I haven't been able to solve. I have several subjects for which trac-all -preproc ends with Segmentation fault (core dumped) I don't think it's a mistake with my directories, they appear correct and I've ran numerous subjects successfully like this already. The dti data and aparc+aseg also appear normal. I'm attaching the trac-all log and error log from one of these problematic subjects. Any insight would be greatly appreciate! Thank you, Kristina Jelinkova

2 1

white matter errors due to inhomogeneities (bright spots) in cortex
by Benjamin Baird 01 Sep '16

01 Sep '16

Dear Freesurfer experts, We are currently working with some scans that were collected on a GE 3T scanner. The goal is to analyze cortical thickness. The scans seem to be relatively high quality with the exception that there are what appear to be inhomogeneities in the intensity of the gray matter (appears too bright in places), which is causing the WM to extend/jump into cortex (see attached image). We're wondering if there are any parameter adjustments to recon that might help with this as the errors occur frequently enough that fixing them all manually will be fairly cumbersome. This type of error doesn’t seem to be discussed very much in the available information on freesurfer quality control as far as we’ve seen. Thanks in advance for any thoughts recommendations or advice you might be able to offer. Best regards, Ben

2 1

bigventricles, inaccurate segmentation
by Carol Nguyen 01 Sep '16

01 Sep '16

Hello FreeSurfer Developers, I am attempting to segment a brain with large ventricles. I was able to create a decent brainmask.mgz but the aseg segmentation after running autorecon2 and autorecon3 is neglecting a part of one hemisphere (see a picture attached). I tried to readjust the talairach parameters with tkregister without success. Running autorecon2 with "-bigventricles" flag did yield a similar result as running without it. Lastly, for your information, I use FS v5.3. I am also attaching the recon-all.log from the most recent attempt. Can you please advise me how to get the correct segmentation of such a brain? Thank you! Best regards, Carol *Carol Nguyen* University of Minnesota, Twin Cities Researcher | Department of Pediatrics Division of Neuropsychology nguy1903(a)umn.edu

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white matter errors due to inhomogeneities (bright spots) in cortex
by Benjamin Baird 01 Sep '16

01 Sep '16

Dear Freesurfer experts, We are currently working with some scans that were collected on a GE 3T scanner. The goal is to analyze cortical thickness. The scans seem to be relatively high quality with the exception that there are what appear to be inhomogeneities in the intensity of the gray matter (appears too bright in places), which is causing the WM to extend/jump into cortex (see attached image). We're wondering if there are any parameter adjustments to recon that might help with this as the errors occur frequently enough that fixing them all manually will be fairly cumbersome. This type of error doesn’t seem to be discussed very much in the available information on freesurfer quality control as far as we’ve seen. (ps I tried to post this yesterday but I think I made a mistake and it didn't go through so I am resending) Thanks in advance for any advice you might be able to offer. Best regards, Ben

1 0

Re: [Freesurfer] data from different MRI scanner
by Bruce Fischl 01 Sep '16

01 Sep '16

Hi rujing that can be tough. If all your group1 are on one scanner and all group2 are on the other how can you tell the difference between a group effect and a site effect? At the very least you should scan some people on both scanners. cheers Bruce On Wed, 31 Aug 2016, charujing123 wrote: > Hi all > I collected two groups: each participant in group A collected from site 1; > Part of group B collected from site 1 and part of group B collected from > site 2. Can I compare the cortical thickness between these two groups > directly? > thanks. > rujing > > 2016-08-31 > > ____________________________________________________________________________ > charujing123 > >

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Pial refinement with FLAIR
by Eelco van Duinkerken 01 Sep '16

01 Sep '16

Dear all, Sorry for spamming, as I have posted this message about 2 weeks ago, but didn't receive an answer just yet. I probably did something wrong :). I've been preprocessing, in FS5.3, 3T GE data in controls, obese and diabetes patients and adding the available flair to do the pial refinement as follows: recon-all -i t1 -s participant -all -FLAIR flair -FLAIRpial This works excellent for most of the scans. Unfortunately, for some scans adding the flair leads to some interesting refinements, either extending outside of the brain.mgz or going deep into the white matter. I didn't notice any misregistrations of the flair to the T1 scan when checking the bb-registration. I have added some screenshots and the recon-all.log files. The red lines represent the pial with the flair refinement, and the blue lines the pial without the refinement. As you can see, these interesting segmentations are not there when the flair is no used. Does anyone know what is going on? Thanks a lot, Eelco -- Eelco van Duinkerken, PhD Pontifícia Universidade Católica | Department of Psychology | R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900 | Brasil | E-mail: e.vanduinkerken(a)vumc.nl | Phone: +55-21-35271855 | http://lattes.cnpq.br/7180895567820901 & VU University Medical Center | Department of Medical Psychology | De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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inclusion of both T1 and T2 in a recon-all run
by Krieger, Donald N. 01 Sep '16

01 Sep '16

Dear list: What are the advantages of including a T2 scan when running recon-all -all ? Which results can it effect and to what extent? And how sensitive is freesurfer to artifacts in the T2 scan? Is there a good reference for this/ Thanks and best - Don

5 8

nu_correct crashed
by Fanny Munsch 01 Sep '16

01 Sep '16

Hi everyone, I just installed the latest version of Ubuntu (Ubuntu 16.04 LTS) and I reinstalled FreeSurfer (centos4). When I computed recon-all it exited with errors (nu_correct crashed). I have attached the .log files. I have already used FreeSurfer with older versions of Ubuntu and I have never had this error. Do you have any idea what needs to be done? Thanks a lot ----------------- Fanny Munsch PhD in Neurosciences Engineer in MRI post-processing

1 0

3 fixed factors and matrix design
by Shady Rahayel 01 Sep '16

01 Sep '16

Greetings, I want to design a matrix that contains 3 fixed factors. The first is diagnosis (3 levels), the second is gender (2 levels), and the last is imaging site (2 levels). However, the thing is that the imaging site factor only applies to only one level of the diagnosis factor (i.e. patients from the first level of the diagnosis factor were seen in 2 different imaging sites, whereas for the two other groups of patients the same imaging site was used). I have followed the tutorials but I still be am confused concerning how I should go about creating the design matrix with 3 fixed factors. Would it be: GroupDescriptorFile 1 Title xx Class Diagnosis1-Male-Site1 Class Diagnosis1-Female-Site1 Class Diagnosis1-Male-Site2 Class Diagnosis1-Female-Site2 Class Diagnosis2-Male-Site1 Class Diagnosis2-Female-Site1 Class Diagnosis3-Male-Site1 Class Diagnosis3-Female-Site1 Input etc etc... Afterwards, if I'm looking for a difference between Diagnosis1 and Diagnosis2, what would be the contrast? 0.25 0.25 0.25 0.25 -0.5 0.5 0 0 ? Thank you very much for your help, Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

2 1

mri_glmfit: Cannot allocate memory
by Heidi Foo 01 Sep '16

01 Sep '16

Dear FreeSurfer team, I tried to run glm_fit to fit group membership. For this model, I have 3 diagnostic groups namely, HC, MCI, AD, and added lobar (Frontal, Parietal, Occipital, Temporal) WMH as the covariates. My contrasts are as follow: Group membership: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal MCI_HC: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal MCI_AD: 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0 Frontal/Parietal/Occipital/Temporal AD_HC: 0 0 0 -1 0 1 0 0 0 0 0 0 0 0 0 However, I got the error message that matlab element type is not a matrix and another error that it cannot allocate memory. Attached the error log and the command for your reference. I am not sure what went wrong, any help will be great. Many thanks, Heidi

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Freesurfer September 2016