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30099 discussions

Tracula_critical issue
by Alshikho, Mohamad J. 24 Nov '14

24 Nov '14

Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file "pathstats.overal.txt" regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three "pathstats.overal.txt" files for the same subject after three consecutive runs for the "trac-all -path -c" (the same subject) Looking forward for your support Thanks

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Regarding recon-all
by Gunjan Gautam 24 Nov '14

24 Nov '14

Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan

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Amygdala subfields
by stdp82＠virgilio.it 24 Nov '14

24 Nov '14

Dear all, is the amygdala subfields segmentation available or you are working on it? Thanks, Stefano

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Re: [Freesurfer] Repost: estimating lesion size on surface
by Timothy Meier 23 Nov '14

23 Nov '14

Hi Bruce, Sorry, I did a poor job of describing the problem. We are trying to do an analysis of subject specific abnormalities on the surface. Instead of a traditional analysis assuming that patients have homogenous abnormalities (for example cortical thinning in anterior cingulate) relative to a control group, we want to count the number of abnormalities over the entire surface in each subject. On the surface, abnormalities can be defined as average thickness in a small region that is >2 SD away from mean thickness in a control group in that same region. Following that, we can compare the average number of subject specific abnormalities between groups. This method has been used to identify white matter abnormalities in patient populations in which heterogenous abnormalities are expected, such as TBI patients. However, it requires an a priori decision about what constitutes an abnormality. In this case, we need to specify it in number of vertices. We have previously used 128 ul as our defined abnormality size in the volume. Our first thought was to use that as a starting point and translate the volume to surface area or number of vertices. Is there a reasonable way to approximate how many voxels get translated into surface space? And is there a reasonable way to approximate how much area each data point would have on the surface? One approach we are considering is to calculate the average gray matter volume, surface area, and number of vertices from the aparc.stats file. With this information we'd have an approximate relationship between volume, surface area, and # vertices. We are curious if this seems like a reasonable choice, or if you have any thoughts on how to go about this. Thanks a lot, Tim On Fri, Nov 21, 2014 at 11:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Repost: estimating lesion size on surface (Bruce Fischl) > 2. Odd thing about mris_convert? Position changed from > freesurfer format to .stl (ting xu) > 3. prefrontal cortex label (Anna Jonsson) > 4. Re: Odd thing about mris_convert? Position changed from > freesurfer format to .stl (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Nov 2014 16:45:17 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Repost: estimating lesion size on surface > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.11.1411201644480.6947(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Tim > > can you elaborate what the issue is? If you have binary lesion maps inthe > volume, can't you just sample those onto the surface and measure surface > area directly? I think I am missing something > > Bruce > On Wed, 19 Nov 2014, Timothy > Meier wrote: > > > Hello, > > I just wanted to repost this to see if anyone had any thoughts on an > > appropriate 'lesion' size for a pothole analysis performed on the > surface. > > We want to compare the average number of small surface lesions (estimated > > from cortical thickness) across single subjects for a control group > relative > > to our patient group. > > > > We have done similar analyses in the volume for white matter, so one > thought > > was to use that same lesion size. However, that requires estimating a > > surface area from our previously used volume. > > > > Any thoughts on how to approach this, or thoughts on an appropriate > lesion > > size to use would be appreciated. > > > > Thanks, > > > > -Tim > > > >

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1-minute Science writing Survey
by Alejandro Vicente Grabovetsky 23 Nov '14

23 Nov '14

Dear Freesurfers, Please fill in my 1-minute anonymous survey (for more info, see text below): https://qtrial2014az1.az1.qualtrics.com/SE/?SID=SV_8HdufImIrB3JXyR My name is Alejandro (Sasha) Vicente Grabovetsky. I took a break from Neuroimaging to work on my other passion, science communication and programming tools to help scientists write more effectively and I want to find out what other scientists would like to have to make paper (and grant) writing easier and better. Constructive feedback on survey and idea very welcome. Best, Sasha -- Vicente Grabovetsky, Alejandro (Sasha) Entrepreneur, PhD uk.linkedin.com/in/sashavg

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tractstats2table for dwi motion
by Chung, Yoonho 21 Nov '14

21 Nov '14

Hi Anastasia, I was wondering if there is a flag in the tractstats2table function that extracts all the variables in the dwi_motion.txt file for all subjects and put them into a single spreadsheet. Thanks! Best, Yoon

2 1

Command '-qa' in TRACULA
by Anri WATANABE 21 Nov '14

21 Nov '14

Dear FreeSurfer experts, I'm running pre-processing steps in TRACULA separatelly and could neither find the context about quality assessment step nor run the command 'trac-all -qa -c <configulation file>. I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion (64-bit). Could anyone solve this problem? Thank you. Anri ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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TRACULA - Error: bvecs and bvals don't have the same number of entries
by Tadeu Kubo 21 Nov '14

21 Nov '14

Dear FS Experts, I'm trying to work with the DTI Siemens (non MGH) and is not working. An error occurs in step "Tensor Fit”. II tried a solution that have worked as substitute bvecs values before this step manual (by original bvecs) and it works great (is meant by: continued)!. Surely I'm doing something wrong, but not yet identified. I would like your help. Sorry for the basic question, but I’m starting with TRACULA. Attached files: .log bvecs.txt bvals.txt

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TRACULA bedpost error
by Worker, Amanda 21 Nov '14

21 Nov '14

Hello, I am trying to run the second step of the TRACULA processing which is: trac-all -bedp -c /home/... I am currently using freesurfer v5.3.0 and I get the following error: WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri subjectdir is /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS006/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage Unable to read script file because of error: error opening bedpostx: No such file or directory Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Exiting. I have read that this may be a bedpostx FSL problem, however I am not familiar with this. Do you have any advice on how to overcome this problem? Thanks in advance, Amanda

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Tracula_average_average center
by Alshikho, Mohamad J. 21 Nov '14

21 Nov '14

Hi Anastasia, One of Tracula's output is the "pathstats.overal.txt" and in this file we have a list of numbers. Kindly what is the difference between the metrics average and the metrics average center also which one do you recommend to do statistic? Thanks, Mohamad

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