Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

Cortical Parcellation
by Heidi Foo 08 May '16

08 May '16

Dear FreeSurfer experts, I apologise for posting this again. I am unable to get the volumes for the cortical regions despite following the commands on https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation I am using FS5.3 to do the parcellation. I created a folder called "labels" inside each of my subject folder. Attached the output. I tried to use mri_mergelabels -i label1 -i label2 -o outputlabel. Attached the command as well as the output. *I am not sure if the output is correct and also, how should I get the total volume for each lobe out? * Thank you so much for your help. Regards, Heidi Foo

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correcting defects
by Bruce Fischl 07 May '16

07 May '16

Hi Katarina how did you create the orig.mgz for these subjects? Either some registration failed badly or you tried to average data from different subjects (see attached tiff of one of the orig.mgz you uploaded) cheers Bruce On Thu, 5 May 2016, Katarina Trojacanec wrote: > Hi Bruce, > > I uploaded the subject dirs (base for TP1_4 and TP2_4, as well as the > cross-sectionally processed time points for TP1, TP2, and TP4). In the > meantime, one of them, template TP1_4 has finished with error. The other one > (base TP2_4) is still running. > > What do you suggest in this situation. > > Sorry for the inconvenience. > > Cheers. > > Katarina Trojacanec, M.Sc. > Teaching and research assistant > > Faculty of Computer Science and Engineering > Ss. Cyril and Methodius University - Skopje, Republic of Macedonia > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> > Sent: Thursday, May 5, 2016 4:20:31 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > Hi Katarina > > if you want us to look you need to upload the entire subject dirs (tarred > and gzipped). TO visualize it, look at the inflated.nofix in freeview in 3D > mode and just see what the big defects look like. If you load the > orig.nofix at the same time you can goto a vertex in the big defect you see > on the inflated by typing its index into the info winwo for the orig.nofix. > This will be automated in v6 > > Bruce > > > On Thu, 5 May 2016, Katarina Trojacanec wrote: > >> Thank you. >> I have uploaded the files (lh.inflated_TP_1_4.nofix and >> lh.inflated_TP_2_4.nofix). >> >> What should I do as a next step? >> >> Cheers >> Katarina Trojacanec, M.Sc. >> Teaching and research assistant >> >> Faculty of Computer Science and Engineering >> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >> >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> Sent: Wednesday, May 4, 2016 2:35 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Correcting defect >> >> sure. Or you can load the ?h.inflated.nofix and look at it - it should be >> obvious if there is a huge defect (you can also load the file >> ?h.defect_labels as an overlay on that surface and it will show you the >> segmentation of the defects) >> >> cheers >> Bruce >> On Wed, 4 May 2016, Katarina Trojacanec wrote: >> >>> >>> Dear FreeSurfer Team, >>> >>> >>> I have been trying to run creation of template with FreeSurfer. However, >>> for two cases for one patient (case 1: template based on TP1 and TP4, case >>> 2: template based on TP2 and TP4), the correcting defect step is running >>> too long. According to the information in the mail archive, the defects are >>> probably too big, and that is the reason for the long processing. >>> >>> >>> May I send you via ftp the subjects directories so you can help me to >>> proceed with this subject, because I am not able to figure out and correct >>> the problem? Should I send you the base directories in their current state >>> or the cross-sectionally processed time points as well? >>> >>> >>> Best Regards, >>> >>> >>> Katarina Trojacanec, M.Sc. >>> Teaching and research assistant >>> >>> Faculty of Computer Science and Engineering >>> Ss. Cyril and Methodius University - Skopje, Republic of Macedonia >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Freesurfer
by Shyam Limachia 06 May '16

06 May '16

To whom it may concern: I had question about Freesurfer, I am trying to correct the gray matter volume. So I made changes by adding pixels to the contour, and ran recon-all. Subsequently, when I opened up the file after performing recon-all I saw were the pixels (which are white) that I added when I was making the changes. How do you make changes to the gray matter, and what type of recon command should I run after making the changes. I searched through the various tutorials, but that further confused me. Thank you for your time. Best Regards, Gaurang Shyam Limachia

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Resting-state fcMRI analysis with GLM
by Eun Young Choi 06 May '16

06 May '16

Hi all, I'd like to run a resting-state fcMRI analysis within the GLM (mri_glmfit), but I'm not completely sure how to set this up in the FSGD file. I've seen the online tutorial of age vs cortical thickness, but I'm not sure how to specify a regressor with a timeseries. Does anyone have an example of an FSGD file for this? Thanks! Eun Young

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does lGI needs correction for any global measure?
by maaike rive 06 May '16

06 May '16

Dear freesurfer experts,I have a question regarding correction of cortical measures or global measures (ICV, total surface area). As I understand from literature and the freesurfer wiki, a model for thickness should not be corrected for ICV (since thickness does not scale with total brain volume), but surface area should be corrected since is does scale with total brain volume. Three questions:1. should I use ICV or should I use total surface area (TSA) as covariate in the model to correct surface area (by the way, average ICV and TSA do not differ between the groups to compare )?2. does lGI also need correction? does it scale with volume? If so, do I need to correct for ICV or for TSA? Usually I see no correction but some do use ICV...3. even if the average of certain measures (like ICV/TSA, or gender, or age) does not differ between groups, should they be added to the model? If I do not correct for gender, for example, my results change and most papers do use age and gender as covariates if they compare groups despite a lack of differences between groups... Thanks,Maaike

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patient case study at two time points
by Zeng, Qi 06 May '16

06 May '16

Hi All, I was running freesurfer for a patient case of two time points. Will you suggest to run it as a group, such as one time point as a template and followed by longitudinal study, discussing atrophy or run these two time points separately as two individual, running everything such recon-all, dt-recon twice and comparing the result, such as thickness, volume and FA? BTW, I post a question about FA display before: will anything lead to a rectangular FA display, with extra diffusion out of the brain skull (no errors during recon and dt …)? Best, Qi

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Cortical Thickness of a Volume-defined ROI
by Mahtab Farahbakhsh 06 May '16

06 May '16

Dear FreeSurfer, I am trying to find the cortical thickness of my ROI which is the perisylvian region of the left hemisphere. What I did was to define a label based on the anatomical area of this region and tried to define a ROI based on this label and the command -mri_label2volume. Howevere, I am using freeview and the tutorial that I found about this issue was based on tkmedit. Would you please guide me how I should get this done? Best Regards, Mahtab Farahbakhsh.

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Automatic parcellation of the postcentral gyrus
by pfannmoelj＠uni-greifswald.de 06 May '16

06 May '16

Dear Experts, in most of my subjects the cortical parcellation with the Desikan-Killiany atlas is all fine. I am especially interested in the postcentral gyrus. In several of my participants there is a typical problem with the automatic parcellation in this region. About half the postcentral gyrus is parcellated correctly (the lower half), but the upper half is shifted to a posterior part of the brain and the upper half of the postcentral gyrus is parcellated as the precentral gyrus. Attached you find a typical example, one hemisphere is parcellated correctly (left_hemisphere.jpg), the other one shows the problem (right_hemisphere.jpg). The postcentral gyrus is shown in red and the precentral gyrus in blue. The only difference that I can spot is in the anatomy of the superiorparietal and supramarginal regions. These regions are disconnected in the left hemisphere, but have a gyrus which connects them in the right hemisphere. May that cause the difference in the parcellations? Yours pfannmoe

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glmfit --table (by tract TRACULA outputs)
by Pedro Rosa 05 May '16

05 May '16

Dear list, I am trying to use mri_glmfit to run statistics on TRACULA outputs (by tract), as suggested by the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics) I used the following command line: mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C 2G1V-1100.mtx It ends without errors. How should I proceed with correction for multiple comparisons, as I cannot use Monte Carlo? Best, Pedro.

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no recon button
by Burke,Sarah E 05 May '16

05 May '16

Hello, I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do? Thank you

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Freesurfer May 2016