Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Free surfer Gray Matter
by Limachia, Gaurang (NIH/NINDS) [F] 09 May '16

09 May '16

Hello Dr. Fischl, 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. I am attaching a screen shot of the brain as well as the tool that I used to add the pixel, and you will be able to see the white pixels I am mentioning above. Thank you for your time. Best Regards, Gaurang Shyam Limachia

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Freesurfer for other species
by Daya P 09 May '16

09 May '16

Hi all, I was wondering if anybody else is using Freesurfer on non-human subjects? Thank you, Daiana

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Re: [Freesurfer] Cortical Thickness of a Volume-defined ROI
by Mahtab Farahbakhsh 09 May '16

09 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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Manual correction for brainstem module
by Jacky Lee 09 May '16

09 May '16

Hi freesurfer experts, I have successfully run the brainstem module for some subjects. On visual checking, I can see there are voxels with T1 hypointense lesions mislabelled as non-brainstem tissue. I manually corrected them on the brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected volume of the brainstem substructures? Thanks. Regards, Jacky

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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

2 1

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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