Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

R: Re: Perirhinal 6.0 error
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

I have resolved my error in running old script Thanks Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 6-feb-2017 19.12 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] Perirhinal 6.0 error > >please send more info > > >On 02/03/2017 04:09 PM, stdp82(a)virgilio.it wrote: >> Hi, >> >> by running the mri_label2label to calculate perirhinal morphometry the >> following error occurs with FS6.0 >> >> ERROR reading sub_DIR/label/rh.perirhinal.label >> >> >> Thanks >> >> >> Stefano >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >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. > >

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Using the "Smooth Surface" tool in Freeview
by Huang, Caleb (NIH/NINDS) [F] 06 Feb '17

06 Feb '17

Hi, I'm new to Freesurfer and am still figuring out the ins and outs of cortical reconstructions. One option I've been looking into is the "Smooth Surface" tool in Freeview. It seems to make it easier to identify handles and other errors especially in subjects with significant atrophy, but I'm not sure what's the best way to use it. I did a few trial runs with various smoothing parameters, and it looks like running autorecon2-wm and autorecon2-pial with autorecon3 both eliminate the effects of the smoothing (parcellation stats don't change), while running autorecon3 alone changes all the stats other than the number of vertices and thickness averages. In particular, the surface area and gray matter volume decrease by 5-10% depending on the parameters I choose (taubin vs. standard, number of iterations, lambda/frequency cutoff), which isn't unexpected. Would you recommend using smoothing to help fix small errors and if so, what parameters would you recommend? Thanks, -Caleb

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Re: [Freesurfer] Error: if: Expression Syntax.
by Anderson Napolitano 06 Feb '17

06 Feb '17

Hi Dr. Greve, Thank you very much. That worked beautifully. For those who are having the same problem as I did, the command: mri_coreg --s subject_name --mov static_template.nii.gz --reg registration_matrix.reg.lta creates a text file named registration_matrix.reg.lta on your current directory. Before, I was overwriting static_template.nii.gz by registration_matrix.reg.lta which in turn makes the command: tkregisterfv --mov static_template.nii.gz --reg registration_matrix.reg.lta --surfs fail as static_template.nii is the same as registration_matrix.reg.lta. I highly doubt others will make the same stupid mistake as I did but I outlined it nonetheless. Again, thank you Dr.Greve for all the help. I appreciate every bit of it. -Anderson

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Perirhinal 6.0 error
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Hi, by running the mri_label2label to calculate perirhinal morphometry the following error occurs with FS6.0ERROR reading sub_DIR/label/rh.perirhinal.label Thanks Stefano

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Re: [Freesurfer] Error: if: Expression Syntax.
by Anderson Napolitano 06 Feb '17

06 Feb '17

Hi Dr. Greve, Ah I see. If that's the case, is the command: mri_coreg --s subject_name --move dicom_template --reg registration_matrix generating the registration matrix? I have ran a search on the subject folder for any *.reg* file and has only found lh.sphere.reg and rh.sphere.reg on the subject's folder. Are those the registration matrices that I am looking for? Thank you for your time. I really appreciate the help. -Anderson

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entorhinal cortex
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Hi list,for entorhinal and perirhional cortices in FS-FAST should I use 1006 ctx-lh-entorhinal or 216 entorhinal_cortex?Thanks Stefano

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FS-FAST 6.0
by stdp82＠virgilio.it 06 Feb '17

06 Feb '17

Hi list,I wonder which are the main changes in FS-FAST 6.0?The links used in previous version are still useful? ThanksStefano

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Recon-all finished with errors
by Bunday, Karen 06 Feb '17

06 Feb '17

Dear FS members My previous email was flagged by the fraud detection checks, perhaps due to the attachment. I am sending this again to see if that was the problem. Apologies for the repeat of information. I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log. Could someone help interpret the log so that I may be able to process this subject? Many thanks Karen Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG

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Probability Maps
by Pascal Goodman 06 Feb '17

06 Feb '17

Hello Freesurfer, I do have a question. Can FS take probability maps of tissue segmentation as prior? Thanks, Pascal

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Whole brain mediation analysis
by Michael Kranz 06 Feb '17

06 Feb '17

Hi, I was wondering if you guys had any suggestions for developing a whole brain mediation analysis through Freesurfer or can think of any examples (e.g., does thickness mediate the relationship between age and cognition)? It looks like SPM has something (whole brain mediation analysis), and given the outputs from mri_glmfit, it seems like it would be possible with Freesurfer. Best, Mike -- Michael Kranz Graduate Research Assistant | Beckman Institute University of Illinois 314-323-1329

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Freesurfer February 2017