Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

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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[FSFAST] Matlab parallel
by Seung-Goo KIM 06 Feb '17

06 Feb '17

Hi all, So this is a question about running FAST through matlab parallel desktop: I know it is very funny (and inefficient) because I open up a bash in the matlab to run a csh script that generates and runs a matlab code, but just I’m familiar with matlab in doing many things including string manipulation, so that’s how I’m doing now. If there are matlab scripts that does a similar thing as csh scripts, it would be nice. Anyway, I realized that I cannot run all the fitting with different parameters and with the identical name of model (the GLM directory name) at the same time because the code appears to refer to the directory at $SUBJECTS_DIR. But I tried to run multiple subjects (with all different GLM names in their own native spaces) through MATLAB on a server, it returns (seems just one of random subject): > ERROR: could not read /tmp/tmp354512.nii > rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory > ERROR: loading ${filename}.nii.gz as analyze So I traced back to the functions that return those errors (i.e., load_nifti.m run in MRIread.m) and it seems to be something with the temporary directory managed by matlab workers. The temporary file seems to be only necessary for nii.gz file. If so, I would rather just use .nii file format (or maybe .mgz?) format instead of dealing with the void complexity. Then can it be done by just putting: > setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) before I run "preproc-sess" and "selxavg3-sess” in my scripts? Best regards, -- Seung-Goo KIM

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possible atlas error to report
by Levman, Jacob 06 Feb '17

06 Feb '17

Hi there, I've been conducting an asymmetry analysis based on FreeSurfer measurements. There are regions of the brain with known left-right asymmetry such as BA44 which exhibits strong leftward asymmetry (the left side is bigger than the right). This is accurately reflected when you compare the BA44 GrayVol measurement from lh.BA.thresh to rh.BA.thresh. However, in the lh.BA and rh.BA results, the BA44 GrayVol measurements consistently indicate a rightward asymmetry (right side larger than the left side) though this conflicts with known findings in the literature for this region of the brain and is the opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh. This indicates that the lh.BA and rh.BA results may be left-right inverted in BA44 and possibly in other regions as well. Thanks, Jacob ?

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