Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Recon error
by Michele Placci 29 Jun '10

29 Jun '10

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, NIFTI format (converted from DICOM) to calculate brain volume. I ran recon-all -autorecon1 -autorecon2 -subjid <..."file with extension.mgz, after the conversion with mri_convert from a unique file .nii" > and I obtained the errors that you can see in the attachments. Any suggestion? Thank you in advance. Michele.

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recon error
by Michele Placci 29 Jun '10

29 Jun '10

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, DICOM format (I have NIFTI too) to calculate brain volume. I ran recon-all -autorecon1 -autorecon2 -subjid <..."file with extension .mgz, after the conversion with mri_convert from a unique file .nii" > and I obtained the errors that you can see in the attachments. Any suggestion? Thank you in advance. Michele.

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Re: [Freesurfer] mne_analyze unable to read inflated surface
by Onerva Korhonen 29 Jun '10

29 Jun '10

Him the disk space doesn't seem to be problem - at least mne_analyze and tksurfer are working fine with other subjects with the same space. Best regards, Onerva K. Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > usually that means you ran out of disk space. Did you check? > > cheers > Bruce > On Mon, 28 Jun > 2010, Onerva Korhonen wrote: > >> Hi all, >> >> I have problems with mne_analyze - I need to do the coordinate >> alignment, but when I try to load the inflated surface (or in fact any >> surface), I get error message: >> >> mne_read_int could not read data >> >> Inflated surface doesn't work with tksurfer either. Instead I get a message: >> >> freadFloat: fread failed >> >> I don't know if it would say something more later - there seems to be >> a loop, so I have killed the program at this point. >> >> I have no idea what to do - redoing recon-all doesn't seem to help. So >> I hope someone could help me with this. >> >> Many thanks, >> Onerva K. >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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. > >

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FSGD file problems
by Theodor R?ber 28 Jun '10

28 Jun '10

Dear Freesurfers, I recently tried to correlate age in a group of subjects with their cortical thickness. After having set up an FSDG file and my contrasts, I ran mris_preproc and mri_surf2surf, and finally mri_glmfit. This, however, did not work and I got this errormessage: gdfReadHeader: reading age.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = xxx Found 1 variables, expected. 0 FSGDF Format Error: file = age.fsgd, tag=Input It looks like an error in the FSGD file but I set it up in exact accordance with the example on the website. Having one group and one covariate, my FSDG file looks like this: GroupDescriptorFile 1 Title OSGM Class Main Variable Age Input xxx Main 23.5 Input yyy Main 47.3 ... Here are my contrasts: Contrast1: 1 0 Contrast2: 0 1 and the mri_glmfit command I run: mri_glmfit --glmdir lh.age.thickness.10B.mgh --y lh.age.thickness.10B.mgh --fsgd age.fsgd --C Contrast1.mtx --C Contrast2.mtx --cortex --surf What is the problem? Thank you very much for your help! It is highly appreciated. Best, Theodor

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references to clusterwise correction for multiple comparisons
by Joonkoo Park 28 Jun '10

28 Jun '10

Dear FreeSurfers Is there a published reference to the clusterwise correction approach implemented in FreeSurfer ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwi… I'd like to cite it for those readers and reviewers who aren't familiar with this. Joon

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heterotopias
by Juranek, Jenifer 28 Jun '10

28 Jun '10

Any suggestions from anyone wrt handling heterotopias? Is it best to use a custom labelname to label them as such? Current labelname="WM-hypointensities". Cheers, Jenifer

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recon for pial and wm edits
by York, Philip 28 Jun '10

28 Jun '10

Hi all, I am currently finishing a number of wm and pial edits. Is there a command to string both autorecon2-cp and autorecon2-pial together? Thanks, Philip

2 1

(no subject)
by Elvira Fischer 28 Jun '10

28 Jun '10

Dear freesurfer users, Maybe somebody could help me with the following problem: On my retinotopic map I observe extensive blobs with max. values (turquoise and yellow, heat color map), that rather look like noise. However these blobs always appear in the same region, around the anterior portion of the calcarine sulcus in every subject, independent of which paradigm we used for the retinotopy. I use the standard protocol as described for freesurfer/FsFast Individual Retinotopy Analysis on FreeSurferWiki, to analyze my data, however use sfa2fieldsign to display the color map on the inflated surface. If someone has an explanation or a clue why I observe these blobs and/or has suggestions how to prevent them , I'm very thankful. Thanks a lot Best, Elvira

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Serious failure of surface reconstruction
by Cindy Eckart 28 Jun '10

28 Jun '10

My last email seemed to be too big because of the picture, so I try it without the picture.... Dear FreeSurfers, after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yesterday) I realized that the white and pial surfaces were reconstructed very badly (see tiff attached). Searching within the mailing list, I found a case that might be very symilar to my problem. Unfortunatly the discussion aborts at this entry http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11770.html without offering a solution. Thus, I wanted to ask if you might have any idea what might have caused this problem and how I could fix it? Thank you very much in advance! Kind regards Cindy ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de

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mne_analyze unable to read inflated surface
by Onerva Korhonen 28 Jun '10

28 Jun '10

Hi all, I have problems with mne_analyze - I need to do the coordinate alignment, but when I try to load the inflated surface (or in fact any surface), I get error message: mne_read_float could not read data Inflated surface doesn't work with tksurfer either. Instead I get a message: freadFloat: fread failed I don't know if it would say something more later - there seems to be a loop, so I have killed the program at this point. I have no idea what to do - redoing recon-all doesn't seem to help. So I hope someone could help me with this. Many thanks, Onerva K.

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Freesurfer June 2010