Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] tksurfer display problem
by Xiangzhen Kong 29 Jun '13

29 Jun '13

Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" <bnucon(a)gmail.com> wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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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Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
by Koolschijn, Cédric 28 Jun '13

28 Jun '13

Hi Martin, Unfortunately it is not a single subject, it happens to many. If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software. FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs. I'll get back to you when results of FS 5.3 are available. Cheers, Cédric On 6/28/13 2:43 AM, "Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> wrote: Hi Cedric, Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)? It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long). Best, Martin On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote: Hi Martin, Thanks for your fast response. It makes sense that in the longi-stream results should be more reliable. However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion. Any thoughts on this? Cheers, Cédric From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn <P.C.M.P.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl>> Cc: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing Hi Cedric, this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable. Cheers, Martin On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers, I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there. Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently. Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal? Many thanks! Cheers, Cédric ------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl> W http://www.dutcharc.nl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu 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. -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu

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re gcareg ?
by Dov Sadan 28 Jun '13

28 Jun '13

Hi, Thank you all for the wonderful project! >From time to time while reading some of the wiki pages it has the feeling of reading ancient Chinese. https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg I'd be happy if anyone help me understand what GCA ? and ismri/no. are ? Thanks in advance, Dov

4 6

Order of Edits + Intensity Normalization
by Peter Boulos 28 Jun '13

28 Jun '13

Hello, I have a fairly basic question regarding the order in which I should perform the edits. After running the full recon on all of my subjects I have now completed the Talairach edits and the skull strip edits on my subjects. At this point I am attempting to seek out help in terms of performing the edits on white/grey matter border from a more experienced user but have a couple of days before I can meet with them. Therefore, can I go ahead and do the pial surface edits before or does the intensity normalization and white/grey boundary edits need to be done first before the pial surface? As in will those edits alter what I do in later steps? Also, I am having a hard time understanding what I am doing with intensity normalization. Am I just ensuring that there are sections of an intensity of 110 in the white matter boundaries of each subject? Am I only looking for white matter that appears to be left out in a disastrous way in this step or should I be very meticulous about this? I am confused because I have areas considered white matter in free surfer that appear to be white matter by visual inspection that have intensities as low as 70 but then areas of the same intensity outside of the boundary. I realize that the program is probably using intensity data along with location data but do not understand how I am supposed to ensure that whether something with an intensity lower than 110 is indeed white matter by visual inspection alone. I apologize for the simplicity of my understanding at this point and thank you for your time. Peter

1 0

mri_label2vol problem
by LAOUCHEDI MAKHLOUF 28 Jun '13

28 Jun '13

Hi i run mri_label2annot to get individual annot files for all labels, then i run mri_label2vol to get nifti volumes of my labels using the following command : mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 but the result is a volume with zero values (i changed --fillthresh .5 to --fillthresh 0 and i got the same probleme) Thanks

2 2

(no subject)
by LAOUCHEDI MAKHLOUF 28 Jun '13

28 Jun '13

excuse me but i don't understand what you mean by "terminal of mri_label2volume" Thank you for help

2 3

longitudinal analyses for one group
by Sandra Preissler 28 Jun '13

28 Jun '13

Dear freesurfer experts, we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepa…) Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we dont have a control group. So we couldn't choose the group variable as discrete factor. Its an pre-post-design with only one group. Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor? Can you help us in fixing this problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

3 2

mri_label2vol problem
by LAOUCHEDI MAKHLOUF 28 Jun '13

28 Jun '13

excuse me but i don't understand what you mean by "terminal of mri_label2vol" Thank you for help

1 0

trouble in freesurfer v5.3
by R B 28 Jun '13

28 Jun '13

Hi Freesurfer Experts, i have earlier worked in freesurfer previous versions. i was able to get preliminary results. i have trouble with freesurfer version V 5.3, i have error in this step of the analysis " minc_modify_header: posixio.c:210: px_pgin:Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed." progressively the subsequent steps are showing error. requesting your assistance in troubleshooting this issue thanks hsekar

1 0

tksurfer display problem
by Xiangzhen Kong 27 Jun '13

27 Jun '13

Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net

2 1

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