Freesurfer

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30132 discussions

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by Efrat Kliper 01 Nov '12

01 Nov '12

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. I am dealing with some problems with recon_checker command. I cannot open the html file to see the figures. The command generates the images but they are not saved. It is written that: *converting snapshots to tiff and making html page...* *Convert: command not found* Any suggestions? Thanks in advance, efrat

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Re: [Freesurfer] fieldsign-sess problem in retinotopy
by Zhou, Wei 31 Oct '12

31 Oct '12

Hi, Doug Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg. So what should SUBJECTS_DIR be exported to for this analysis? Best Wei >Hi Wei, this is a bug in the error msg. It is trying to say that your >source subject is not in the $SUBJECTS_DIR. >doug >On 10/27/2012 02:27 PM, Zhou, Wei wrote: > Dear freesurfers, > > I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I > encounter the following problem when I type "fieldsign-sess -a > rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh > -occip -sf sessid": > > */media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* > *subject: Undefined variable.* > > my structure of retinotopy fold is : > retinotopy > | |--sessid > |--SUBJ01 > |--subjectname > > |--bold > |--001 > |--f.nii > |--rtopy.par| > > I really appreciate it if you could give me some idea about that > problem. Thanks a lot in advance. > > Best > Wei Zhou > Medical Physics Ph.D. Student > Diagnostic Imaging Track > cgxz...(a)gmail.com <mailto:cgxz...@gmail.com> > zho...(a)livemail.uthscsa.edu <mailto:zho...@livemail.uthscsa.edu> > > > _______________________________________________ > 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 gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Error during recon-all with notal-check on
by Darshan P 31 Oct '12

31 Oct '12

I have a MRI data which has a lesion on the left side . recon-all fails with errors . I was hoping to recover from this error . The last few lines of the log file is as follows'

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Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
by Anastasia Yendiki 31 Oct '12

31 Oct '12

If FSL isn't happy with the directions, that's going to be fatal b/c trac-all relies on bedpostx running properly. I'm going to look into this further to try to figure out what it is about this data that's causing the discrepancy. On Wed, 31 Oct 2012, Fernando Ventrice wrote: > Dear Anastasia, > When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions actually are OK, but when I open them with FSLview they are similar to your screen-shot. Here I also send a screen-shot with the comparison between the two softwares in each monitor. > Best, > Fernando > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Tuesday, October 30, 2012 1:24 PM > To: Fernando Ventrice > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small > > See screenshot now :) > > On Tue, 30 Oct 2012, Anastasia Yendiki wrote: > >> >> Hi Fernando - Thanks for uploading your data. Looking at the primary >> directions from tensor fit on the data that you sent me (see screenshot), >> they seem to be off by a 90 degree angle from what you'd expect them. This >> means that your gradient table is probably off as well. >> >> Hope this helps, >> a.y >> >> On Thu, 18 Oct 2012, Fernando Ventrice wrote: >> >>> Dear Freesurfer/Tracula users, >>> Finally I could successfully test Tracula and I think it is amazing what >>> it can do automatically. These are the commands I used: >>> >>> export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source >>> $FREESURFER_HOME/SetUpFreeSurfer.sh >>> source /etc/fsl/fsl.sh >>> export FSLPARALLEL=condor >>> trac-all -prep -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> trac-all -bedp -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> # "trac-all -bedp" gave some errors so I used bedpostx directly: >>> bedpostx >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri >>> trac-all -path -c >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice >>> freeview -tv >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz >>> -v >>> /home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz >>> & >>> >>> All finished without errors, but there seems to be a problem with CC >>> Forceps Mayor volume, which gave very small values. Is this OK or I made >>> some mistake? First I tested with some patient and other fiber tracks also >>> gave very small volumes. I attached some pictures and the dmrirc and >>> trac-all log files. >>> Best, >>> Fernando Ventrice >>> >>> El contenido del presente mensaje y el de sus adjuntos, es confidencial, >>> privado y de uso exclusivo de los destinatarios a los cuales está >>> dirigido, pudiendo contener información legalmente protegida. Queda >>> prohibida la revisión, divulgación, publicación, modificación, copia, >>> distribución o acción en relación con esta información, por personas o >>> entidades distintas al destinatario. Si usted, por alguna razón, lo ha >>> recibido por error, por favor tenga la amabilidad de eliminarlo de su >>> sistema. Las opiniones contenidas, son exclusivas de su autor, y no >>> representa necesariamente, la opinión de FLENI. >>> http://www.fleni.org.ar >>> >> > > > 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. > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar > > El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. > http://www.fleni.org.ar >

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Re: [Freesurfer] average measure of cortical thickness
by Bruce Fischl 31 Oct '12

31 Oct '12

yes, I think so Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: > So, as a measure of whole brain cortical thickness average is it better to > "Mean Thickness" from aparc.stats file? > > > 2012/10/30 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel > > the parcellations are not uniform in size, and therefore the > average of them will not be the same as averaging over the > cortex. > > cheers > Bruce > On Tue, 30 Oct 2012, Daniel Ferreira wrote: > > Hi, > I was wondering what should I use as an average of > cortical thickness for > the whole cortex. > > The aparc.stats output gives a value of "Mean > Thickness" for each > hemisphere. But this value does not coincide with > the one I get if I average > the 34 variables from aparc.stats. Do you know why? > > thanks so much in advance > > Daniel > > > > > 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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SPM VBM and Freesurfer group analysis
by Infinity 31 Oct '12

31 Oct '12

Hi, I did a SPM VBM (using dartel) analysis as well as a freesurfer group analysis. After correcting for multiple comparisons. Both maps give me pretty different results. From the literature review both sets of results make sense but the fact that the results don't agree is troubling me. I have checked everything multiple times and still get the same results. Is it common that the two methods give different results? I also wanted to know the interpretation of the surface measures that freesurfer reports, especially the curv and sulc measures. What does it mean exactly when two groups have different sulc or curv measures? In my results I get a negative correlation between curv measure and volume measure in the same region. So in that region for curv measure group1 > group 2 while in the same region for the volume measure group1 < group2. How exactly is the curv measure related to volume and area measures? Is there a standard reference where all the details for these measures are mentioned? Thank you.

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Phase-Sensitive Inversion Recovery
by Lena Palaniyappan 31 Oct '12

31 Oct '12

Hi all Our local team of physicists recommend Phase-Sensitive Inversion Recovery instead of MPRAGE for anatomical imaging in 7T. So far, I have had no issues with 7T MPRAGEs with regard to freesurfer processing. I am not sure about PSIR and freesurfer compatibility. Does anyone have experience with PSIR sequences. Any suggestions/thoughts will be helpful. Cheers, Lena Palaniyappan This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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recon-all
by Efrat Kliper 31 Oct '12

31 Oct '12

Dear Freesurfer expert, I am using Freesurfer version 5.1.0. After I ran the freesurfer recon-all -autorecon-all and checked the data I saw that the skull wasn't removed as a whole (yet it is not part of the pial or white matter margin). I was wondering if it just doesn't look good or that part of the skull that was not removed was calculated as part of the ICV or somthing else. Thanks in advance, efrat

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Hurricane Sandy
by Ed Gronenschild 31 Oct '12

31 Oct '12

Hi Bruce and colleagues, I hope you did survive Sandy without too much damage. Cheers, Ed

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No result differences v5.1.0 between MacOSX 10.6 and 10.7
by Ed Gronenschild 31 Oct '12

31 Oct '12

Hi, For your information: for version 5.1.0 we have found no differences in the results between MacOSX 10.6 and 10.7 (53 subjects). Cheers, Ed

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