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30132 discussions

Re: [Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks
by Thomas Yeo 26 Nov '11

26 Nov '11

Hi Yolanda, Just to understand what you are doing, you have run BASGU throughrecon-all and you are trying to project the surface parcellation intothe anatomical volume of BASGU? The annotation we are providing is actually in fsaverage space, so youneed to first project the parcellation from fsaverage space to BASGUnative surface space before running mris_annot_to_segmentation toproject the parcellation into his/her anatomical volume. To project the parcellation from freesurfer surface space to thesubject's native surface space, I think you can use mri_surf2surf,although I am not sure if there's a more specific freesurfer functionthat is specialized for transferring annotation files. --Thomas On Sun, Nov 27, 2011 at 12:40 AM, Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > Hi Yolanda, > > Just to understand what you are doing, you have run BASGU through > recon-all and you are trying to project the surface parcellation into > the anatomical volume of BASGU? > > The annotation we are providing is actually in fsaverage space, so you > need to first project the parcellation from fsaverage space to BASGU > native surface space before running mris_annot_to_segmentation to > project the parcellation into his/her anatomical volume. > > To project the parcellation from freesurfer surface space to the > subject's native surface space, I think you can use mri_surf2surf, > although I am not sure if there's a more specific freesurfer function > that is specialized for transferring annotation files. > > --Thomas > > On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives <yvives(a)pic.es> wrote: >> Dear Freesurfer experts, >> >> I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with my >> dataset and I am not sure what I have to do. I have used the >> mris_annot_to_segmentation command but I have the following error: >> >> mris_annot_to_segmentation BASGU lh inflated >> ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot >> ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test >> reading /freesurfer/BASGU/surf/lh.inflated... >> reading colortable from annotation file... >> colortable with 18 entries read (originally MyColorLUT) >> mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 >> (null): could not read T1 for template volume >> >> I have a T1.mgz file inside mri/. Where could be the problem? Is this >> command appropriate? >> >> Thank you in advance, >> Yolanda >> >> _______________________________________________ >> 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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Bad nu_noneck
by Jeff Sadino 26 Nov '11

26 Nov '11

Hello, I am having problems creating the nu_noneck file in fs500. Using the default stream, the front and back of the brain is clipped off, which seems to be causing significantly bad surfaces downstream. I changed the radius to 45 so that all of the brain is included, but then too much neck is left over, causing bad surfaces and a bad aseg downstream. I am running now in fs510 to see if I can copy over from there. If not, are there any recommendations on how to get a useful nu_noneck file? Thank you, Jeff Sadino

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what does the tk stand for in tksurfer?
by Martina Papmeyer 24 Nov '11

24 Nov '11

Hello, I have a very simple question but couldn't find an answer yet. What does the "tk" actually stand for in tksurfer and tkmedit? Many thanks for this info, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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intensity normalisation and aseg
by Mahinda Yogarajah 24 Nov '11

24 Nov '11

Dear Experts, I am a beginner to the use of Freesurfer and having just installed version 5.1.0 (Centos 64bit) I have been going through the processing pipeline with one of our own datasets (3T GE Excite II scanner - coronal T1-weighted volumetric acquisition sequence with 1.1-mm thick slices). recon-all works fine and I have been looking at the outputs. I have a question regarding the subcortical segmentation especially around the basal ganglia - during the intensity normalisation it appears to have assigned similar high (110) voxel values to parts of the internal capsule, pallidum and thalamus (pic1- brainmask.mgz), though the actual segmentation (pic2-aseg) looks reasonable when compared with the native image (pic3-raw T1) (though I appreciate one is normalised and the other is not). Should I be worried about this (and if so how can I correct ?) or is this intensity normalisation used only in the surface stream with a different intensity normalisation used in the volume stream ? Or ... is it used in the volume stream but the other parts of the model (eg priors from atlas etc) compensate in some way. Thanks. Mo PS I can post screen

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difference between recon-all 4.3 and 5.1
by Knut J Bjuland 24 Nov '11

24 Nov '11

Hi I have two different folders where one is processed by recon-all 4.3 and another by recon-all 5.1. When I compare these two folders I get similar results for fwhm 30 for group difference which is survives fdr, but when I compare results that are do not survived fdr I get very different results. Is there anything wrong? The folder where I used recon-all 5.1 has all automatic segmentation with manual pial surface edit, while the other have manual editions of putamen and manual segmentation of corpus callosum. Knut J

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Postdoctoral Fellowship fMRI of Reaching and Grasping
by angelika lingnau 24 Nov '11

24 Nov '11

*Postdoc fMRI of Reaching and Grasping, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC), University of Trento there is soon going to be an opening for a Postdoctoral Fellowship to work with Dr. Angelika Lingnau (http://www.unitn.it/en/cimec/11702/angelika-lingnau) in collaboration with Prof. Raffaella Rumiati, SISSA. In this project, we will use fMRI and kinematic recordings to study the effects of parietal and premotor lesions on reaching and grasping movements. *Start date:* as soon as possible *Requirements: * PhD in related field Experience with fMRI design and analysis Experience with kinematic recordings Programming skills (Matlab or C) The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The University of Trento is ranked first among research universities in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Dr Angelika Lingnau, Center for Mind/ Brain Sciences, University of Trento, Via delle Regole, 101, Mattarello (TN), Italy. Tel.: ++39-0461-283067, email: angelika.lingnau(a)unitn.it or angelika.lingnau(a)gmail.com <Angelika.lingnau(a)gmail.com>by December 5th, 2011.

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GROUP ANALYSIS ON QDEC
by Luisa Leo 24 Nov '11

24 Nov '11

Hi, I've done the recon-all for all my subjects, and everyone ended with no errors. First of all, I don't understand if the recon-all do a volume normalization: why subjects have different number of vertex?if the comparison isnt't vertex by vertex, how is it done? Now I want to do a group Analysis using QDEC, so I've done the recon-all -qcache to create a common space for my subjects. I would know how I have to set parameters in the DiSPLAY and how can I use the "correction for multiple-comparisons" to see the results of my analysis. Is there a way to have all the values of the cortical thickness vertex by vertex and not only the average? Sincerely, Luisa Leo

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Yeo_JNeurophysiol11_FreeSurfer networks
by Yolanda Vives 24 Nov '11

24 Nov '11

Dear Freesurfer experts, I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with my dataset and I am not sure what I have to do. I have used the mris_annot_to_segmentation command but I have the following error: mris_annot_to_segmentation BASGU lh inflated ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test reading /freesurfer/BASGU/surf/lh.inflated... reading colortable from annotation file... colortable with 18 entries read (originally MyColorLUT) mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 (null): could not read T1 for template volume I have a T1.mgz file inside mri/. Where could be the problem? Is this command appropriate? Thank you in advance, Yolanda

1 0

flat surfaces and negative indices
by Gabriele Arnulfo 23 Nov '11

23 Nov '11

Dear freesurfer experts, I'm curious to understand the meaning of negative indices in flatten surfaces.

2 1

Bad nu_noneck
by Jeff Sadino 23 Nov '11

23 Nov '11

Hello, I am having problems creating the nu_noneck file in fs500. Using the default stream, the front and back of the brain is clipped off, which seems to be causing significantly bad surfaces downstream. I changed the radius to 45 so that all of the brain is included, but then too much neck is left over, causing bad surfaces and a bad aseg downstream. The nu_noneck file seems to be fine from the fs510 reconstruction. Can I just copy it over from there? If not, are there any recommendations on how to get a useful nu_noneck file? Thank you, Jeff Sadino

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